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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
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@@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
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</div>
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<div class="section level2">
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<h2 id="read-more-on-our-website-">Read more on Our Website!<a class="anchor" aria-label="anchor" href="#read-more-on-our-website-"></a></h2>
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<p>On our website <a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a> you can find <a href="https://msberends.github.io/AMR/articles/AMR.html">a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href="https://msberends.github.io/AMR/reference/">complete documentation of all functions</a> and <a href="https://msberends.github.io/AMR/articles/WHONET.html">an example analysis using WHONET data</a>.</p>
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<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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</div>
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<div class="section level2">
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<h2 id="contact-us">Contact Us<a class="anchor" aria-label="anchor" href="#contact-us"></a></h2>
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<p>For suggestions, comments or questions, please contact us at:</p>
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<p>Matthijs S. Berends <br>
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<p>For suggestions, comments or questions, please contact us via:</p>
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<p>Dr. Matthijs S. Berends <br>
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m.s.berends [at] umcg [dot] nl <br>
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University of Groningen
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Department of Medical Microbiology and Infection Prevention <br>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 500 observations and 53 variables:</p><ul><li><p><code>Identification number</code><br> ID of the sample</p></li>
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<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 500 observations and 53 variables:</p><ul><li><p><code>Identification number</code><br> ID of the sample</p></li>
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<li><p><code>Specimen number</code><br> ID of the specimen</p></li>
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<li><p><code>Organism</code><br> Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using <code><a href="as.mo.html">as.mo()</a></code>.</p></li>
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<li><p><code>Country</code><br> Country of origin</p></li>
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@@ -166,78 +166,33 @@
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<li><p><code>AMP_ND10:CIP_EE</code><br> 28 different antibiotics. You can lookup the abbreviations in the <a href="antibiotics.html">antibiotics</a> data set, or use e.g. <code><a href="ab_property.html">ab_name("AMP")</a></code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href="as.rsi.html">as.rsi()</a></code>.</p></li>
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</ul></div>
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<div class="section level2">
|
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
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<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">WHONET</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Identification number Specimen number Organism Country</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 fe41d7bafa 1748 SPN Belgium</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 91f175ec37 1767 eco The Netherlands</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 cc4015056e 1343 eco The Netherlands</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 e864b692f5 1894 MAP Denmark</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 3d051fe345 1739 PVU Belgium</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 c80762a08d 1846 103 The Netherlands</span>
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<span class="r-out co"><span class="r-pr">#></span> Laboratory Last name First name Sex Age</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 National Laboratory of Belgium Abel B. F 68</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 National Laboratory of The Netherlands Delacroix F. M 89</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 National Laboratory of The Netherlands Steensen F. M 85</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 National Laboratory of Denmark Beyersdorf L. M 62</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 National Laboratory of Belgium Hummel W. M 86</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 National Laboratory of The Netherlands Eikenboom J. F 53</span>
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<span class="r-out co"><span class="r-pr">#></span> Age category Date of admission Specimen date Specimen type</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 55-74 2005-01-12 2005-01-30 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 75+ 2006-07-30 2006-08-16 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 75+ 2014-03-05 2014-03-14 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 55-74 2014-10-22 2014-11-01 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 75+ 2016-10-28 2016-11-17 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 25-54 2017-12-21 2018-01-02 Urine</span>
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<span class="r-out co"><span class="r-pr">#></span> Specimen type (Numeric) Reason Isolate number Organism type Serotype</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 2 Unknown 1748 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 2 2 Unknown 1767 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 3 2 Unknown 1343 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 4 2 Unknown 1894 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 5 2 Unknown 1739 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> 6 2 Unknown 1846 Bacteria </span>
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<span class="r-out co"><span class="r-pr">#></span> Beta-lactamase ESBL Carbapenemase MRSA screening test</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> Inducible clindamycin resistance Comment Date of data entry AMP_ND10 AMC_ED20</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 FALSE 2005-01-30 S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 FALSE 2006-08-16 <NA> S</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 FALSE 2014-03-14 S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 FALSE 2014-11-01 R <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 FALSE 2016-11-17 R R</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 FALSE 2018-01-02 S S</span>
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<span class="r-out co"><span class="r-pr">#></span> TZP_ED30 FEP_ED30 CTX_ED5 FOX_ED30 CAZ_ED10 CRO_ED30 CIP_ED5 AMK_ED30</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 S <NA> <NA> <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 2 <NA> <NA> <NA> <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 3 S <NA> <NA> <NA> <NA> <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 4 <NA> <NA> <NA> <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 S <NA> S R S S S <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 6 S <NA> S S S S S <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> GEN_ED10 TOB_ED10 SXT_ED1.2 IPM_ND10 PEN_ND1 AMP_ND2 AMC_ND2 CHL_ND30 VAN_ED5</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 R R S <NA> S S S <NA> S</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 S <NA> R <NA> R <NA> S <NA> S</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 <NA> <NA> <NA> <NA> S S S <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 4 R R <NA> <NA> R R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 S S R I R R R <NA> R</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 S S S S R S S <NA> R</span>
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<span class="r-out co"><span class="r-pr">#></span> OXA_ED1 ERY_ED15 CLI_ED2 TCY_ED30 RIF_ED5 PEN_EE AMP_EE CRO_EE CIP_EE</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 <NA> S <NA> S <NA> S S <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 2 <NA> S S S <NA> R <NA> <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 3 <NA> <NA> S <NA> <NA> S S <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 4 <NA> <NA> S <NA> <NA> R R <NA> <NA></span>
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<span class="r-out co"><span class="r-pr">#></span> 5 <NA> R <NA> R R R R S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 <NA> R <NA> <NA> R R S S S</span>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">WHONET</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 500 × 53</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Identif…¹ Speci…² Organ…³ Country Labor…⁴ Last …⁵ First…⁶ Sex Age Age c…⁷</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> fe41d7ba… <span style="text-decoration: underline;">1</span>748 SPN Belgium Nation… Abel B. F 68 55-74 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 91f175ec… <span style="text-decoration: underline;">1</span>767 eco The Ne… Nation… Delacr… F. M 89 75+ </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> cc401505… <span style="text-decoration: underline;">1</span>343 eco The Ne… Nation… Steens… F. M 85 75+ </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> e864b692… <span style="text-decoration: underline;">1</span>894 MAP Denmark Nation… Beyers… L. M 62 55-74 </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 3d051fe3… <span style="text-decoration: underline;">1</span>739 PVU Belgium Nation… Hummel W. M 86 75+ </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> c80762a0… <span style="text-decoration: underline;">1</span>846 103 The Ne… Nation… Eikenb… J. F 53 25-54 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 8022d372… <span style="text-decoration: underline;">1</span>628 103 Denmark Nation… Leclerc S. F 77 75+ </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> f3dc5f55… <span style="text-decoration: underline;">1</span>493 eco The Ne… Nation… Delacr… W. M 53 25-54 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 15add38f… <span style="text-decoration: underline;">1</span>847 eco France Nation… Van La… S. F 63 55-74 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> fd41248d… <span style="text-decoration: underline;">1</span>458 eco Germany Nation… Moulin O. F 75 75+ </span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 490 more rows, 43 more variables: `Date of admission` <date>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Specimen date` <date>, `Specimen type` <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Specimen type (Numeric)` <dbl>, Reason <chr>, `Isolate number` <int>,</span></span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Organism type` <chr>, Serotype <chr>, `Beta-lactamase` <lgl>, ESBL <lgl>,</span></span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Carbapenemase <lgl>, `MRSA screening test` <lgl>,</span></span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Inducible clindamycin resistance` <lgl>, Comment <chr>,</span></span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `Date of data entry` <date>, AMP_ND10 <rsi>, AMC_ED20 <rsi>, …</span></span>
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</code></pre></div>
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</div>
|
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -206,7 +206,7 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># mind the bad spelling of amoxicillin in this line, </span></span></span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># mind the bad spelling of amoxicillin in this line,</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># straight from a true health care record:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"28/03/2020 regular amoxicilliin 500mg po tds"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [[1]]</span>
|
||||
@@ -237,22 +237,28 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins" "Quinolones" </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a></span><span class="op">(</span>clinical_text <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"given 400mg cipro and 500 mg amox"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"started on doxy iv today"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>abx_codes <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_doses <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>, type <span class="op">=</span> <span class="st">"doses"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_admin <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>, type <span class="op">=</span> <span class="st">"admin"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_coll <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>, collapse <span class="op">=</span> <span class="st">"|"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_coll_names <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>,</span></span>
|
||||
<span class="r-in"><span> collapse <span class="op">=</span> <span class="st">"|"</span>,</span></span>
|
||||
<span class="r-in"><span> translate_ab <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_coll_doses <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>,</span></span>
|
||||
<span class="r-in"><span> type <span class="op">=</span> <span class="st">"doses"</span>,</span></span>
|
||||
<span class="r-in"><span> collapse <span class="op">=</span> <span class="st">"|"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_coll_admin <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>,</span></span>
|
||||
<span class="r-in"><span> type <span class="op">=</span> <span class="st">"admin"</span>,</span></span>
|
||||
<span class="r-in"><span> collapse <span class="op">=</span> <span class="st">"|"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a></span><span class="op">(</span>clinical_text <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="st">"given 400mg cipro and 500 mg amox"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"started on doxy iv today"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> abx_codes <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_doses <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>, type <span class="op">=</span> <span class="st">"doses"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_admin <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>, type <span class="op">=</span> <span class="st">"admin"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_coll <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>, collapse <span class="op">=</span> <span class="st">"|"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_coll_names <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>,</span></span>
|
||||
<span class="r-in"><span> collapse <span class="op">=</span> <span class="st">"|"</span>,</span></span>
|
||||
<span class="r-in"><span> translate_ab <span class="op">=</span> <span class="st">"name"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_coll_doses <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>,</span></span>
|
||||
<span class="r-in"><span> type <span class="op">=</span> <span class="st">"doses"</span>,</span></span>
|
||||
<span class="r-in"><span> collapse <span class="op">=</span> <span class="st">"|"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> abx_coll_admin <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>,</span></span>
|
||||
<span class="r-in"><span> type <span class="op">=</span> <span class="st">"admin"</span>,</span></span>
|
||||
<span class="r-in"><span> collapse <span class="op">=</span> <span class="st">"|"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Loading required package: dplyr</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -239,7 +239,7 @@
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
@@ -249,13 +249,13 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># all properties:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Amoxicillin"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Amoxicillin"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Amoxicillin"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "J01CA04" (ATC code from the WHO)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "J01CA04" (ATC code from the WHO)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA04"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_cid</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># 33613 (Compound ID from PubChem)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_cid</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># 33613 (Compound ID from PubChem)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 33613</span>
|
||||
<span class="r-in"><span><span class="fu">ab_synonyms</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># a list with brand names of amoxicillin</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_synonyms</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># a list with brand names of amoxicillin</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "actimoxi" "amoclen" "amolin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
|
||||
@@ -287,34 +287,36 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] "ospamox" "pamoxicillin" "piramox" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [40] "robamox" "sawamox pm" "tolodina" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [43] "unicillin" "utimox" "vetramox" </span>
|
||||
<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Beta-lactams/penicillins"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Beta-lactams/penicillins"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc_group1</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Beta-lactam antibacterials, penicillins"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactam antibacterials, penicillins"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc_group2</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Penicillins with extended spectrum"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Penicillins with extended spectrum"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_url</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># link to the official WHO page</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_url</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># link to the official WHO page</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Amoxicillin </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> "https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no" </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># smart lowercase tranformation</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"PLB"</span><span class="op">)</span><span class="op">)</span> <span class="co"># "Amoxicillin/clavulanic acid" "Polymyxin B"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"PLB"</span><span class="op">)</span><span class="op">)</span> <span class="co"># "Amoxicillin/clavulanic acid" "Polymyxin B"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Amoxicillin/clavulanic acid" "Polymyxin B" </span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"PLB"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> tolower <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "amoxicillin/clavulanic acid" "polymyxin B"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"PLB"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> tolower <span class="op">=</span> <span class="cn">TRUE</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span> <span class="co"># "amoxicillin/clavulanic acid" "polymyxin B"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "amoxicillin/clavulanic acid" "polymyxin B" </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># defined daily doses (DDD)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_ddd</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"oral"</span><span class="op">)</span> <span class="co"># 1.5</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_ddd</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"oral"</span><span class="op">)</span> <span class="co"># 1.5</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1.5</span>
|
||||
<span class="r-in"><span><span class="fu">ab_ddd_units</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"oral"</span><span class="op">)</span> <span class="co"># "g"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_ddd</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"iv"</span><span class="op">)</span> <span class="co"># 3</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_ddd</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"iv"</span><span class="op">)</span> <span class="co"># 3</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 3</span>
|
||||
<span class="r-in"><span><span class="fu">ab_ddd_units</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"iv"</span><span class="op">)</span> <span class="co"># "g"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_ddd_units</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"iv"</span><span class="op">)</span> <span class="co"># "g"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_info</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># all properties as a list</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_info</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># all properties as a list</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $ab</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "AMX"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
@@ -376,17 +378,17 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMP"</span><span class="op">)</span> <span class="co"># ATC code of AMP (ampicillin)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMP"</span><span class="op">)</span> <span class="co"># ATC code of AMP (ampicillin)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA01" "S01AA19"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span> <span class="co"># Drug group of ampicillins ATC code</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span> <span class="co"># Drug group of ampicillins ATC code</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_loinc</span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># LOINC codes of ampicillin</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_loinc</span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># LOINC codes of ampicillin</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span> <span class="co"># "Ampicillin" (using LOINC)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span> <span class="co"># "Ampicillin" (using LOINC)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="fl">6249</span><span class="op">)</span> <span class="co"># "Ampicillin" (using CID)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="fl">6249</span><span class="op">)</span> <span class="co"># "Ampicillin" (using CID)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span> <span class="co"># "Ampicillin" (using ATC)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span> <span class="co"># "Ampicillin" (using ATC)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>
|
||||
@@ -401,96 +403,86 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># use set_ab_names() for renaming columns</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "hospital_id" "ward_icu" "ward_clinical" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "ward_outpatient" "age" "gender" "patient_id" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] "mo" "PEN" "OXA" "FLC" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] "AMX" "AMC" "AMP" "TZP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [17] "CZO" "FEP" "CXM" "FOX" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] "CTX" "CAZ" "CRO" "GEN" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] "TOB" "AMK" "KAN" "TMP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [29] "SXT" "NIT" "FOS" "LNZ" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [33] "CIP" "MFX" "VAN" "TEC" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] "TCY" "TGC" "DOX" "ERY" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [41] "CLI" "AZM" "IPM" "MEM" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [45] "MTR" "CHL" "COL" "MUP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] "RIF" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "patient" "age" "gender" "ward" "mo" "PEN" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [8] "OXA" "FLC" "AMX" "AMC" "AMP" "TZP" "CZO" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [15] "FEP" "CXM" "FOX" "CTX" "CAZ" "CRO" "GEN" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [22] "TOB" "AMK" "KAN" "TMP" "SXT" "NIT" "FOS" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [29] "LNZ" "CIP" "MFX" "VAN" "TEC" "TCY" "TGC" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [36] "DOX" "ERY" "CLI" "AZM" "IPM" "MEM" "MTR" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [43] "CHL" "COL" "MUP" "RIF" </span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="fu">set_ab_names</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "hospital_id" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [3] "ward_icu" "ward_clinical" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "ward_outpatient" "age" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] "gender" "patient_id" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] "mo" "benzylpenicillin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] "oxacillin" "flucloxacillin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] "amoxicillin" "amoxicillin_clavulanic_acid" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [15] "ampicillin" "piperacillin_tazobactam" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [17] "cefazolin" "cefepime" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] "cefuroxime" "cefoxitin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] "cefotaxime" "ceftazidime" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [23] "ceftriaxone" "gentamicin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] "tobramycin" "amikacin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [27] "kanamycin" "trimethoprim" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [29] "trimethoprim_sulfamethoxazole" "nitrofurantoin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [31] "fosfomycin" "linezolid" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [33] "ciprofloxacin" "moxifloxacin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [35] "vancomycin" "teicoplanin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] "tetracycline" "tigecycline" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [39] "doxycycline" "erythromycin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [41] "clindamycin" "azithromycin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [43] "imipenem" "meropenem" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [45] "metronidazole" "chloramphenicol" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [47] "colistin" "mupirocin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] "rifampicin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "patient" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [3] "age" "gender" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "ward" "mo" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [7] "benzylpenicillin" "oxacillin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] "flucloxacillin" "amoxicillin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] "amoxicillin_clavulanic_acid" "ampicillin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] "piperacillin_tazobactam" "cefazolin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [15] "cefepime" "cefuroxime" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [17] "cefoxitin" "cefotaxime" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] "ceftazidime" "ceftriaxone" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] "gentamicin" "tobramycin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [23] "amikacin" "kanamycin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] "trimethoprim" "trimethoprim_sulfamethoxazole"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [27] "nitrofurantoin" "fosfomycin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [29] "linezolid" "ciprofloxacin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [31] "moxifloxacin" "vancomycin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [33] "teicoplanin" "tetracycline" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [35] "tigecycline" "doxycycline" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] "erythromycin" "clindamycin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [39] "azithromycin" "imipenem" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [41] "meropenem" "metronidazole" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [43] "chloramphenicol" "colistin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [45] "mupirocin" "rifampicin" </span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="fu">set_ab_names</span><span class="op">(</span><span class="va">example_isolates</span>, <span class="va">NIT</span><span class="op">:</span><span class="va">VAN</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "hospital_id" "ward_icu" "ward_clinical" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "ward_outpatient" "age" "gender" "patient_id" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] "mo" "PEN" "OXA" "FLC" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] "AMX" "AMC" "AMP" "TZP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [17] "CZO" "FEP" "CXM" "FOX" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] "CTX" "CAZ" "CRO" "GEN" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] "TOB" "AMK" "KAN" "TMP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [29] "SXT" "nitrofurantoin" "fosfomycin" "linezolid" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [33] "ciprofloxacin" "moxifloxacin" "vancomycin" "TEC" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] "TCY" "TGC" "DOX" "ERY" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [41] "CLI" "AZM" "IPM" "MEM" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [45] "MTR" "CHL" "COL" "MUP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] "RIF" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "patient" "age" "gender" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "ward" "mo" "PEN" "OXA" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] "FLC" "AMX" "AMC" "AMP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] "TZP" "CZO" "FEP" "CXM" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [17] "FOX" "CTX" "CAZ" "CRO" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] "GEN" "TOB" "AMK" "KAN" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] "TMP" "SXT" "nitrofurantoin" "fosfomycin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [29] "linezolid" "ciprofloxacin" "moxifloxacin" "vancomycin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [33] "TEC" "TCY" "TGC" "DOX" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] "ERY" "CLI" "AZM" "IPM" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [41] "MEM" "MTR" "CHL" "COL" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [45] "MUP" "RIF" </span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># this does the same:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html" class="external-link">rename_with</a></span><span class="op">(</span><span class="va">set_ab_names</span><span class="op">)</span><span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html" class="external-link">rename_with</a></span><span class="op">(</span><span class="va">set_ab_names</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># set_ab_names() works with any AB property:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span><span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span><span class="va">NIT</span><span class="op">:</span><span class="va">VAN</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span><span class="va">NIT</span><span class="op">:</span><span class="va">VAN</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "hospital_id" "ward_icu" "ward_clinical" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "ward_outpatient" "age" "gender" "patient_id" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] "mo" "PEN" "OXA" "FLC" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] "AMX" "AMC" "AMP" "TZP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [17] "CZO" "FEP" "CXM" "FOX" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] "CTX" "CAZ" "CRO" "GEN" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] "TOB" "AMK" "KAN" "TMP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [29] "SXT" "nitrofurantoin" "fosfomycin" "linezolid" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [33] "ciprofloxacin" "moxifloxacin" "vancomycin" "TEC" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] "TCY" "TGC" "DOX" "ERY" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [41] "CLI" "AZM" "IPM" "MEM" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [45] "MTR" "CHL" "COL" "MUP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] "RIF" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "patient" "age" "gender" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "ward" "mo" "PEN" "OXA" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [9] "FLC" "AMX" "AMC" "AMP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] "TZP" "CZO" "FEP" "CXM" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [17] "FOX" "CTX" "CAZ" "CRO" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] "GEN" "TOB" "AMK" "KAN" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] "TMP" "SXT" "nitrofurantoin" "fosfomycin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [29] "linezolid" "ciprofloxacin" "moxifloxacin" "vancomycin" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [33] "TEC" "TCY" "TGC" "DOX" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] "ERY" "CLI" "AZM" "IPM" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [41] "MEM" "MTR" "CHL" "COL" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [45] "MUP" "RIF" </span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -190,16 +190,16 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1941-07-07 81 81.13699 58</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1938-12-21 83 83.67945 61</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1986-07-22 36 36.09589 13</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1959-10-17 62 62.85753 40</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1975-01-14 47 47.61370 24</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1973-12-13 48 48.70137 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1954-03-31 68 68.40548 45</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1961-10-20 60 60.84932 38</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1959-01-07 63 63.63288 40</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1967-08-20 55 55.01644 32</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1982-03-20 40 40.44110 17</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1996-11-03 25 25.81644 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1970-05-07 52 52.30959 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1970-11-29 51 51.74521 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1934-01-13 88 88.62192 65</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1953-11-17 68 68.77808 46</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1970-08-02 52 52.07123 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1965-04-20 57 57.35616 34</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1943-07-28 79 79.08493 56</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1992-11-12 29 29.79178 7</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -216,16 +216,17 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">mo</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">mo</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span>age_group <span class="op">=</span> <span class="fu">age_groups</span><span class="op">(</span><span class="va">age</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">age_group</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="ggplot_rsi.html">ggplot_rsi</a></span><span class="op">(</span>x <span class="op">=</span> <span class="st">"age_group"</span>,</span></span>
|
||||
<span class="r-in"><span> minimum <span class="op">=</span> <span class="fl">0</span>,</span></span>
|
||||
<span class="r-in"><span> x.title <span class="op">=</span> <span class="st">"Age Group"</span>,</span></span>
|
||||
<span class="r-in"><span> title <span class="op">=</span> <span class="st">"Ciprofloxacin resistance per age group"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="ggplot_rsi.html">ggplot_rsi</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="st">"age_group"</span>,</span></span>
|
||||
<span class="r-in"><span> minimum <span class="op">=</span> <span class="fl">0</span>,</span></span>
|
||||
<span class="r-in"><span> x.title <span class="op">=</span> <span class="st">"Age Group"</span>,</span></span>
|
||||
<span class="r-in"><span> title <span class="op">=</span> <span class="st">"Ciprofloxacin resistance per age group"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-plt img"><img src="age_groups-1.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -280,21 +280,39 @@
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># `example_isolates` is a data set available in the AMR package.</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># See ?example_isolates.</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span> , <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"hospital_id"</span>, <span class="st">"mo"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"AMP"</span>, <span class="st">"AMC"</span>, <span class="st">"TZP"</span>, <span class="st">"CXM"</span>, <span class="st">"CRO"</span>, <span class="st">"GEN"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"TOB"</span>, <span class="st">"COL"</span>, <span class="st">"IPM"</span>, <span class="st">"MEM"</span>, <span class="st">"TEC"</span>, <span class="st">"VAN"</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># base R ------------------------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># select columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> IPM MEM </span>
|
||||
@@ -312,157 +330,192 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin) and 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 3</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo GEN TOB </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_ESCHR_COLI NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_STPHY_EPDR NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B_STPHY_EPDR NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B_STPHY_EPDR NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B_STPHY_EPDR NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B_STPHY_AURS NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_STPHY_EPDR NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B_STPHY_EPDR NA NA </span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo GEN TOB AMK KAN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_ESCHR_COLI NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B_STPHY_AURS NA S NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS NA S NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># select only antibiotic columns with DDDs for oral treatment</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `administrable_per_os()` using columns 'AMP' (ampicillin), 'AMC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (amoxicillin/clavulanic acid), 'CXM' (cefuroxime), 'COL' (colistin) and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'VAN' (vancomycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMP AMC CXM COL VAN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> NA I I NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> NA I I NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> NA NA R R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> NA NA R R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> NA NA R R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> NA NA R R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> R S S R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> R S S R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA NA R R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA NA S R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `administrable_per_os()` using columns 'OXA' (oxacillin), 'FLC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin) and 'RIF'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (rifampicin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 23</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX AMC AMP CXM KAN TMP NIT FOS LNZ CIP MFX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> NA NA NA I NA I NA R NA NA R NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> NA NA NA I NA I NA R NA NA R NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> NA R NA NA NA R NA S NA NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> NA R NA NA NA R NA S NA NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> NA R NA NA NA R NA R NA NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> NA R NA NA NA R NA R NA NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> NA S R S R S NA R NA NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> NA S R S R S NA R NA NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA R NA NA NA R NA S NA NA NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA S NA NA NA S NA S NA NA NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 10 more variables: VAN <rsi>, TCY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter using any() or all()</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 55 × 14</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> hospital…¹ mo AMP AMC TZP CXM CRO GEN TOB COL IPM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> A B_ENTRC_FACM NA NA NA R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> A B_ENTRC_FACM NA NA NA R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B B_STNTR_MLTP R R R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B B_ENTRC NA NA R NA NA NA NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B B_ENTRC NA NA R NA NA NA NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B B_ENTRC_FACM NA NA R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> D B_ENTRC_FACM NA NA R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> A B_ENTRC_FACM NA NA R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> A B_PROTS_MRBL NA S S S S S S R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> A B_PROTS_MRBL NA S S S S S S R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 45 more rows, 3 more variables: MEM <rsi>, TEC <rsi>, VAN <rsi>, and</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable name ¹hospital_id</span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">df</span>, <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 55 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2004-06-09 529296 69 M ICU B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2004-06-09 529296 69 M ICU B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2004-11-03 D65308 80 F ICU B_STNTR_MLTP R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2005-04-21 452212 82 F ICU B_ENTRC NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2005-04-22 452212 82 F ICU B_ENTRC NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2005-04-22 452212 82 F ICU B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2007-02-21 8BBC46 61 F Clinical B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2007-12-15 401043 72 M Clinical B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2008-01-22 1710B8 82 M Clinical B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2008-01-22 1710B8 82 M Clinical B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 45 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">example_isolates</span>, <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 55 × 14</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> hospital…¹ mo AMP AMC TZP CXM CRO GEN TOB COL IPM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> A B_ENTRC_FACM NA NA NA R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> A B_ENTRC_FACM NA NA NA R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B B_STNTR_MLTP R R R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B B_ENTRC NA NA R NA NA NA NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B B_ENTRC NA NA R NA NA NA NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B B_ENTRC_FACM NA NA R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> D B_ENTRC_FACM NA NA R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> A B_ENTRC_FACM NA NA R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> A B_PROTS_MRBL NA S S S S S S R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> A B_PROTS_MRBL NA S S S S S S R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 45 more rows, 3 more variables: MEM <rsi>, TEC <rsi>, VAN <rsi>, and</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable name ¹hospital_id</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 55 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2004-06-09 529296 69 M ICU B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2004-06-09 529296 69 M ICU B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2004-11-03 D65308 80 F ICU B_STNTR_MLTP R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2005-04-21 452212 82 F ICU B_ENTRC NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2005-04-22 452212 82 F ICU B_ENTRC NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2005-04-22 452212 82 F ICU B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2007-02-21 8BBC46 61 F Clinical B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2007-12-15 401043 72 M Clinical B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2008-01-22 1710B8 82 M Clinical B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2008-01-22 1710B8 82 M Clinical B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 45 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter on any or all results in the carbapenem columns (i.e., IPM, MEM):</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Filtering any of columns 'IPM' and 'MEM' to contain value "R", "S" or "I"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 962 × 14</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> hospital…¹ mo AMP AMC TZP CXM CRO GEN TOB COL IPM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> D B_ESCHR_COLI NA I NA S S NA S NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> D B_ESCHR_COLI NA I NA S S NA S NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B B_PROTS_MRBL NA I NA S S NA NA R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B B_PROTS_MRBL NA I NA S S NA NA R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B B_SERRT_MRCS R R NA R NA NA NA R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B B_SERRT_MRCS R R NA R NA NA NA R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B B_SERRT_MRCS R R NA R NA NA NA R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> D B_KLBSL_PNMN R I NA S S S S NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> D B_KLBSL_PNMN R I NA S S S S NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> C B_ESCHR_COLI R R NA R S S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 952 more rows, 3 more variables: MEM <rsi>, TEC <rsi>, VAN <rsi>, and</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable name ¹hospital_id</span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 962 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-02-27 066895 85 F Clinical B_KLBSL_PNMN R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-02-27 066895 85 F Clinical B_KLBSL_PNMN R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-03-08 4FC193 69 M Clinical B_ESCHR_COLI R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 952 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value "R", "S" or "I"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 756 × 14</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> hospita…¹ mo AMP AMC TZP CXM CRO GEN TOB COL IPM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> C B_STRPT_GRPB S S S S S R R R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B B_STRPT_PYGN S S S S S R R R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B B_STRPT_GRPA S S S S S R R R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B B_STRPT_GRPA S S S S S R R R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> D B_STRPT_GRPB S S S S S R R R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B B_ESCHR_COLI R R S S S S S NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B B_ENTRBC_CLOC R R S R NA S S NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B B_ENTRBC_CLOC R R S R NA S S NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B B_ESCHR_COLI NA S S S S S S NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B B_ESCHR_COLI NA S S S S S S NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 746 more rows, 3 more variables: MEM <rsi>, TEC <rsi>, VAN <rsi>, and</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable name ¹hospital_id</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 756 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-04-14 F30196 73 M Outpat… B_STRPT_GRPB S NA S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2003-04-08 114570 74 M ICU B_STRPT_PYGN S NA S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2003-04-08 114570 74 M ICU B_STRPT_GRPA S NA S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2003-04-08 114570 74 M ICU B_STRPT_GRPA S NA S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2003-08-14 F71508 0 F Clinic… B_STRPT_GRPB S NA S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2003-10-16 650870 63 F ICU B_ESCHR_COLI R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2003-10-20 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2003-10-20 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2003-11-04 2FC253 87 F ICU B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2003-11-04 2FC253 87 F ICU B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 746 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter with multiple antibiotic selectors using c()</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin) and 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 26 × 14</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> hospital…¹ mo AMP AMC TZP CXM CRO GEN TOB COL IPM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B B_STNTR_MLTP R R R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B B_ENTRC_FACM NA NA R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> D B_ENTRC_FACM NA NA R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> A B_ENTRC_FACM NA NA R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> D B_STNTR_MLTP R R R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> D B_ENTRC_FACM NA NA R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B B_STPHY_CONS R R R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> A B_STPHY_CONS R R R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> D B_STPHY_CONS R R R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> D B_STPHY_CONS R R R R R R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 16 more rows, 3 more variables: MEM <rsi>, TEC <rsi>, VAN <rsi>, and</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable name ¹hospital_id</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 26 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2004-11-03 D65308 80 F ICU B_STNTR_MLTP R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2005-04-22 452212 82 F ICU B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2007-02-21 8BBC46 61 F Clinical B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2007-12-15 401043 72 M Clinical B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2008-12-06 501361 43 F Clinical B_STNTR_MLTP R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2011-05-09 207325 82 F ICU B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2012-03-12 582258 80 M ICU B_STPHY_CONS R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2012-05-19 C25552 89 F Outpati… B_STPHY_CONS R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2012-07-17 F05015 83 M ICU B_STPHY_CONS R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2012-07-20 404299 66 F Clinical B_STPHY_CONS R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 16 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter + select in one go: get penicillins in carbapenems-resistant strains</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `penicillins()` using columns 'AMP' (ampicillin), 'AMC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (amoxicillin/clavulanic acid) and 'TZP' (piperacillin/tazobactam)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 55 × 3</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMP AMC TZP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA S S </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `penicillins()` using columns 'PEN' (benzylpenicillin), 'OXA'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin) and 'TZP'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (piperacillin/tazobactam)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 55 × 7</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> PEN OXA FLC AMX AMC AMP TZP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> NA NA NA NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> NA NA NA NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> R NA NA R R R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> NA NA NA NA NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> NA NA NA NA NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> NA NA NA NA NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> NA NA NA NA NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> NA NA NA NA NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> R NA NA NA S NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> R NA NA NA S NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 45 more rows</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># You can combine selectors with '&' to be more specific. For example,</span></span></span>
|
||||
@@ -470,132 +523,457 @@
|
||||
<span class="r-in"><span><span class="co"># administrable_per_os() would select erythromycin. Yet, when combined these</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># drugs are both omitted since benzylpenicillin is not administrable per os</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># and erythromycin is not a penicillin:</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span> <span class="op">&</span> <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `penicillins()` using columns 'AMP' (ampicillin), 'AMC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (amoxicillin/clavulanic acid) and 'TZP' (piperacillin/tazobactam)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `administrable_per_os()` using columns 'AMP' (ampicillin), 'AMC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (amoxicillin/clavulanic acid), 'CXM' (cefuroxime), 'COL' (colistin) and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'VAN' (vancomycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMP AMC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> NA I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> NA I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA NA </span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span> <span class="op">&</span> <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `penicillins()` using columns 'PEN' (benzylpenicillin), 'OXA'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin) and 'TZP'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (piperacillin/tazobactam)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `administrable_per_os()` using columns 'OXA' (oxacillin), 'FLC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin) and 'RIF'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (rifampicin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX AMC AMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> NA NA NA I NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> NA NA NA I NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> NA R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> NA R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> NA R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> NA R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> NA S R S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> NA S R S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA S NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># ab_selector() applies a filter in the `antibiotics` data set and is thus very</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># flexible. For instance, to select antibiotic columns with an oral DDD of at</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># least 1 gram:</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu">ab_selector</span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">></span> <span class="fl">1</span> <span class="op">&</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `ab_selector(oral_ddd > 1 & oral_units == "g")` using columns 'AMP'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (ampicillin), 'AMC' (amoxicillin/clavulanic acid) and 'VAN' (vancomycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 3</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMP AMC VAN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> NA I R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> NA I R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> R S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> R S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA NA S </span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">ab_selector</span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">></span> <span class="fl">1</span> <span class="op">&</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `ab_selector(oral_ddd > 1 & oral_units == "g")` using columns 'OXA'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'KAN' (kanamycin), 'FOS'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (fosfomycin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'ERY' (erythromycin),</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'CLI' (clindamycin), 'MTR' (metronidazole) and 'CHL' (chloramphenicol)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 13</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX AMC AMP KAN FOS LNZ VAN ERY CLI MTR CHL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> NA NA NA I NA NA NA R R R R NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> NA NA NA I NA NA NA R R R R NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> NA R NA NA NA NA NA NA S R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> NA R NA NA NA NA NA NA S R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> NA R NA NA NA NA NA NA S R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> NA R NA NA NA NA NA NA S R R NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> NA S R S R NA NA NA S S NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> NA S R S R NA NA NA S S NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA R NA NA NA NA NA NA S R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA S NA NA NA NA NA NA S S NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># get AMR for all aminoglycosides e.g., per hospital:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># get AMR for all aminoglycosides e.g., per ward:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span>, <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 23 results available for KAN in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward GEN TOB AMK KAN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 0.229 0.315 0.626 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 0.290 0.400 0.662 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 0.2 0.368 0.605 <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># You can combine selectors with '&' to be more specific:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span> <span class="op">&</span> <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `penicillins()` using columns 'PEN' (benzylpenicillin), 'OXA'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin) and 'TZP'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (piperacillin/tazobactam)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `administrable_per_os()` using columns 'OXA' (oxacillin), 'FLC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin) and 'RIF'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (rifampicin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX AMC AMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> NA NA NA I NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> NA NA NA I NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> NA R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> NA R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> NA R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> NA R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> NA S R S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> NA S R S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA S NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># get AMR for only drugs that matter - no intrinsic resistance:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia"</span>, <span class="st">"Klebsiella"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia"</span>, <span class="st">"Klebsiella"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">not_intrinsic_resistant</span><span class="op">(</span><span class="op">)</span>, <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_genus()`</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `not_intrinsic_resistant()` removing columns 'PEN'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (benzylpenicillin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'TEC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (teicoplanin), 'ERY' (erythromycin), 'CLI' (clindamycin), 'AZM'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (azithromycin) and 'RIF' (rifampicin)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: ward = "Clinical"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: ward = "Outpatient"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: ward = "Clinical"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: ward = "Outpatient"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for AMX in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for AMC in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for AMP in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 24 results available for TZP in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 23 results available for CZO in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 10 results available for CZO in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 20 results available for FEP in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for CXM in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 22 results available for FOX in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for CTX in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for CAZ in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for CRO in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for GEN in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for TOB in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 15 results available for AMK in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: ward = "Clinical"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: ward = "Outpatient"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 22 results available for TMP in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for SXT in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for NIT in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for FOS in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for FOS in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for CIP in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 15 results available for MFX in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 4 results available for MFX in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 5 results available for TCY in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Clinical" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for TCY in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for TCY in group: ward = "Outpatient"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 13 results available for TGC in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for TGC in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: ward = "Clinical"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: ward = "Outpatient"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 24 results available for IPM in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for MEM in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for MTR in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Clinical" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: ward = "Outpatient"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: ward = "Clinical"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: ward = "Outpatient"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 9 results available for COL in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: ward = "Clinical"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: ward = "ICU"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: ward = "Outpatient"</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (`minimum` = 30).</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 33</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward OXA FLC AMX AMC AMP TZP CZO FEP CXM FOX</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clin… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 0.606 0.121 0.606 0.050<span style="text-decoration: underline;">4</span> 0.065<span style="text-decoration: underline;">6</span> 0.015<span style="text-decoration: underline;">9</span> 0.062<span style="text-decoration: underline;">2</span> 0.064<span style="text-decoration: underline;">8</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 0.535 0.172 0.535 0.119 <span style="color: #BB0000;">NA</span> 0.072<span style="text-decoration: underline;">2</span> 0.082<span style="text-decoration: underline;">8</span> 0.099<span style="text-decoration: underline;">2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outp… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 22 more variables: CTX <dbl>, CAZ <dbl>, CRO <dbl>, GEN <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <dbl>, AMK <dbl>, KAN <dbl>, TMP <dbl>, SXT <dbl>, NIT <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <dbl>, CIP <dbl>, MFX <dbl>, TCY <dbl>, TGC <dbl>, DOX <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <dbl>, MEM <dbl>, MTR <dbl>, CHL <dbl>, COL <dbl>, MUP <dbl></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># get susceptibility for antibiotics whose name contains "trim":</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">ab_selector</span><span class="op">(</span><span class="va">name</span> <span class="op"><a href="like.html">%like%</a></span> <span class="st">"trim"</span><span class="op">)</span>, <span class="va">susceptibility</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `ab_selector(name %like% "trim")` using columns 'TMP' (trimethoprim)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> and 'SXT' (trimethoprim/sulfamethoxazole)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 3</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward TMP SXT</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 0.627 0.808</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 0.549 0.778</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 0.667 0.821</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> IPM MEM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># any() and all() work in dplyr's filter() too:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">cephalosporins_2nd</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># also works with c():</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo GEN TOB AMK KAN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_ESCHR_COLI NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B_STPHY_AURS NA S NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS NA S NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B_STPHY_EPDR NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># any() and all() work in dplyr's filter() too:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">cephalosporins_2nd</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `cephalosporins_2nd()` using columns 'CXM' (cefuroxime) and 'FOX'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (cefoxitin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 112 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 4FC193 69 M Clinical B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-03-16 4FC193 69 M Clinical B_PSDMN_AERG R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-04-08 130252 78 M ICU B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-06-23 798871 82 M Clinical B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-06-23 798871 82 M Clinical B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2003-08-13 F35553 52 M ICU B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2003-09-05 F35553 52 M ICU B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2004-06-09 529296 69 M ICU B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 102 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># also works with c():</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># not setting any/all will automatically apply all():</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 531 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 4FC193 69 M Clinical B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-03-16 4FC193 69 M Clinical B_PSDMN_AERG R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-03-17 B30560 78 M Clinical B_STPHY_CONS R NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-04-04 E61143 67 M Clinical B_STRPT_SNGN S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-04-08 130252 78 M ICU B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-04-14 F30196 73 M Outpati… B_STRPT_GRPB S NA S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-05-07 D91570 83 M Clinical B_STPHY_CONS R NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-05-07 D91570 83 M Clinical B_STPHY_CONS R NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-05-14 077552 86 F Clinical B_STRPT_PNMN S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-05-14 077552 86 F Clinical B_STRPT_PNMN S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 521 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># not setting any/all will automatically apply all():</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming a filter on all 4 aminoglycosides. Wrap around `all()` or</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> `any()` to prevent this note.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 427 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 4FC193 69 M Clinical B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-03-17 B30560 78 M Clinical B_STPHY_CONS R NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-04-04 E61143 67 M Clinical B_STRPT_SNGN S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-04-08 130252 78 M ICU B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-04-14 F30196 73 M Outpati… B_STRPT_GRPB S NA S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-05-07 D91570 83 M Clinical B_STPHY_CONS R NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-05-07 D91570 83 M Clinical B_STPHY_CONS R NA R R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-05-14 077552 86 F Clinical B_STRPT_PNMN S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-05-14 077552 86 F Clinical B_STRPT_PNMN S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-05-16 D25302 65 F ICU B_STRPT_ANGN S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 417 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># this will select columns 'mo' and all antimycobacterial drugs ('RIF'):</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu">ab_class</span><span class="op">(</span><span class="st">"mycobact"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `ab_class("mycobact")` using column 'RIF' (rifampicin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo RIF </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_ESCHR_COLI R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_STPHY_EPDR NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B_STPHY_EPDR NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B_STPHY_EPDR NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B_STPHY_EPDR NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B_STPHY_AURS NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_STPHY_EPDR NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B_STPHY_EPDR NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># get bug/drug combinations for only glycopeptides in Gram-positives:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_is_gram_positive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu">glycopeptides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_is_gram_positive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu">glycopeptides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>some_column <span class="op">=</span> <span class="st">"some_value"</span>,</span></span>
|
||||
<span class="r-in"><span> J01CA01 <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># ATC code of ampicillin</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># only the 'J01CA01' column will be selected</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># with recent versions of dplyr this is all equal:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">x</span> <span class="op"><-</span> <span class="va">df</span><span class="op">[</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">y</span> <span class="op"><-</span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">z</span> <span class="op"><-</span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">if_all</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="op">~</span><span class="va">.x</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">y</span>, <span class="va">z</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin) and 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `penicillins()` using columns 'AMP' (ampicillin), 'AMC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (amoxicillin/clavulanic acid) and 'TZP' (piperacillin/tazobactam)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `administrable_per_os()` using columns 'AMP' (ampicillin), 'AMC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (amoxicillin/clavulanic acid), 'CXM' (cefuroxime), 'COL' (colistin) and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'VAN' (vancomycin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_genus()`</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `not_intrinsic_resistant()` removing columns 'TEC' (teicoplanin) and</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'VAN' (vancomycin)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Introducing NA: only 23 results available for COL in group: hospital_id =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "C" (`minimum` = 30).</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in filter(., first_isolate()):</span> Problem while computing `..1 = first_isolate()`.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="font-weight: bold;">Caused by error:</span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> in first_isolate(): `col_date` must be set</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_is_gram_positive()`</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `glycopeptides()` using columns 'VAN' (vancomycin) and 'TEC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (teicoplanin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 8</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Group Drug CoNS E. fa…¹ S. au…² S. ep…³ S. ho…⁴ S. pn…⁵</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> <span style="color: #949494;">"</span>Glycopeptides<span style="color: #949494;">"</span> Teicoplanin (TE… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span>64.1%… <span style="color: #949494;">"</span> 6.8%… <span style="color: #949494;">""</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> <span style="color: #949494;">""</span> Vancomycin (VAN… <span style="color: #949494;">"</span> 0.… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with abbreviated variable names ¹`E. faecalis`, ²`S. aureus`,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ³`S. epidermidis`, ⁴`S. hominis`, ⁵`S. pneumoniae`</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> some_column <span class="op">=</span> <span class="st">"some_value"</span>,</span></span>
|
||||
<span class="r-in"><span> J01CA01 <span class="op">=</span> <span class="st">"S"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># ATC code of ampicillin</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># only the 'J01CA01' column will be selected</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `penicillins()` using column 'J01CA01' (ampicillin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> J01CA01</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 S</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># with recent versions of dplyr this is all equal:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">x</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">y</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">z</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">if_all</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="op">~</span> <span class="va">.x</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span> <span class="op">&&</span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">y</span>, <span class="va">z</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming a filter on all 2 carbapenems. Wrap around `all()` or `any()` to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> prevent this note.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming a filter on all 2 carbapenems. Wrap around `all()` or `any()` to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> prevent this note.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -142,7 +142,7 @@
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
|
||||
<div class="section">
|
||||
<h3 id="for-the-antibiotics-data-set-a-data-frame-with-observations-and-variables-">For the antibiotics data set: a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 464 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antibiotics-data-set-a-data-frame-with-observations-and-variables-"></a></h3>
|
||||
<h3 id="for-the-antibiotics-data-set-a-tibbletibble-tibble-with-observations-and-variables-">For the antibiotics data set: a [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 464 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antibiotics-data-set-a-tibbletibble-tibble-with-observations-and-variables-"></a></h3>
|
||||
|
||||
<ul><li><p><code>ab</code><br> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
|
||||
<li><p><code>cid</code><br> Compound ID as found in PubChem</p></li>
|
||||
@@ -161,7 +161,7 @@
|
||||
</ul></div>
|
||||
|
||||
<div class="section">
|
||||
<h3 id="for-the-antivirals-data-set-a-data-frame-with-observations-and-variables-">For the antivirals data set: a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 102 observations and 9 variables:<a class="anchor" aria-label="anchor" href="#for-the-antivirals-data-set-a-data-frame-with-observations-and-variables-"></a></h3>
|
||||
<h3 id="for-the-antivirals-data-set-a-tibbletibble-tibble-with-observations-and-variables-">For the antivirals data set: a [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 102 observations and 9 variables:<a class="anchor" aria-label="anchor" href="#for-the-antivirals-data-set-a-tibbletibble-tibble-with-observations-and-variables-"></a></h3>
|
||||
|
||||
<ul><li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
|
||||
<li><p><code>cid</code><br> Compound ID as found in PubChem</p></li>
|
||||
@@ -174,7 +174,7 @@
|
||||
<li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
|
||||
</ul></div>
|
||||
|
||||
<p>An object of class <code>data.frame</code> with 102 rows and 9 columns.</p>
|
||||
<p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 102 rows and 9 columns.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
|
||||
@@ -188,18 +188,9 @@
|
||||
<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
|
||||
|
||||
|
||||
<p>These data sets are available as 'flat files' for use even without <span style="R">R</span> - you can find the files here:</p><ul><li><p><a href="https://github.com/msberends/AMR/raw/main/data-raw/antibiotics.txt" class="external-link">https://github.com/msberends/AMR/raw/main/data-raw/antibiotics.txt</a></p></li>
|
||||
<li><p><a href="https://github.com/msberends/AMR/raw/main/data-raw/antivirals.txt" class="external-link">https://github.com/msberends/AMR/raw/main/data-raw/antivirals.txt</a></p></li>
|
||||
</ul><p>Files in <span style="R">R</span> format (with preserved data structure) can be found here:</p><ul><li><p><a href="https://github.com/msberends/AMR/raw/main/data/antibiotics.rda" class="external-link">https://github.com/msberends/AMR/raw/main/data/antibiotics.rda</a></p></li>
|
||||
<li><p><a href="https://github.com/msberends/AMR/raw/main/data/antivirals.rda" class="external-link">https://github.com/msberends/AMR/raw/main/data/antivirals.rda</a></p></li>
|
||||
</ul></div>
|
||||
<p>Like all data sets in this package, these data sets are publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="whocc">WHOCC<a class="anchor" aria-label="anchor" href="#whocc"></a></h2>
|
||||
@@ -218,78 +209,39 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">antibiotics</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ab cid name group</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 AMA 4649 4-aminosalicylic acid Antimycobacterials</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 FCT 3366 5-fluorocytosine Antifungals/antimycotics</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 ACM 6450012 Acetylmidecamycin Macrolides/lincosamides</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 ASP 49787020 Acetylspiramycin Macrolides/lincosamides</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 ALS 8954 Aldesulfone sodium Other antibacterials</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 AMK 37768 Amikacin Aminoglycosides</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> atc atc_group1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 J04AA01 Drugs for treatment of tuberculosis</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 D01AE21 Antifungals for topical use</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 NA <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 NA <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 J04BA03 Drugs for treatment of lepra</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 D06AX12, J01GB06, S01AA21 Aminoglycoside antibacterials</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> atc_group2 abbreviations</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Aminosalicylic acid and derivatives </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 Other antifungals for topical use 5flc, fcu, fluo, fluy</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 <NA> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 <NA> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Drugs for treatment of lepra </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Other aminoglycosides ak, ami, amik, amk, an</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> synonyms</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 aminopar, aminosalicylic, aminosalicylic acid, aminosalyl, aminox, apacil, deapasil, entepas, ferrosan, gabbropas, helipidyl, hellipidyl, neopasalate, osacyl, pamacyl, pamisyl, paramycin, parasal, parasalicil, parasalindon, pasalon, pasara, pascorbic, pasdium, paser granules, paskalium, pasmed, pasnodia, pasolac, propasa, rezipas, teebacin, wln: zr cq dvq</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 alcobon, ancobon, ancotil, ancotyl, flucitosina, flucystine, flucytosin, flucytosine, flucytosinum, flucytosone, fluocytosine, fluorcytosine</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 acetylspiramycin, foromacidin b, spiramycin ii</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 adesulfone sodium, aldapsone, aldesulfona sodica, aldesulfone, aldesulfone sodique, aldesulfone sodium, diamidin, diasone, diasone sodium, diazon, novotrone, sodium aldesulphone, sodium sulfoxone, sulfoxone sodium</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 amicacin, amikacillin, amikacin, amikacin base, amikacin dihydrate, amikacin sulfate, amikacina, amikacine, amikacinum, amikavet, amikin, amiklin, amikozit, amukin, arikace, briclin, lukadin, mikavir, pierami, potentox</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> oral_ddd oral_units iv_ddd iv_units</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 12.00 g NA <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 NA <NA> NA <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 NA <NA> NA <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 NA <NA> NA <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 0.33 g NA <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 NA <NA> 1 g</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> loinc</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 10974-4, 23805-5, 25142-1, 25143-9, 3639-2, 46218-4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 13546-7, 15098-7, 17798-0, 31097-9, 31098-7, 31099-5, 3319-1, 3320-9, 3321-7, 35669-1, 50802-8, 50803-6, 56628-1, 59378-0, 80972-3</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">antivirals</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> atc cid name</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 J05AF06 441300 Abacavir</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 J05AB01 135398513 Aciclovir</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 J05AF08 60871 Adefovir dipivoxil</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 J05AE05 65016 Amprenavir</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 J05AP06 16076883 Asunaprevir</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 J05AE08 148192 Atazanavir</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> atc_group</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Nucleoside and nucleotide reverse transcriptase inhibitors</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 Nucleosides and nucleotides excl. reverse transcriptase inhibitors</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 Nucleoside and nucleotide reverse transcriptase inhibitors</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 Protease inhibitors</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Antivirals for treatment of HCV infections</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Protease inhibitors</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> synonyms</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Abacavir, Abacavir sulfate, Ziagen</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 Acicloftal, Aciclovier, Aciclovir, Aciclovirum, Activir, AcycloFoam, Acycloguanosine, Acyclovir, Acyclovir Lauriad, ACYCLOVIR SODIUM, Avirax, Cargosil, Cyclovir, Genvir, Gerpevir, Hascovir, Herpevir, Maynar, Poviral, Sitavig, Sitavir, Vipral, Virolex, Viropump, Virorax, Zovirax, Zovirax topical, Zyclir</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, Adefovir dipivoxyl, Adefovir pivoxil, Adefovirdipivoxl, Bisadenine, BISADENINE, BisPMEA, Hepsera, Preveon, YouHeDing</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 Agenerase, Amprenavir, Amprenavirum, Prozei, Vertex</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Asunaprevir, Sunvepra</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Atazanavir, Atazanavir Base, Latazanavir, Reyataz, Zrivada</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> oral_ddd oral_units iv_ddd iv_units</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 0.6 g NA <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 4.0 g 4 g</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 10.0 mg NA <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1.2 g NA <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 NA <NA> NA <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 0.3 g NA <NA></span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">antibiotics</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 464 × 14</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ab cid name group atc atc_g…¹ atc_g…² abbre…³ synon…⁴ oral_…⁵</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lis></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><list></span> <span style="color: #949494; font-style: italic;"><list></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> AMA <span style="text-decoration: underline;">4</span>649 4-aminosal… Anti… <chr> Drugs … Aminos… <chr> <chr> 12 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> FCT <span style="text-decoration: underline;">3</span>366 5-fluorocy… Anti… <chr> Antifu… Other … <chr> <chr> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> ACM 6<span style="text-decoration: underline;">450</span>012 Acetylmide… Macr… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <chr> <chr> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ASP 49<span style="text-decoration: underline;">787</span>020 Acetylspir… Macr… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <chr> <chr> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ALS <span style="text-decoration: underline;">8</span>954 Aldesulfon… Othe… <chr> Drugs … Drugs … <chr> <chr> 0.33</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> AMK <span style="text-decoration: underline;">37</span>768 Amikacin Amin… <chr> Aminog… Other … <chr> <chr> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> AKF <span style="color: #BB0000;">NA</span> Amikacin/f… Amin… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <chr> <chr> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> AMX <span style="text-decoration: underline;">33</span>613 Amoxicillin Beta… <chr> Beta-l… Penici… <chr> <chr> 1.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> AMC 23<span style="text-decoration: underline;">665</span>637 Amoxicilli… Beta… <chr> Beta-l… Combin… <chr> <chr> 1.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> AXS <span style="text-decoration: underline;">465</span>441 Amoxicilli… Beta… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <chr> <chr> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 454 more rows, 4 more variables: oral_units <chr>, iv_ddd <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># iv_units <chr>, loinc <list>, and abbreviated variable names ¹atc_group1,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ²atc_group2, ³abbreviations, ⁴synonyms, ⁵oral_ddd</span></span>
|
||||
<span class="r-in"><span><span class="va">antivirals</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 102 × 9</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> atc cid name atc_g…¹ synon…² oral_…³ oral_…⁴ iv_ddd iv_un…⁵</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><list></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> J05AF06 <span style="text-decoration: underline;">441</span>300 Abacavir Nucleo… <chr> 0.6 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> J05AB01 135<span style="text-decoration: underline;">398</span>513 Aciclovir Nucleo… <chr> 4 g 4 g </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> J05AF08 <span style="text-decoration: underline;">60</span>871 Adefovir di… Nucleo… <chr> 10 mg <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> J05AE05 <span style="text-decoration: underline;">65</span>016 Amprenavir Protea… <chr> 1.2 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> J05AP06 16<span style="text-decoration: underline;">076</span>883 Asunaprevir Antivi… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> J05AE08 <span style="text-decoration: underline;">148</span>192 Atazanavir Protea… <chr> 0.3 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> J05AR15 86<span style="text-decoration: underline;">583</span>336 Atazanavir … Antivi… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> J05AR23 <span style="color: #BB0000;">NA</span> Atazanavir … Antivi… <chr> 0.3 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> J05AP03 10<span style="text-decoration: underline;">324</span>367 Boceprevir Antivi… <chr> 2.4 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> J05AB15 <span style="text-decoration: underline;">446</span>727 Brivudine Nucleo… <chr> 0.125 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 92 more rows, and abbreviated variable names ¹atc_group, ²synonyms,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ³oral_ddd, ⁴oral_units, ⁵iv_units</span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -197,7 +197,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
@@ -234,28 +234,28 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"eritromicine"</span><span class="op">)</span> <span class="co"># spelled wrong, yet works</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythrocin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythrocin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Romycin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Romycin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"ceftriaxon"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"cephtriaxone"</span><span class="op">)</span> <span class="co"># small spelling error</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"cephtriaxone"</span><span class="op">)</span> <span class="co"># small spelling error</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"cephthriaxone"</span><span class="op">)</span> <span class="co"># or a bit more severe</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"cephthriaxone"</span><span class="op">)</span> <span class="co"># or a bit more severe</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"seephthriaaksone"</span><span class="op">)</span> <span class="co"># and even this works</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># use ab_* functions to get a specific properties (see ?ab_property);</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># they use as.ab() internally:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01FA01"</span><span class="op">)</span> <span class="co"># "Erythromycin"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01FA01"</span><span class="op">)</span> <span class="co"># "Erythromycin"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Erythromycin"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"eryt"</span><span class="op">)</span> <span class="co"># "Erythromycin"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"eryt"</span><span class="op">)</span> <span class="co"># "Erythromycin"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Erythromycin"</span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
@@ -263,28 +263,27 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
<span class="r-in"><span> <span class="co"># you can quickly rename <rsi> columns using dplyr >= 1.0.0:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html" class="external-link">rename_with</a></span><span class="op">(</span><span class="va">as.ab</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospit…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 B TRUE FALSE FALSE 79 F 858515 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -175,11 +175,13 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># transform existing disk zones to the `disk` class (using base R)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
|
||||
<span class="r-in"><span> AMP <span class="op">=</span> <span class="fl">20</span>,</span></span>
|
||||
<span class="r-in"><span> CIP <span class="op">=</span> <span class="fl">14</span>,</span></span>
|
||||
<span class="r-in"><span> GEN <span class="op">=</span> <span class="fl">18</span>,</span></span>
|
||||
<span class="r-in"><span> TOB <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
|
||||
<span class="r-in"><span> AMP <span class="op">=</span> <span class="fl">20</span>,</span></span>
|
||||
<span class="r-in"><span> CIP <span class="op">=</span> <span class="fl">14</span>,</span></span>
|
||||
<span class="r-in"><span> GEN <span class="op">=</span> <span class="fl">18</span>,</span></span>
|
||||
<span class="r-in"><span> TOB <span class="op">=</span> <span class="fl">16</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fl">2</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">df</span><span class="op">[</span>, <span class="fl">2</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span>, <span class="va">as.disk</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 'data.frame': 1 obs. of 5 variables:</span>
|
||||
@@ -199,10 +201,12 @@
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># interpret disk values, see ?as.rsi</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span>x <span class="op">=</span> <span class="fu">as.disk</span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"Strep pneu"</span>, <span class="co"># `mo` will be coerced with as.mo()</span></span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu">as.disk</span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"Strep pneu"</span>, <span class="co"># `mo` will be coerced with as.mo()</span></span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'ampicillin' according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
@@ -212,17 +216,17 @@
|
||||
<span class="r-in"><span><span class="co"># interpret whole data set, pretend to be all from urinary tract infections:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="va">df</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'microorganism' as input for `col_mo`.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'AMP' (AMP, ampicillin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'AMP' (ampicillin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'CIP' (ciprofloxacin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'CIP' (CIP, ciprofloxacin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'GEN' (gentamicin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'GEN' (GEN, gentamicin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'TOB' (TOB, tobramycin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'TOB' (tobramycin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S R S S</span>
|
||||
|
||||
BIN
reference/as.mic-3.png
Normal file
BIN
reference/as.mic-3.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 49 KiB |
BIN
reference/as.mic-4.png
Normal file
BIN
reference/as.mic-4.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 47 KiB |
BIN
reference/as.mic-5.png
Normal file
BIN
reference/as.mic-5.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 48 KiB |
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -232,20 +232,24 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># interpret MIC values</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span>x <span class="op">=</span> <span class="fu">as.mic</span><span class="op">(</span><span class="fl">2</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Streptococcus pneumoniae"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMX' (AMX, amoxicillin) according to EUCAST</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu">as.mic</span><span class="op">(</span><span class="fl">2</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Streptococcus pneumoniae"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span>x <span class="op">=</span> <span class="fu">as.mic</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.01</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">8</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Streptococcus pneumoniae"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMX' (AMX, amoxicillin) according to EUCAST</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu">as.mic</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.01</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">8</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Streptococcus pneumoniae"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
@@ -258,12 +262,26 @@
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-plt img"><img src="as.mic-2.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="fu">autoplot</span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in autoplot(mic_data, mo = "E. coli", ab = "cipro"):</span> could not find function "autoplot"</span>
|
||||
<span class="r-in"><span><span class="fu">autoplot</span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># Dutch</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl"):</span> could not find function "autoplot"</span>
|
||||
<span class="r-in"><span><span class="fu">autoplot</span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "uk"):</span> could not find function "autoplot"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Loading required package: ggplot2</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-plt img"><img src="as.mic-3.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># Dutch</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-plt img"><img src="as.mic-4.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_data</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-plt img"><img src="as.mic-5.png" alt="" width="700" height="433"></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -299,7 +299,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
@@ -350,13 +350,13 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Staphylococcus aureus). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS</span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># Methicillin Resistant S. aureus</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># Methicillin Resistant S. aureus</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS</span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># Vancomycin Intermediate S. aureus</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># Vancomycin Intermediate S. aureus</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS</span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span> <span class="co"># Vancomycin Resistant S. aureus</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span> <span class="co"># Vancomycin Resistant S. aureus</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS</span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span> <span class="co"># SNOMED CT code</span></span></span>
|
||||
@@ -393,14 +393,14 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STRPT_GRPB</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span> <span class="co"># will remain species: B_STPHY_EPDR</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span> <span class="co"># will remain species: B_STPHY_EPDR</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_EPDR</span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STPHY_CONS</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STPHY_CONS</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_CONS</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span> <span class="co"># will remain species: B_STRPT_PYGN</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span> <span class="co"># will remain species: B_STRPT_PYGN</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STRPT_PYGN</span>
|
||||
<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STRPT_GRPA</span></span></span>
|
||||
@@ -408,11 +408,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] B_STRPT_GRPA</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Escherichia"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Escherichia"</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Escherichia"</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Gram negative"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Gram negative"</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative"</span>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -305,7 +305,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
@@ -315,172 +315,167 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">example_isolates</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospit…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 B TRUE FALSE FALSE 79 F 858515 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span> <span class="co"># see all R/SI results at a glance</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospital_id ward_icu ward_clinical </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Min. :2002-01-02 A:321 Mode :logical Mode :logical </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1st Qu.:2005-07-31 B:663 FALSE:1354 FALSE:536 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Median :2009-07-31 C:254 TRUE :646 TRUE :1464 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Mean :2009-11-20 D:762 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3rd Qu.:2014-05-30 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Max. :2017-12-28 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward_outpatient age gender patient_id </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Mode :logical Min. : 0.00 Length:2000 Length:2000 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FALSE:1880 1st Qu.:63.00 Class :character Class :character </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TRUE :120 Median :74.00 Mode :character Mode :character </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Mean :70.69 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3rd Qu.:82.00 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Max. :97.00 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo PEN OXA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class :mo Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <NA> :0 %R :73.7% (n=1201) %R :31.2% (n=114) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Unique:90 %SI :26.3% (n=428) %SI :68.8% (n=251) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #1 :B_ESCHR_COLI - %S :25.6% (n=417) - %S :68.8% (n=251) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #2 :B_STPHY_CONS - %I : 0.7% (n=11) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #3 :B_STPHY_AURS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FLC AMX AMC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Min. :2002-01-02 Length:2000 Min. : 0.00 Length:2000 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1st Qu.:2005-07-31 Class :character 1st Qu.:63.00 Class :character </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Median :2009-07-31 Mode :character Median :74.00 Mode :character </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Mean :2009-11-20 Mean :70.69 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3rd Qu.:2014-05-30 3rd Qu.:82.00 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Max. :2017-12-28 Max. :97.00 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward mo PEN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Length:2000 Class :mo Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class :character <NA> :0 %R :73.7% (n=1201) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Mode :character Unique:90 %SI :26.3% (n=428) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #1 :B_ESCHR_COLI - %S :25.6% (n=417) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #2 :B_STPHY_CONS - %I : 0.7% (n=11) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> #3 :B_STPHY_AURS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :31.2% (n=114) %R :29.5% (n=278) %R :59.6% (n=804) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :68.8% (n=251) %SI :70.5% (n=665) %SI :40.4% (n=546) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :68.8% (n=251) - %S :70.5% (n=665) - %S :40.2% (n=543) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.2% (n=3) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMC AMP TZP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :23.7% (n=446) %R :59.6% (n=804) %R :12.6% (n=126) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :76.3% (n=1433) %SI :40.4% (n=546) %SI :87.4% (n=875) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :71.4% (n=1342) - %S :40.2% (n=543) - %S :86.1% (n=862) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 4.8% (n=91) - %I : 0.2% (n=3) - %I : 1.3% (n=13) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CZO FEP CXM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :29.5% (n=278) %R :59.6% (n=804) %R :23.7% (n=446) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :70.5% (n=665) %SI :40.4% (n=546) %SI :76.3% (n=1433) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :70.5% (n=665) - %S :40.2% (n=543) - %S :71.4% (n=1342) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.2% (n=3) - %I : 4.8% (n=91) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :44.6% (n=199) %R :14.2% (n=103) %R :26.3% (n=470) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :55.4% (n=247) %SI :85.8% (n=621) %SI :73.7% (n=1319) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :54.9% (n=245) - %S :85.6% (n=620) - %S :72.5% (n=1297) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.4% (n=2) - %I : 0.1% (n=1) - %I : 1.2% (n=22) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMP TZP CZO </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :59.6% (n=804) %R :12.6% (n=126) %R :44.6% (n=199) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :40.4% (n=546) %SI :87.4% (n=875) %SI :55.4% (n=247) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :40.2% (n=543) - %S :86.1% (n=862) - %S :54.9% (n=245) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.2% (n=3) - %I : 1.3% (n=13) - %I : 0.4% (n=2) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FEP CXM FOX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FOX CTX CAZ </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :27.4% (n=224) %R :15.5% (n=146) %R :66.5% (n=1204) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :72.6% (n=594) %SI :84.5% (n=797) %SI :33.5% (n=607) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :71.6% (n=586) - %S :84.4% (n=796) - %S :33.5% (n=607) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 1.0% (n=8) - %I : 0.1% (n=1) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CRO GEN TOB </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :14.2% (n=103) %R :26.3% (n=470) %R :27.4% (n=224) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :85.8% (n=621) %SI :73.7% (n=1319) %SI :72.6% (n=594) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :85.6% (n=620) - %S :72.5% (n=1297) - %S :71.6% (n=586) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.1% (n=1) - %I : 1.2% (n=22) - %I : 1.0% (n=8) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :15.5% (n=146) %R :24.6% (n=456) %R :34.4% (n=465) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :84.5% (n=797) %SI :75.4% (n=1399) %SI :65.6% (n=886) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :84.4% (n=796) - %S :74.0% (n=1372) - %S :65.1% (n=879) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.1% (n=1) - %I : 1.5% (n=27) - %I : 0.5% (n=7) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CTX CAZ CRO </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMK KAN TMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :15.5% (n=146) %R :66.5% (n=1204) %R :15.5% (n=146) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :84.5% (n=797) %SI :33.5% (n=607) %SI :84.5% (n=797) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :84.4% (n=796) - %S :33.5% (n=607) - %S :84.4% (n=796) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.1% (n=1) - %I : 0.0% (n=0) - %I : 0.1% (n=1) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :63.7% (n=441) %R :100.0% (n=471) %R :38.1% (n=571) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :36.3% (n=251) %SI : 0.0% (n=0) %SI :61.9% (n=928) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :36.3% (n=251) - %S : 0.0% (n=0) - %S :61.2% (n=918) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.7% (n=10) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> GEN TOB AMK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> SXT NIT FOS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :24.6% (n=456) %R :34.4% (n=465) %R :63.7% (n=441) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :75.4% (n=1399) %SI :65.6% (n=886) %SI :36.3% (n=251) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :74.0% (n=1372) - %S :65.1% (n=879) - %S :36.3% (n=251) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 1.5% (n=27) - %I : 0.5% (n=7) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :20.5% (n=361) %R :17.1% (n=127) %R :42.2% (n=148) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :79.5% (n=1398) %SI :82.9% (n=616) %SI :57.8% (n=203) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :79.1% (n=1392) - %S :76.0% (n=565) - %S :57.8% (n=203) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.3% (n=6) - %I : 6.9% (n=51) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> KAN TMP SXT </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :100.0% (n=471) %R :38.1% (n=571) %R :20.5% (n=361) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI : 0.0% (n=0) %SI :61.9% (n=928) %SI :79.5% (n=1398) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S : 0.0% (n=0) - %S :61.2% (n=918) - %S :79.1% (n=1392) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.7% (n=10) - %I : 0.3% (n=6) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> NIT FOS LNZ </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :17.1% (n=127) %R :42.2% (n=148) %R :69.3% (n=709) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :82.9% (n=616) %SI :57.8% (n=203) %SI :30.7% (n=314) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :76.0% (n=565) - %S :57.8% (n=203) - %S :30.7% (n=314) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 6.9% (n=51) - %I : 0.0% (n=0) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CIP MFX VAN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :16.2% (n=228) %R :33.6% (n=71) %R :38.3% (n=712) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :83.8% (n=1181) %SI :66.4% (n=140) %SI :61.7% (n=1149) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :78.9% (n=1112) - %S :64.5% (n=136) - %S :61.7% (n=1149) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 4.9% (n=69) - %I : 1.9% (n=4) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TEC TCY TGC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :75.7% (n=739) %R :29.8% (n=357) %R :12.7% (n=101) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :24.3% (n=237) %SI :70.3% (n=843) %SI :87.3% (n=697) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :24.3% (n=237) - %S :68.3% (n=820) - %S :87.3% (n=697) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 1.9% (n=23) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> DOX ERY CLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> LNZ CIP MFX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :27.7% (n=315) %R :57.2% (n=1084) %R :61.2% (n=930) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :72.3% (n=821) %SI :42.8% (n=810) %SI :38.8% (n=590) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :71.7% (n=814) - %S :42.3% (n=801) - %S :38.6% (n=586) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.6% (n=7) - %I : 0.5% (n=9) - %I : 0.3% (n=4) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :69.3% (n=709) %R :16.2% (n=228) %R :33.6% (n=71) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :30.7% (n=314) %SI :83.8% (n=1181) %SI :66.4% (n=140) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :30.7% (n=314) - %S :78.9% (n=1112) - %S :64.5% (n=136) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 4.9% (n=69) - %I : 1.9% (n=4) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AZM IPM MEM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> VAN TEC TCY </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :57.2% (n=1084) %R : 6.2% (n=55) %R : 5.9% (n=49) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :42.8% (n=810) %SI :93.8% (n=834) %SI :94.1% (n=780) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :42.3% (n=801) - %S :92.7% (n=824) - %S :94.1% (n=780) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.5% (n=9) - %I : 1.1% (n=10) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :38.3% (n=712) %R :75.7% (n=739) %R :29.8% (n=357) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :61.7% (n=1149) %SI :24.3% (n=237) %SI :70.3% (n=843) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :61.7% (n=1149) - %S :24.3% (n=237) - %S :68.3% (n=820) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 1.9% (n=23) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TGC DOX ERY </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :12.7% (n=101) %R :27.7% (n=315) %R :57.2% (n=1084) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :87.3% (n=697) %SI :72.3% (n=821) %SI :42.8% (n=810) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :87.3% (n=697) - %S :71.7% (n=814) - %S :42.3% (n=801) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.6% (n=7) - %I : 0.5% (n=9) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CLI AZM IPM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :61.2% (n=930) %R :57.2% (n=1084) %R : 6.2% (n=55) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :38.8% (n=590) %SI :42.8% (n=810) %SI :93.8% (n=834) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :38.6% (n=586) - %S :42.3% (n=801) - %S :92.7% (n=824) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.3% (n=4) - %I : 0.5% (n=9) - %I : 1.1% (n=10) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MEM MTR CHL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R : 5.9% (n=49) %R :14.7% (n=5) %R :21.4% (n=33) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :94.1% (n=780) %SI :85.3% (n=29) %SI :78.6% (n=121) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :94.1% (n=780) - %S :85.3% (n=29) - %S :78.6% (n=121) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> COL MUP RIF </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :81.2% (n=1331) %R : 5.9% (n=16) %R :69.6% (n=698) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :18.8% (n=309) %SI :94.1% (n=254) %SI :30.4% (n=305) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :18.8% (n=309) - %S :93.0% (n=251) - %S :30.2% (n=303) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 1.1% (n=3) - %I : 0.2% (n=2) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MTR CHL COL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :14.7% (n=5) %R :21.4% (n=33) %R :81.2% (n=1331) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :85.3% (n=29) %SI :78.6% (n=121) %SI :18.8% (n=309) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :85.3% (n=29) - %S :78.6% (n=121) - %S :18.8% (n=309) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MUP RIF </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R : 5.9% (n=16) %R :69.6% (n=698) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :94.1% (n=254) %SI :30.4% (n=305) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :93.0% (n=251) - %S :30.2% (n=303) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 1.1% (n=3) - %I : 0.2% (n=2) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># a whole data set, even with combined MIC values and disk zones</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
|
||||
<span class="r-in"><span> AMP <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">8</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> CIP <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.256</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> GEN <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> TOB <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">16</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ERY <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
|
||||
<span class="r-in"><span> AMP <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">8</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> CIP <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.256</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> GEN <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> TOB <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">16</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ERY <span class="op">=</span> <span class="st">"R"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'microorganism' as input for `col_mo`.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'AMP' (AMP, ampicillin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'CIP' (ciprofloxacin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'CIP' (CIP, ciprofloxacin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'GEN' (gentamicin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'GEN' (GEN, gentamicin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'TOB' (TOB, tobramycin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'TOB' (tobramycin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (NIT, nitrofurantoin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
@@ -491,22 +486,26 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S <NA> R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># for single values</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S. pneumoniae"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMP"</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S. pneumoniae"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMP"</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "S. pneumoniae" (assuming</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Streptococcus pneumoniae). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"Strep pneu"</span>, <span class="co"># `mo` will be coerced with as.mo()</span></span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"Strep pneu"</span>, <span class="co"># `mo` will be coerced with as.mo()</span></span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'ampicillin' according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
@@ -521,122 +520,126 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="va">.</span><span class="op">$</span><span class="va">microorganism</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># to include information about urinary tract infections (UTI)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> from_the_bladder <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> from_the_bladder <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">as.rsi</span><span class="op">(</span>uti <span class="op">=</span> <span class="st">"from_the_bladder"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> specimen <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"urine"</span>, <span class="st">"blood"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> specimen <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"urine"</span>, <span class="st">"blood"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">as.rsi</span><span class="op">(</span><span class="op">)</span> <span class="co"># automatically determines urine isolates</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">NIT</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">NIT</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
@@ -644,8 +647,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (NIT, nitrofurantoin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> infection.</span>
|
||||
@@ -653,26 +656,26 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (NIT, nitrofurantoin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (nitrofurantoin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB NIT ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S S R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@@ -689,7 +692,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span><span class="va">rsi_data</span> <span class="op"><-</span> <span class="fu">as.rsi</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="fl">474</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"I"</span>, <span class="fl">36</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"R"</span>, <span class="fl">370</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">is.rsi</span><span class="op">(</span><span class="va">rsi_data</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">rsi_data</span><span class="op">)</span> <span class="co"># for percentages</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">rsi_data</span><span class="op">)</span> <span class="co"># for percentages</span></span></span>
|
||||
<span class="r-plt img"><img src="as.rsi-1.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot</a></span><span class="op">(</span><span class="va">rsi_data</span><span class="op">)</span> <span class="co"># for frequencies</span></span></span>
|
||||
<span class="r-plt img"><img src="as.rsi-2.png" alt="" width="700" height="433"></span>
|
||||
@@ -698,38 +701,38 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">PEN</span><span class="op">:</span><span class="va">RIF</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># same: </span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># same:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">as.rsi</span><span class="op">(</span><span class="va">PEN</span><span class="op">:</span><span class="va">RIF</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># fastest way to transform all columns with already valid AMR results to class `rsi`:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.rsi.eligible</span>, <span class="va">as.rsi</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># since dplyr 1.0.0, this can also be: </span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># since dplyr 1.0.0, this can also be:</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># example_isolates %>%</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># mutate(across(where(is.rsi.eligible), as.rsi))</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospit…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 B TRUE FALSE FALSE 79 F 858515 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -204,7 +204,7 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"curl"</span><span class="op">)</span> <span class="op">&&</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"rvest"</span><span class="op">)</span> <span class="op">&&</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"xml2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> </span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"curl"</span><span class="op">)</span> <span class="op">&&</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"rvest"</span><span class="op">)</span> <span class="op">&&</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"xml2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># oral DDD (Defined Daily Dose) of amoxicillin</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, <span class="st">"DDD"</span>, <span class="st">"O"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">atc_online_ddd</span><span class="op">(</span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"amox"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -160,65 +160,60 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">availability</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> count available visual_availabilty resistant visual_resistance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date 2000 100.0% |################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> hospital_id 2000 100.0% |################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward_icu 2000 100.0% |################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward_clinical 2000 100.0% |################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward_outpatient 2000 100.0% |################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> age 2000 100.0% |################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> gender 2000 100.0% |################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient_id 2000 100.0% |################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo 2000 100.0% |################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> PEN 1629 81.5% |############----| 73.7% |###########-----|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA 365 18.3% |##--------------| 31.2% |#####-----------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FLC 943 47.2% |#######---------| 29.5% |####------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMX 1350 67.5% |##########------| 59.6% |#########-------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMC 1879 94.0% |###############-| 23.7% |###-------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMP 1350 67.5% |##########------| 59.6% |#########-------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TZP 1001 50.0% |########--------| 12.6% |##--------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CZO 446 22.3% |###-------------| 44.6% |#######---------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FEP 724 36.2% |#####-----------| 14.2% |##--------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CXM 1789 89.5% |##############--| 26.3% |####------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FOX 818 40.9% |######----------| 27.4% |####------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CTX 943 47.2% |#######---------| 15.5% |##--------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CAZ 1811 90.6% |##############--| 66.5% |##########------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CRO 943 47.2% |#######---------| 15.5% |##--------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> GEN 1855 92.8% |##############--| 24.6% |###-------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TOB 1351 67.6% |##########------| 34.4% |#####-----------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMK 692 34.6% |#####-----------| 63.7% |##########------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> KAN 471 23.6% |###-------------| 100.0% |################|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TMP 1499 75.0% |############----| 38.1% |######----------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> SXT 1759 88.0% |##############--| 20.5% |###-------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> NIT 743 37.2% |#####-----------| 17.1% |##--------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FOS 351 17.6% |##--------------| 42.2% |######----------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> LNZ 1023 51.2% |########--------| 69.3% |###########-----|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CIP 1409 70.5% |###########-----| 16.2% |##--------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MFX 211 10.6% |#---------------| 33.6% |#####-----------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> VAN 1861 93.1% |##############--| 38.3% |######----------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TEC 976 48.8% |#######---------| 75.7% |############----|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TCY 1200 60.0% |#########-------| 29.8% |####------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TGC 798 39.9% |######----------| 12.7% |##--------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> DOX 1136 56.8% |#########-------| 27.7% |####------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ERY 1894 94.7% |###############-| 57.2% |#########-------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CLI 1520 76.0% |############----| 61.2% |#########-------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AZM 1894 94.7% |###############-| 57.2% |#########-------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> IPM 889 44.5% |#######---------| 6.2% |----------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MEM 829 41.5% |######----------| 5.9% |----------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MTR 34 1.7% |----------------| 14.7% |##--------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CHL 154 7.7% |#---------------| 21.4% |###-------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> COL 1640 82.0% |#############---| 81.2% |############----|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MUP 270 13.5% |##--------------| 5.9% |----------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> RIF 1003 50.2% |########--------| 69.6% |###########-----|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> count available visual_availabilty resistant visual_resistance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date 2000 100.0% |####################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient 2000 100.0% |####################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> age 2000 100.0% |####################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> gender 2000 100.0% |####################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward 2000 100.0% |####################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo 2000 100.0% |####################| </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> PEN 1629 81.5% |################----| 73.7% |##############------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA 365 18.3% |###-----------------| 31.2% |######--------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FLC 943 47.2% |#########-----------| 29.5% |#####---------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMX 1350 67.5% |#############-------| 59.6% |###########---------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMC 1879 94.0% |##################--| 23.7% |####----------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMP 1350 67.5% |#############-------| 59.6% |###########---------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TZP 1001 50.0% |##########----------| 12.6% |##------------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CZO 446 22.3% |####----------------| 44.6% |########------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FEP 724 36.2% |#######-------------| 14.2% |##------------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CXM 1789 89.5% |#################---| 26.3% |#####---------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FOX 818 40.9% |########------------| 27.4% |#####---------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CTX 943 47.2% |#########-----------| 15.5% |###-----------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CAZ 1811 90.6% |##################--| 66.5% |#############-------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CRO 943 47.2% |#########-----------| 15.5% |###-----------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> GEN 1855 92.8% |##################--| 24.6% |####----------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TOB 1351 67.6% |#############-------| 34.4% |######--------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMK 692 34.6% |######--------------| 63.7% |############--------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> KAN 471 23.6% |####----------------| 100.0% |####################|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TMP 1499 75.0% |###############-----| 38.1% |#######-------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> SXT 1759 88.0% |#################---| 20.5% |####----------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> NIT 743 37.2% |#######-------------| 17.1% |###-----------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> FOS 351 17.6% |###-----------------| 42.2% |########------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> LNZ 1023 51.2% |##########----------| 69.3% |#############-------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CIP 1409 70.5% |#############-------| 16.2% |###-----------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MFX 211 10.6% |##------------------| 33.6% |######--------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> VAN 1861 93.1% |##################--| 38.3% |#######-------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TEC 976 48.8% |#########-----------| 75.7% |###############-----|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TCY 1200 60.0% |###########---------| 29.8% |#####---------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TGC 798 39.9% |########------------| 12.7% |##------------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> DOX 1136 56.8% |###########---------| 27.7% |#####---------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ERY 1894 94.7% |##################--| 57.2% |###########---------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CLI 1520 76.0% |###############-----| 61.2% |############--------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AZM 1894 94.7% |##################--| 57.2% |###########---------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> IPM 889 44.5% |########------------| 6.2% |#-------------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MEM 829 41.5% |########------------| 5.9% |#-------------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MTR 34 1.7% |--------------------| 14.7% |##------------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CHL 154 7.7% |#-------------------| 21.4% |####----------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> COL 1640 82.0% |################----| 81.2% |################----|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MUP 270 13.5% |##------------------| 5.9% |#-------------------|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> RIF 1003 50.2% |##########----------| 69.6% |#############-------|</span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">mo</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">mo</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select_all.html" class="external-link">select_if</a></span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">availability</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> count available visual_availabilty resistant visual_resistance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> PEN 467 100.0% |######################| 100.0% |######################|</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> OXA 0 0.0% |----------------------| </span>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -158,7 +158,7 @@
|
||||
<div class="section level2">
|
||||
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
|
||||
<dl><dt>x</dt>
|
||||
<dd><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
|
||||
<dd><p>a data set with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
|
||||
|
||||
|
||||
<dt>col_mo</dt>
|
||||
@@ -229,351 +229,79 @@
|
||||
<span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo ab S I R total</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 (unknown species) PEN 14 0 1 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 (unknown species) OXA 0 0 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 (unknown species) FLC 0 0 0 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 (unknown species) AMX 15 0 1 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 (unknown species) AMC 15 0 0 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 (unknown species) AMP 15 0 1 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 6 × 6</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo ab S I R total</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> (unknown species) PEN 14 0 1 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> (unknown species) OXA 0 0 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> (unknown species) FLC 0 0 0 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> (unknown species) AMX 15 0 1 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> (unknown species) AMC 15 0 0 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">6</span> (unknown species) AMP 15 0 1 16</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, translate_ab <span class="op">=</span> <span class="st">"name (atc)"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Group Drug</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Aminoglycosides Amikacin (J01GB06)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 Gentamicin (J01GB03)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 Kanamycin (J01GB04)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 Tobramycin (J01GB01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Amphenicols Chloramphenicol (J01BA01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Antimycobacterials Rifampicin (J04AB02)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 Beta-lactams/penicillins Amoxicillin (J01CA04)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 Amoxicillin/clavulanic acid (J01CR02)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 Ampicillin (J01CA01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 Benzylpenicillin (J01CE01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 11 Flucloxacillin (J01CF05)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 12 Oxacillin (J01CF04)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 13 Piperacillin/tazobactam (J01CR05)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 14 Carbapenems Imipenem (J01DH51)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 15 Meropenem (J01DH02)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 16 Cephalosporins (1st gen.) Cefazolin (J01DB04)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 17 Cephalosporins (2nd gen.) Cefoxitin (J01DC01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 18 Cefuroxime (J01DC02)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 19 Cephalosporins (3rd gen.) Cefotaxime (J01DD01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 20 Ceftazidime (J01DD02)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 21 Ceftriaxone (J01DD04)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 22 Cephalosporins (4th gen.) Cefepime (J01DE01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 23 Glycopeptides Teicoplanin (J01XA02)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 24 Vancomycin (J01XA01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 25 Macrolides/lincosamides Azithromycin (J01FA10)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 26 Clindamycin (J01FF01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 27 Erythromycin (J01FA01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 28 Other antibacterials Fosfomycin (J01XX01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 29 Mupirocin (D06AX09)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 30 Nitrofurantoin (J01XE01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 31 Oxazolidinones Linezolid (J01XX08)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 32 Polymyxins Colistin (J01XB01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 33 Quinolones Ciprofloxacin (J01MA02)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 34 Moxifloxacin (J01MA14)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 35 Tetracyclines Doxycycline (J01AA02)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 36 Tetracycline (J01AA07)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 37 Tigecycline (J01AA12)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 38 Trimethoprims Trimethoprim (J01EA01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 39 Trimethoprim/sulfamethoxazole (J01EE01)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CoNS E. coli E. faecalis K. pneumoniae</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 100.0% (43/43) 0.0% (0/171) 100.0% (39/39) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 13.6% (42/309) 2.0% (9/460) 100.0% (39/39) 10.3% (6/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 100.0% (43/43) 100.0% (39/39) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 78.2% (43/55) 2.6% (12/462) 100.0% (39/39) 10.3% (6/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 100.0% (467/467) 100.0% (58/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 93.0% (132/142) 50.0% (196/392) 100.0% (58/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 42.6% (132/310) 13.1% (61/467) 10.3% (6/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 93.0% (132/142) 50.0% (196/392) 100.0% (58/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 77.6% (228/294) 100.0% (467/467) 100.0% (58/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 11 42.8% (134/313) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 12 54.8% (34/62) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 13 69.7% (23/33) 5.5% (23/416) 11.3% (6/53)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 14 47.9% (23/48) 0.0% (0/422) 0.0% (0/38) 0.0% (0/51)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 15 47.9% (23/48) 0.0% (0/418) 0.0% (0/53)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 16 47.9% (23/48) 2.4% (2/82) 100.0% (39/39) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 17 47.9% (23/48) 6.9% (26/377) 100.0% (39/39) 2.2% (1/46)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 18 42.6% (133/312) 5.4% (25/465) 100.0% (39/39) 10.3% (6/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 19 47.9% (23/48) 2.4% (11/459) 100.0% (39/39) 5.2% (3/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 20 100.0% (313/313) 2.4% (11/460) 100.0% (39/39) 5.2% (3/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 21 47.9% (23/48) 2.4% (11/459) 100.0% (39/39) 5.2% (3/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 22 47.9% (23/48) 2.8% (9/317) 100.0% (39/39) 5.3% (2/38)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 23 100.0% (467/467) 100.0% (58/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 24 0.3% (1/304) 100.0% (467/467) 0.0% (0/39) 100.0% (58/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 25 44.1% (138/313) 100.0% (467/467) 100.0% (39/39) 100.0% (58/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 26 33.5% (59/176) 100.0% (467/467) 100.0% (39/39) 100.0% (58/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 27 44.1% (138/313) 100.0% (467/467) 100.0% (39/39) 100.0% (58/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 28 0.0% (0/61) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 29 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 30 2.8% (13/458) 19.0% (11/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 31 100.0% (467/467) 100.0% (58/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 32 100.0% (313/313) 0.0% (0/240) 100.0% (39/39) 5.9% (2/34)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 33 27.4% (69/252) 12.5% (57/456) 3.6% (2/55)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 34 100.0% (57/57) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 35 22.2% (67/302) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 36 22.5% (59/262) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 37 0.0% (0/195) 0.0% (0/68) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 38 41.4% (126/304) 39.1% (155/396) 100.0% (39/39) 18.4% (9/49)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 39 12.2% (30/246) 31.6% (147/465) 100.0% (39/39) 10.3% (6/58)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> P. aeruginosa P. mirabilis S. aureus S. epidermidis</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 100.0% (44/44)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 0.0% (0/30) 5.9% (2/34) 0.9% (2/233) 21.5% (35/163)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 100.0% (30/30) 100.0% (44/44)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 0.0% (0/30) 5.9% (2/34) 2.3% (2/86) 49.4% (44/89)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 100.0% (30/30) 0.0% (0/46) 3.1% (1/32)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 100.0% (30/30) 100.0% (36/36) 0.0% (0/108) 2.7% (2/73)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 100.0% (30/30) 93.9% (123/131) 98.9% (90/91)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 100.0% (30/30) 2.8% (1/36) 0.4% (1/235) 54.5% (90/165)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 100.0% (30/30) 93.9% (123/131) 98.9% (90/91)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 100.0% (30/30) 100.0% (36/36) 80.9% (123/152) 89.4% (93/104)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 11 0.4% (1/235) 55.7% (97/174)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 12 0.0% (0/99) 50.0% (37/74)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 13 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 14 6.3% (2/32) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 15 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 16 100.0% (30/30) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 17 100.0% (30/30) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 18 100.0% (30/30) 0.0% (0/36) 0.4% (1/235) 56.1% (97/173)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 19 100.0% (30/30) 0.0% (0/36) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 20 3.3% (1/30) 0.0% (0/36) 100.0% (235/235) 100.0% (174/174)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 21 100.0% (30/30) 0.0% (0/36) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 22 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 23 100.0% (30/30) 100.0% (36/36) 0.0% (0/80) 64.1% (25/39)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 24 100.0% (30/30) 100.0% (36/36) 0.0% (0/232) 0.0% (0/171)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 25 100.0% (30/30) 100.0% (36/36) 8.9% (21/235) 53.8% (93/173)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 26 100.0% (30/30) 100.0% (36/36) 6.0% (9/151) 37.5% (42/112)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 27 100.0% (30/30) 100.0% (36/36) 8.9% (21/235) 53.8% (93/173)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 28 0.0% (0/80) 21.9% (14/64)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 29 0.0% (0/84) 8.7% (6/69)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 30 100.0% (36/36) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 31 100.0% (30/30) 100.0% (36/36) 0.0% (0/82) 0.0% (0/68)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 32 100.0% (36/36) 100.0% (235/235) 100.0% (174/174)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 33 0.0% (0/30) 5.6% (2/36) 10.5% (20/191) 36.0% (49/136)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 34 2.2% (1/46) 0.0% (0/31)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 35 100.0% (30/30) 100.0% (36/36) 3.0% (7/231) 32.4% (55/170)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 36 100.0% (30/30) 100.0% (36/36) 3.2% (7/217) 32.9% (55/167)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 37 100.0% (30/30) 100.0% (36/36) 0.0% (0/209) 0.0% (0/109)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 38 100.0% (30/30) 36.4% (12/33) 8.4% (13/155) 58.5% (69/118)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 39 100.0% (30/30) 25.0% (9/36) 3.9% (9/231) 17.5% (24/137)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> S. hominis S. pneumoniae</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 100.0% (117/117)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 7.5% (6/80) 100.0% (117/117)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 100.0% (117/117)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 14.5% (9/62) 100.0% (117/117)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 6.5% (2/31) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 0.0% (0/61) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 0.0% (0/112)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 35.0% (28/80) 0.0% (0/112)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 0.0% (0/112)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 0.0% (0/117)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 11 34.6% (28/81) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 12 39.7% (23/58) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 13 0.0% (0/112)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 14 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 15 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 17 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 18 33.3% (27/81) 0.0% (0/61)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 19 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 20 100.0% (81/81) 100.0% (117/117)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 21 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 22 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 23 6.8% (4/59) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 24 0.0% (0/81) 0.0% (0/94)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 25 40.7% (33/81) 7.8% (9/116)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 26 29.4% (20/68) 6.5% (4/62)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 27 40.7% (33/81) 7.8% (9/116)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 28 100.0% (59/59) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 29 1.6% (1/61) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 30 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 31 0.0% (0/60) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 32 100.0% (81/81) 100.0% (117/117)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 33 20.0% (14/70) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 34 0.0% (0/32) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 35 55.0% (44/80) 4.5% (5/112)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 36 54.3% (44/81) 4.7% (5/106)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 37 0.0% (0/36) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 38 57.9% (22/38) 17.9% (17/95)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 39 24.7% (20/81) 7.3% (8/109)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 39 × 12</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Group Drug CoNS E. co…¹ E. fa…² K. pn…³ P. ae…⁴ P. mi…⁵ S. au…⁶ S. ep…⁷</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">"</span>Aminogl… Amik… <span style="color: #949494;">"</span>100… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">""</span> Gent… <span style="color: #949494;">"</span> 13… <span style="color: #949494;">"</span> 2.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 10.3… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 5.9… <span style="color: #949494;">"</span> 0.9… <span style="color: #949494;">"</span> 21.5…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">""</span> Kana… <span style="color: #949494;">"</span>100… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">""</span> Tobr… <span style="color: #949494;">"</span> 78… <span style="color: #949494;">"</span> 2.6… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 10.3… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 5.9… <span style="color: #949494;">"</span> 2.3… <span style="color: #949494;">"</span> 49.4…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">"</span>Ampheni… Chlo… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 3.1…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">"</span>Antimyc… Rifa… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 2.7…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">"</span>Beta-la… Amox… <span style="color: #949494;">"</span> 93… <span style="color: #949494;">"</span> 50.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 93.9… <span style="color: #949494;">"</span> 98.9…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">""</span> Amox… <span style="color: #949494;">"</span> 42… <span style="color: #949494;">"</span> 13.1… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 10.3… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 2.8… <span style="color: #949494;">"</span> 0.4… <span style="color: #949494;">"</span> 54.5…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">""</span> Ampi… <span style="color: #949494;">"</span> 93… <span style="color: #949494;">"</span> 50.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 93.9… <span style="color: #949494;">"</span> 98.9…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">""</span> Benz… <span style="color: #949494;">"</span> 77… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 80.9… <span style="color: #949494;">"</span> 89.4…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 29 more rows, 2 more variables: `S. hominis` <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `S. pneumoniae` <chr>, and abbreviated variable names ¹`E. coli`,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ²`E. faecalis`, ³`K. pneumoniae`, ⁴`P. aeruginosa`, ⁵`P. mirabilis`,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ⁶`S. aureus`, ⁷`S. epidermidis`</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Use FUN to change to transformation of microorganism codes</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>, </span></span>
|
||||
<span class="r-in"><span> FUN <span class="op">=</span> <span class="va">mo_gramstain</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo ab S I R total</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Gram-negative PEN 8 0 717 725</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 Gram-negative OXA 6 0 0 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 Gram-negative FLC 6 0 0 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 Gram-negative AMX 226 0 405 631</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Gram-negative AMC 463 89 174 726</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Gram-negative AMP 226 0 405 631</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 Gram-negative TZP 554 11 76 641</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 Gram-negative CZO 94 2 110 206</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 Gram-negative FEP 470 1 14 485</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 Gram-negative CXM 539 22 142 703</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 11 Gram-negative FOX 435 8 135 578</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 12 Gram-negative CTX 578 1 57 636</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 13 Gram-negative CAZ 607 0 27 634</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 14 Gram-negative CRO 578 1 57 636</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 15 Gram-negative GEN 651 8 25 684</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 16 Gram-negative TOB 651 7 28 686</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 17 Gram-negative AMK 251 0 5 256</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 18 Gram-negative KAN 0 0 35 35</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 19 Gram-negative TMP 364 1 223 588</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 20 Gram-negative SXT 506 0 197 703</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 21 Gram-negative NIT 491 51 122 664</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 22 Gram-negative FOS 71 0 7 78</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 23 Gram-negative LNZ 0 0 707 707</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 24 Gram-negative CIP 610 11 63 684</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 25 Gram-negative MFX 0 0 63 63</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 26 Gram-negative VAN 0 0 707 707</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 27 Gram-negative TEC 0 0 707 707</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 28 Gram-negative TCY 15 1 110 126</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 29 Gram-negative TGC 87 0 101 188</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 30 Gram-negative DOX 10 0 108 118</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 31 Gram-negative ERY 1 2 696 699</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 32 Gram-negative CLI 18 1 709 728</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 33 Gram-negative AZM 1 2 696 699</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 34 Gram-negative IPM 616 10 5 631</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 35 Gram-negative MEM 624 0 2 626</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 36 Gram-negative MTR 21 0 2 23</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 37 Gram-negative CHL 1 0 30 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 38 Gram-negative COL 309 0 78 387</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 39 Gram-negative MUP 0 0 0 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 40 Gram-negative RIF 1 0 695 696</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 41 Gram-positive PEN 395 11 483 889</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 42 Gram-positive OXA 245 0 113 358</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 43 Gram-positive FLC 659 0 278 937</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 44 Gram-positive AMX 302 3 398 703</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 45 Gram-positive AMC 864 2 272 1138</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 46 Gram-positive AMP 302 3 398 703</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 47 Gram-positive TZP 294 2 49 345</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 48 Gram-positive CZO 151 0 89 240</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 49 Gram-positive FEP 150 0 89 239</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 50 Gram-positive CXM 756 0 328 1084</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 51 Gram-positive FOX 151 0 89 240</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 52 Gram-positive CTX 218 0 89 307</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 53 Gram-positive CAZ 0 0 1177 1177</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 54 Gram-positive CRO 218 0 89 307</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 55 Gram-positive GEN 721 19 430 1170</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 56 Gram-positive TOB 228 0 437 665</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 57 Gram-positive AMK 0 0 436 436</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 58 Gram-positive KAN 0 0 436 436</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 59 Gram-positive TMP 553 9 343 905</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 60 Gram-positive SXT 883 6 163 1052</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 61 Gram-positive NIT 73 0 5 78</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 62 Gram-positive FOS 132 0 141 273</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 63 Gram-positive LNZ 312 0 2 314</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 64 Gram-positive CIP 502 58 164 724</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 65 Gram-positive MFX 136 4 8 148</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 66 Gram-positive VAN 1141 0 5 1146</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 67 Gram-positive TEC 237 0 32 269</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 68 Gram-positive TCY 800 22 245 1067</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 69 Gram-positive TGC 610 0 0 610</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 70 Gram-positive DOX 802 7 206 1015</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 71 Gram-positive ERY 797 7 385 1189</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 72 Gram-positive CLI 556 3 220 779</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 73 Gram-positive AZM 797 7 385 1189</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 74 Gram-positive IPM 207 0 50 257</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 75 Gram-positive MEM 156 0 47 203</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 76 Gram-positive MTR 1 0 2 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 77 Gram-positive CHL 120 0 3 123</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 78 Gram-positive COL 0 0 1237 1237</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 79 Gram-positive MUP 251 3 16 270</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 80 Gram-positive RIF 301 2 3 306</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||||
<span class="r-in"><span> FUN <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">x</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"Others"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> FUN <span class="op">=</span> <span class="va">mo_gramstain</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo ab S I R total</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 E. coli PEN 0 0 467 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 E. coli OXA 0 0 0 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 E. coli FLC 0 0 0 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 E. coli AMX 196 0 196 392</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 E. coli AMC 332 74 61 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 E. coli AMP 196 0 196 392</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 E. coli TZP 388 5 23 416</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 E. coli CZO 79 1 2 82</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 E. coli FEP 308 0 9 317</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 E. coli CXM 425 15 25 465</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 11 E. coli FOX 347 4 26 377</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 12 E. coli CTX 448 0 11 459</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 13 E. coli CAZ 449 0 11 460</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 14 E. coli CRO 448 0 11 459</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 15 E. coli GEN 451 0 9 460</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 16 E. coli TOB 450 0 12 462</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 17 E. coli AMK 171 0 0 171</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 18 E. coli KAN 0 0 0 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 19 E. coli TMP 241 0 155 396</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 20 E. coli SXT 318 0 147 465</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 21 E. coli NIT 429 16 13 458</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 22 E. coli FOS 61 0 0 61</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 23 E. coli LNZ 0 0 467 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 24 E. coli CIP 398 1 57 456</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 25 E. coli MFX 0 0 57 57</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 26 E. coli VAN 0 0 467 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 27 E. coli TEC 0 0 467 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 28 E. coli TCY 1 0 2 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 29 E. coli TGC 68 0 0 68</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 30 E. coli DOX 0 0 0 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 31 E. coli ERY 0 0 467 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 32 E. coli CLI 0 0 467 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 33 E. coli AZM 0 0 467 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 34 E. coli IPM 422 0 0 422</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 35 E. coli MEM 418 0 0 418</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 36 E. coli MTR 2 0 0 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 37 E. coli CHL 0 0 0 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 38 E. coli COL 240 0 0 240</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 39 E. coli MUP 0 0 0 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 40 E. coli RIF 0 0 467 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 41 Others PEN 417 11 734 1162</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 42 Others OXA 251 0 114 365</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 43 Others FLC 665 0 278 943</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 44 Others AMX 347 3 608 958</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 45 Others AMC 1010 17 385 1412</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 46 Others AMP 347 3 608 958</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 47 Others TZP 474 8 103 585</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 48 Others CZO 166 1 197 364</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 49 Others FEP 312 1 94 407</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 50 Others CXM 872 7 445 1324</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 51 Others FOX 239 4 198 441</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 52 Others CTX 348 1 135 484</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 53 Others CAZ 158 0 1193 1351</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 54 Others CRO 348 1 135 484</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 55 Others GEN 921 27 447 1395</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 56 Others TOB 429 7 453 889</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 57 Others AMK 80 0 441 521</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 58 Others KAN 0 0 471 471</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 59 Others TMP 677 10 416 1103</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 60 Others SXT 1074 6 214 1294</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 61 Others NIT 136 35 114 285</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 62 Others FOS 142 0 148 290</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 63 Others LNZ 314 0 242 556</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 64 Others CIP 714 68 171 953</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 65 Others MFX 136 4 14 154</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 66 Others VAN 1149 0 245 1394</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 67 Others TEC 237 0 272 509</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 68 Others TCY 819 23 355 1197</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 69 Others TGC 629 0 101 730</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 70 Others DOX 814 7 315 1136</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 71 Others ERY 801 9 617 1427</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 72 Others CLI 586 4 463 1053</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 73 Others AZM 801 9 617 1427</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 74 Others IPM 402 10 55 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 75 Others MEM 362 0 49 411</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 76 Others MTR 27 0 5 32</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 77 Others CHL 121 0 33 154</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 78 Others COL 69 0 1331 1400</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 79 Others MUP 251 3 16 270</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 80 Others RIF 303 2 231 536</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 80 × 6</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo ab S I R total</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Gram-negative PEN 8 0 717 725</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Gram-negative OXA 6 0 0 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Gram-negative FLC 6 0 0 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 226 0 405 631</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AMC 463 89 174 726</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Gram-negative AMP 226 0 405 631</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Gram-negative TZP 554 11 76 641</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CZO 94 2 110 206</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Gram-negative FEP 470 1 14 485</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Gram-negative CXM 539 22 142 703</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 70 more rows</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||||
<span class="r-in"><span> FUN <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">x</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"Others"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">}</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 80 × 6</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo ab S I R total</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> E. coli PEN 0 0 467 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> E. coli OXA 0 0 0 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> E. coli FLC 0 0 0 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> E. coli AMX 196 0 196 392</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> E. coli AMC 332 74 61 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> E. coli AMP 196 0 196 392</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> E. coli TZP 388 5 23 416</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> E. coli CZO 79 1 2 82</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> E. coli FEP 308 0 9 317</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> E. coli CXM 425 15 25 465</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 70 more rows</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -163,7 +163,7 @@ Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intel
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Get version info of included data set</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="catalogue_of_life_version.html">catalogue_of_life_version</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Included in this AMR package (v1.8.1.9030) are:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Included in this AMR package (v1.8.1.9045) are:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Catalogue of Life: 2019 Annual Checklist</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Available at: http://www.catalogueoflife.org</span>
|
||||
@@ -185,24 +185,16 @@ Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intel
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "C. psittaci"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Get any property from the entire taxonomic tree for all included species</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_class</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_class</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gammaproteobacteria"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacteriaceae"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># based on kingdom and phylum, see ?mo_gramstain</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span> <span class="co"># based on kingdom and phylum, see ?mo_gramstain</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_ref</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_ref</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Castellani et al., 1919"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Do not get mistaken - this package is about microorganisms</span></span></span>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -260,11 +260,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span><span class="co"># run ?example_isolates for more info.</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># base R ------------------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">count_resistant</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "R"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">count_resistant</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "R"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 804</span>
|
||||
<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S" and "I"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 546</span>
|
||||
<span class="r-in"><span><span class="fu">count_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">count_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1350</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># be more specific</span></span></span>
|
||||
@@ -304,62 +304,62 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>R <span class="op">=</span> <span class="fu">count_R</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> I <span class="op">=</span> <span class="fu">count_I</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> S <span class="op">=</span> <span class="fu">count_S</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n1 <span class="op">=</span> <span class="fu">count_all</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># the actual total; sum of all three</span></span></span>
|
||||
<span class="r-in"><span> n2 <span class="op">=</span> <span class="fu">n_rsi</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># same - analogous to n_distinct</span></span></span>
|
||||
<span class="r-in"><span> total <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># NOT the number of tested isolates!</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> R <span class="op">=</span> <span class="fu">count_R</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> I <span class="op">=</span> <span class="fu">count_I</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> S <span class="op">=</span> <span class="fu">count_S</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n1 <span class="op">=</span> <span class="fu">count_all</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># the actual total; sum of all three</span></span></span>
|
||||
<span class="r-in"><span> n2 <span class="op">=</span> <span class="fu">n_rsi</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># same - analogous to n_distinct</span></span></span>
|
||||
<span class="r-in"><span> total <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="co"># NOT the number of tested isolates!</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># Number of available isolates for a whole antibiotic class</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># (i.e., in this data set columns GEN, TOB, AMK, KAN)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">n_rsi</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># Count co-resistance between amoxicillin/clav acid and gentamicin,</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># so we can see that combination therapy does a lot more than mono therapy.</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># Please mind that `susceptibility()` calculates percentages right away instead.</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_susceptible</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># 1433</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_all</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># 1879</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_all</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># 1879</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_susceptible</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># 1399</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_all</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># 1855</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_all</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># 1855</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_susceptible</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># 1764</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_all</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># 1936</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_all</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># 1936</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># Get number of S+I vs. R immediately of selected columns</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">count_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># It also supports grouping variables</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">hospital_id</span>, <span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">ward</span>, <span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">count_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> hospital_id antibiotic interpretation value</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A AMX SI 70</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 A AMX R 108</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 A CIP SI 181</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 A CIP R 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 B AMX SI 170</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 B AMX R 271</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 B CIP SI 414</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 B CIP R 85</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 C AMX SI 65</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 C AMX R 110</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 11 C CIP SI 161</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 12 C CIP R 41</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 13 D AMX SI 241</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 14 D AMX R 315</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 15 D CIP SI 425</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 16 D CIP R 76</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 12 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward antibiotic interpretation value</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ord></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical AMX SI 357</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical AMX R 487</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical CIP SI 741</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical CIP R 128</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU AMX SI 158</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU AMX R 270</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU CIP SI 362</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU CIP R 85</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Outpatient AMX SI 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Outpatient AMX R 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Outpatient CIP SI 78</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Outpatient CIP R 15</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -139,7 +139,7 @@
|
||||
<div class="section level2">
|
||||
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
|
||||
<dl><dt>...</dt>
|
||||
<dd><p>rules in formula notation, see <em>Examples</em></p></dd>
|
||||
<dd><p>rules in <a href="https://rdrr.io/r/base/tilde.html" class="external-link">formula</a> notation, see <em>Examples</em></p></dd>
|
||||
|
||||
</dl></div>
|
||||
<div class="section level2">
|
||||
@@ -240,8 +240,10 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu">custom_eucast_rules</span><span class="op">(</span><span class="va">AMC</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="va">AMC</span> <span class="op">==</span> <span class="st">"I"</span> <span class="op">&</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"I"</span><span class="op">)</span></span></span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu">custom_eucast_rules</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">AMC</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="va">AMC</span> <span class="op">==</span> <span class="st">"I"</span> <span class="op">&</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"I"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">x</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> A set of custom EUCAST rules:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
@@ -253,50 +255,29 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># run the custom rule set (verbose = TRUE will return a logbook instead of the data set):</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||||
<span class="r-in"><span> rules <span class="op">=</span> <span class="st">"custom"</span>,</span></span>
|
||||
<span class="r-in"><span> custom_rules <span class="op">=</span> <span class="va">x</span>,</span></span>
|
||||
<span class="r-in"><span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
|
||||
<span class="r-in"><span> verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> row col mo_fullname old new</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 33 AMP Klebsiella pneumoniae R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 33 AMX Klebsiella pneumoniae R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 34 AMP Klebsiella pneumoniae R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 34 AMX Klebsiella pneumoniae R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 531 AMP Klebsiella pneumoniae R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 531 AMX Klebsiella pneumoniae R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1485 AMP Klebsiella oxytoca R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1485 AMX Klebsiella oxytoca R I</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> rule</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> rule_group rule_name</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Custom EUCAST rules Custom EUCAST rule 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 Custom EUCAST rules Custom EUCAST rule 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 Custom EUCAST rules Custom EUCAST rule 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 Custom EUCAST rules Custom EUCAST rule 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Custom EUCAST rules Custom EUCAST rule 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Custom EUCAST rules Custom EUCAST rule 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 Custom EUCAST rules Custom EUCAST rule 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 Custom EUCAST rules Custom EUCAST rule 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> rule_source</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Object 'x' consisting of 2 custom rules</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 Object 'x' consisting of 2 custom rules</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 Object 'x' consisting of 2 custom rules</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 Object 'x' consisting of 2 custom rules</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Object 'x' consisting of 2 custom rules</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Object 'x' consisting of 2 custom rules</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 Object 'x' consisting of 2 custom rules</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 Object 'x' consisting of 2 custom rules</span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> rules <span class="op">=</span> <span class="st">"custom"</span>,</span></span>
|
||||
<span class="r-in"><span> custom_rules <span class="op">=</span> <span class="va">x</span>,</span></span>
|
||||
<span class="r-in"><span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
|
||||
<span class="r-in"><span> verbose <span class="op">=</span> <span class="cn">TRUE</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 8 × 9</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> row col mo_fullname old new rule rule_…¹ rule_…² rule_…³</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ord></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 33 AMP Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 33 AMX Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 34 AMP Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 34 AMX Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> 531 AMP Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">6</span> 531 AMX Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">7</span> <span style="text-decoration: underline;">1</span>485 AMP Klebsiella oxytoca R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">8</span> <span style="text-decoration: underline;">1</span>485 AMX Klebsiella oxytoca R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with abbreviated variable names ¹rule_group, ²rule_name, ³rule_source</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># combine rule sets</span></span></span>
|
||||
<span class="r-in"><span><span class="va">x2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">x</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="fu">custom_eucast_rules</span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="va">carbapenems</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">x2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">x</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="fu">custom_eucast_rules</span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="va">carbapenems</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">x2</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> A set of custom EUCAST rules:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -138,7 +138,7 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 169 observations and 9 variables:</p><ul><li><p><code>ab</code><br> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
|
||||
<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 169 observations and 9 variables:</p><ul><li><p><code>ab</code><br> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
|
||||
<li><p><code>name</code><br> Official name of the antimicrobial agent as used by WHONET/EARS-Net or the WHO</p></li>
|
||||
<li><p><code>type</code><br> Type of the dosage, either "high_dosage", "standard_dosage" or "uncomplicated_uti"</p></li>
|
||||
<li><p><code>dose</code><br> Dose, such as "2 g" or "25 mg/kg"</p></li>
|
||||
@@ -150,32 +150,33 @@
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p><a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">'EUCAST Clinical Breakpoint Tables' v11.0</a> (2021) are based on the dosages in this data set.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
<p>This data set is based on <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">'EUCAST Clinical Breakpoint Tables' v11.0</a> (2021).</p><div class="section">
|
||||
<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
|
||||
|
||||
|
||||
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">dosage</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ab name type dose dose_times administration notes</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 AMK Amikacin standard_dosage 25-30 mg/kg 1 iv </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 AMX Amoxicillin high_dosage 2 g 6 iv </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 AMX Amoxicillin standard_dosage 1 g 3 iv </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 AMX Amoxicillin high_dosage 0.75-1 g 3 oral </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 AMX Amoxicillin standard_dosage 0.5 g 3 oral </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 AMX Amoxicillin uncomplicated_uti 0.5 g 3 oral </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> original_txt eucast_version</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 25-30 mg/kg x 1 iv 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 2 g x 6 iv 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1 g x 3-4 iv 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 0.75-1 g x 3 oral 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 0.5 g x 3 oral 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 0.5 g x 3 oral 11</span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dosage</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 169 × 9</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ab name type dose dose_…¹ admin…² notes origi…³ eucas…⁴</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> AMK Amikacin stan… 25-3… 1 iv <span style="color: #949494;">""</span> 25-30 … 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> AMX Amoxicillin high… 2 g 6 iv <span style="color: #949494;">""</span> 2 g x … 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> AMX Amoxicillin stan… 1 g 3 iv <span style="color: #949494;">""</span> 1 g x … 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> AMX Amoxicillin high… 0.75… 3 oral <span style="color: #949494;">""</span> 0.75-1… 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> AMX Amoxicillin stan… 0.5 g 3 oral <span style="color: #949494;">""</span> 0.5 g … 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> AMX Amoxicillin unco… 0.5 g 3 oral <span style="color: #949494;">""</span> 0.5 g … 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> AMC Amoxicillin/clavulani… high… 2 g … 3 iv <span style="color: #949494;">""</span> (2 g a… 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> AMC Amoxicillin/clavulani… stan… 1 g … 3 iv <span style="color: #949494;">""</span> (1 g a… 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> AMC Amoxicillin/clavulani… high… 0.87… 3 oral <span style="color: #949494;">""</span> (0.875… 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> AMC Amoxicillin/clavulani… stan… 0.5 … 3 oral <span style="color: #949494;">""</span> (0.5 g… 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 159 more rows, and abbreviated variable names ¹dose_times,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ²administration, ³original_txt, ⁴eucast_version</span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -169,7 +169,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
<div class="section level2">
|
||||
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
|
||||
<dl><dt>x</dt>
|
||||
<dd><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
|
||||
<dd><p>a data set with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
|
||||
|
||||
|
||||
<dt>col_mo</dt>
|
||||
@@ -238,26 +238,26 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
<span> <span class="va">AMC</span> <span class="op">==</span> <span class="st">"I"</span> <span class="op">&</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"I"</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">example_isolates</span>, rules <span class="op">=</span> <span class="st">"custom"</span>, custom_rules <span class="op">=</span> <span class="va">x</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> # A tibble: 2,000 x 49</span></span>
|
||||
<span><span class="co">#> date hospit~1 ward_~2 ward_~3 ward_~4 age gender patie~5 mo </span></span>
|
||||
<span><span class="co">#> * <date> <fct> <lgl> <lgl> <lgl> <dbl> <chr> <chr> <mo> </span></span>
|
||||
<span><span class="co">#> 1 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span></span>
|
||||
<span><span class="co">#> 2 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span></span>
|
||||
<span><span class="co">#> 3 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span></span>
|
||||
<span><span class="co">#> 4 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span></span>
|
||||
<span><span class="co">#> 5 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span></span>
|
||||
<span><span class="co">#> 6 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span></span>
|
||||
<span><span class="co">#> 7 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span></span>
|
||||
<span><span class="co">#> 8 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span></span>
|
||||
<span><span class="co">#> 9 2002-01-16 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span></span>
|
||||
<span><span class="co">#> 10 2002-01-17 B TRUE FALSE FALSE 79 F 858515 B_STPHY_EPDR</span></span>
|
||||
<span><span class="co">#> # ... with 1,990 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
||||
<span><span class="co">#> # AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
||||
<span><span class="co">#> # CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
||||
<span><span class="co">#> # TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
||||
<span><span class="co">#> # FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
||||
<span><span class="co">#> # TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
||||
<span><span class="co">#> # IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, ...</span></span>
|
||||
<span><span class="co">#> # A tibble: 2,000 x 46</span></span>
|
||||
<span><span class="co">#> date patient age gender ward mo PEN OXA FLC AMX </span></span>
|
||||
<span><span class="co">#> * <date> <chr> <dbl> <chr> <chr> <mo> <rsi> <rsi> <rsi> <rsi></span></span>
|
||||
<span><span class="co">#> 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span></span>
|
||||
<span><span class="co">#> 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span></span>
|
||||
<span><span class="co">#> 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span></span>
|
||||
<span><span class="co">#> 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span></span>
|
||||
<span><span class="co">#> 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span></span>
|
||||
<span><span class="co">#> 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span></span>
|
||||
<span><span class="co">#> 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span></span>
|
||||
<span><span class="co">#> 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span></span>
|
||||
<span><span class="co">#> 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span></span>
|
||||
<span><span class="co">#> 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span></span>
|
||||
<span><span class="co">#> # ... with 1,990 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
|
||||
<span><span class="co">#> # TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
|
||||
<span><span class="co">#> # CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
|
||||
<span><span class="co">#> # TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
|
||||
<span><span class="co">#> # MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
|
||||
<span><span class="co">#> # ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
|
||||
<span><span class="co">#> # CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span><span class="co">#> # i Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span></code></pre><p></p></div>
|
||||
</div>
|
||||
|
||||
@@ -284,25 +284,29 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="va">a</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"Enterococcus faecalis"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"Escherichia coli"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"Klebsiella pneumoniae"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"Pseudomonas aeruginosa"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> VAN <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span></span></span>
|
||||
<span class="r-in"><span> AMX <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span></span></span>
|
||||
<span class="r-in"><span> COL <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Colistin</span></span></span>
|
||||
<span class="r-in"><span> CAZ <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span></span></span>
|
||||
<span class="r-in"><span> CXM <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span></span></span>
|
||||
<span class="r-in"><span> PEN <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Benzylpenicillin</span></span></span>
|
||||
<span class="r-in"><span> FOX <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span></span></span>
|
||||
<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">a</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="st">"Staphylococcus aureus"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"Enterococcus faecalis"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"Escherichia coli"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"Klebsiella pneumoniae"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"Pseudomonas aeruginosa"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> VAN <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Vancomycin</span></span></span>
|
||||
<span class="r-in"><span> AMX <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Amoxicillin</span></span></span>
|
||||
<span class="r-in"><span> COL <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Colistin</span></span></span>
|
||||
<span class="r-in"><span> CAZ <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Ceftazidime</span></span></span>
|
||||
<span class="r-in"><span> CXM <span class="op">=</span> <span class="st">"-"</span>, <span class="co"># Cefuroxime</span></span></span>
|
||||
<span class="r-in"><span> PEN <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Benzylpenicillin</span></span></span>
|
||||
<span class="r-in"><span> FOX <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span></span></span>
|
||||
<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo VAN AMX COL CAZ CXM PEN FOX</span>
|
||||
@@ -367,18 +371,22 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
<span class="r-in"><span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Tables' v11.0 (2021). This note will be shown once per session.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ab name standard_dosage high_dosage</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 TOB Tobramycin 6-7 mg/kg x 1 iv <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 GEN Gentamicin 6-7 mg/kg x 1 iv <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ab name standard_dosage high_dosage </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> TOB Tobramycin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> GEN Gentamicin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Tables' v10.0 (2020). This note will be shown once per session.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ab name standard_dosage high_dosage</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 TOB Tobramycin 6-7 mg/kg x 1 iv <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 GEN Gentamicin 6-7 mg/kg x 1 iv <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ab name standard_dosage high_dosage </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> TOB Tobramycin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> GEN Gentamicin 6-7 mg/kg x 1 iv <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> CIP Ciprofloxacin 0.4 g x 2 iv 0.4 g x 3 iv</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
<!DOCTYPE html>
|
||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR data analysis. For examples, please read the tutorial on our website."><title>Data Set with 2,000 Example Isolates — example_isolates • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 2,000 Example Isolates — example_isolates"><meta property="og:description" content="A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR data analysis. For examples, please read the tutorial on our website."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
|
||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A data set containing 2,000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read the tutorial on our website."><title>Data Set with 2,000 Example Isolates — example_isolates • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 2,000 Example Isolates — example_isolates"><meta property="og:description" content="A data set containing 2,000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read the tutorial on our website."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<![endif]--></head><body>
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@@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
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|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -128,7 +128,7 @@
|
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</div>
|
||||
|
||||
<div class="ref-description section level2">
|
||||
<p>A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR data analysis. For examples, please read <a href="https://msberends.github.io/AMR/articles/AMR.html">the tutorial on our website</a>.</p>
|
||||
<p>A data set containing 2,000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read <a href="https://msberends.github.io/AMR/articles/AMR.html">the tutorial on our website</a>.</p>
|
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</div>
|
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|
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<div class="section level2">
|
||||
@@ -138,43 +138,42 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 2,000 observations and 49 variables:</p><ul><li><p><code>date</code><br> date of receipt at the laboratory</p></li>
|
||||
<li><p><code>hospital_id</code><br> ID of the hospital, from A to D</p></li>
|
||||
<li><p><code>ward_icu</code><br><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to determine if ward is an intensive care unit</p></li>
|
||||
<li><p><code>ward_clinical</code><br><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to determine if ward is a regular clinical ward</p></li>
|
||||
<li><p><code>ward_outpatient</code><br><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to determine if ward is an outpatient clinic</p></li>
|
||||
<li><p><code>age</code><br> age of the patient</p></li>
|
||||
<li><p><code>gender</code><br> gender of the patient</p></li>
|
||||
<li><p><code>patient_id</code><br> ID of the patient</p></li>
|
||||
<li><p><code>mo</code><br> ID of microorganism created with <code><a href="as.mo.html">as.mo()</a></code>, see also <a href="microorganisms.html">microorganisms</a></p></li>
|
||||
<li><p><code>PEN:RIF</code><br> 40 different antibiotics with class <code><a href="as.rsi.html">rsi</a></code> (see <code><a href="as.rsi.html">as.rsi()</a></code>); these column names occur in the <a href="antibiotics.html">antibiotics</a> data set and can be translated with <code><a href="ab_property.html">ab_name()</a></code></p></li>
|
||||
<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 2,000 observations and 46 variables:</p><ul><li><p><code>date</code><br> Date of receipt at the laboratory</p></li>
|
||||
<li><p><code>patient</code><br> ID of the patient</p></li>
|
||||
<li><p><code>age</code><br> Age of the patient</p></li>
|
||||
<li><p><code>gender</code><br> Gender of the patient, either "F" or "M"</p></li>
|
||||
<li><p><code>ward</code><br> Ward type where the patient was admitted, either "Clinical", "ICU" or "Outpatient"</p></li>
|
||||
<li><p><code>mo</code><br> ID of microorganism created with <code><a href="as.mo.html">as.mo()</a></code>, see also the <a href="microorganisms.html">microorganisms</a> data set</p></li>
|
||||
<li><p><code>PEN:RIF</code><br> 40 different antibiotics with class <code><a href="as.rsi.html">rsi</a></code> (see <code><a href="as.rsi.html">as.rsi()</a></code>); these column names occur in the <a href="antibiotics.html">antibiotics</a> data set and can be translated with <code><a href="ab_property.html">set_ab_names()</a></code> or <code><a href="ab_property.html">ab_name()</a></code></p></li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 6 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospita…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">6</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>, AMX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi>, and …</span></span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">example_isolates</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -138,29 +138,34 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 3,000 observations and 8 variables:</p><ul><li><p><code>patient_id</code><br> ID of the patient</p></li>
|
||||
<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 3,000 observations and 8 variables:</p><ul><li><p><code>patient_id</code><br> ID of the patient</p></li>
|
||||
<li><p><code>date</code><br> date of receipt at the laboratory</p></li>
|
||||
<li><p><code>hospital</code><br> ID of the hospital, from A to C</p></li>
|
||||
<li><p><code>bacteria</code><br> info about microorganism that can be transformed with <code><a href="as.mo.html">as.mo()</a></code>, see also <a href="microorganisms.html">microorganisms</a></p></li>
|
||||
<li><p><code>AMX:GEN</code><br> 4 different antibiotics that have to be transformed with <code><a href="as.rsi.html">as.rsi()</a></code></p></li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">example_isolates_unclean</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient_id hospital date bacteria AMX AMC CIP GEN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 J3 A 2012-11-21 E. coli R I S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 R7 A 2018-04-03 K. pneumoniae R I S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 P3 A 2014-09-19 E. coli R S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 P10 A 2015-12-10 E. coli S I S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 B7 A 2015-03-02 E. coli S S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 W3 A 2018-03-31 S. aureus R S R S</span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">example_isolates_unclean</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3,000 × 8</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient_id hospital date bacteria AMX AMC CIP GEN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 E. coli R I S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 K. pneumoniae R I S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 E. coli R S S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 E. coli S I S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 E. coli S S S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 S. aureus R S R S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> J8 A 2016-06-14 E. coli R S S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 E. coli R S S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 E. coli S S S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 S. aureus S S S S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 2,990 more rows</span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -12,7 +12,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -202,7 +202,7 @@
|
||||
|
||||
|
||||
<dt>col_icu</dt>
|
||||
<dd><p>column name of the logicals (<code>TRUE</code>/<code>FALSE</code>) whether a ward or department is an Intensive Care Unit (ICU)</p></dd>
|
||||
<dd><p>column name of the logicals (<code>TRUE</code>/<code>FALSE</code>) whether a ward or department is an Intensive Care Unit (ICU). This can also be a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector with the same length as rows in <code>x</code>.</p></dd>
|
||||
|
||||
|
||||
<dt>col_keyantimicrobials</dt>
|
||||
@@ -261,7 +261,7 @@
|
||||
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
|
||||
|
||||
|
||||
<p>A <code><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a></code> vector</p>
|
||||
<p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
@@ -324,93 +324,132 @@
|
||||
<span class="r-in"><span><span class="co"># See ?example_isolates.</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu">first_isolate</span><span class="op">(</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,379 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospit…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-17 B TRUE FALSE FALSE 79 F 858515 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 D FALSE TRUE FALSE 67 M 495616 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-19 D FALSE TRUE FALSE 71 M 738003 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-21 D FALSE TRUE FALSE 75 F 462081 B_CTRBC_FRND</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-22 B TRUE FALSE FALSE 50 M F35553 B_PROTS_MRBL</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-02-03 B TRUE FALSE FALSE 76 M 481442 B_STPHY_CONS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-05 A FALSE TRUE FALSE 50 M 023456 B_STPHY_HMNS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,369 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,379 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 495616 67 M Clinical B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-21 462081 75 F Clinical B_CTRBC_FRND R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-02-03 481442 76 M ICU B_STPHY_CONS R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-05 023456 50 M Clinical B_STPHY_HMNS S NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,369 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># get all first Gram-negatives</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_is_gram_negative()`</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 437 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospit…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-19 D FALSE TRUE FALSE 71 M 738003 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-21 D FALSE TRUE FALSE 75 F 462081 B_CTRBC_FRND</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-22 B TRUE FALSE FALSE 50 M F35553 B_PROTS_MRBL</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-02-05 B TRUE FALSE FALSE 45 F 067927 B_SERRT_MRCS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-02-27 D FALSE TRUE FALSE 85 F 066895 B_KLBSL_PNMN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-03-08 C FALSE TRUE FALSE 69 M 4FC193 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-03-16 C FALSE TRUE FALSE 69 M 4FC193 B_PSDMN_AERG</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-04-01 B TRUE FALSE FALSE 46 F 496896 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-04-23 B TRUE FALSE FALSE 69 F EE2510 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 427 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 437 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-21 462081 75 F Clinical B_CTRBC_FRND R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-02-27 066895 85 F Clinical B_KLBSL_PNMN R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-03-08 4FC193 69 M Clinical B_ESCHR_COLI R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-03-16 4FC193 69 M Clinical B_PSDMN_AERG R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-04-01 496896 46 F ICU B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-04-23 EE2510 69 F ICU B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 427 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># filter on first isolates using dplyr:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">first_isolate</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,379 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 495616 67 M Clinical B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-21 462081 75 F Clinical B_CTRBC_FRND R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-02-03 481442 76 M ICU B_STPHY_CONS R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-05 023456 50 M Clinical B_STPHY_HMNS S NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,369 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># short-hand version:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">filter_first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># flag the first isolates per group:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu">first_isolate</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">hospital_id</span>, <span class="va">date</span>, <span class="va">patient_id</span>, <span class="va">mo</span>, <span class="va">first</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># now let's see if first isolates matter:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">A</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>count <span class="op">=</span> <span class="fu"><a href="count.html">n_rsi</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span>, <span class="co"># gentamicin availability</span></span></span>
|
||||
<span class="r-in"><span> resistance <span class="op">=</span> <span class="fu"><a href="proportion.html">resistance</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span><span class="op">)</span> <span class="co"># gentamicin resistance</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">B</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">filter_first_isolate</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># the 1st isolate filter</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>count <span class="op">=</span> <span class="fu"><a href="count.html">n_rsi</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span>, <span class="co"># gentamicin availability</span></span></span>
|
||||
<span class="r-in"><span> resistance <span class="op">=</span> <span class="fu"><a href="proportion.html">resistance</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span><span class="op">)</span> <span class="co"># gentamicin resistance</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># Have a look at A and B.</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">A</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">B</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># B is more reliable because every isolate is counted only once.</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># Gentamicin resistance in hospital D appears to be 4.2% higher than</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># when you (erroneously) would have used all isolates for analysis.</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 3</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> hospital_id count resistance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> A 216 0.204</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> B 407 0.270</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> C 202 0.218</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> D 457 0.293</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1,379 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 495616 67 M Clinical B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-21 462081 75 F Clinical B_CTRBC_FRND R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-02-03 481442 76 M ICU B_STPHY_CONS R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-05 023456 50 M Clinical B_STPHY_HMNS S NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,369 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># flag the first isolates per group:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu">first_isolate</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">ward</span>, <span class="va">date</span>, <span class="va">patient</span>, <span class="va">mo</span>, <span class="va">first</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward [3]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient mo first</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><lgl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2002-01-02 A77334 B_ESCHR_COLI TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2002-01-03 A77334 B_ESCHR_COLI FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> ICU 2002-01-07 067927 B_STPHY_EPDR TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2002-01-07 067927 B_STPHY_EPDR FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU 2002-01-13 067927 B_STPHY_EPDR FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2002-01-13 067927 B_STPHY_EPDR FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2002-01-14 462729 B_STPHY_AURS TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2002-01-14 462729 B_STPHY_AURS FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU 2002-01-16 067927 B_STPHY_EPDR FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> ICU 2002-01-17 858515 B_STPHY_EPDR TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -176,54 +176,56 @@
|
||||
<span class="r-in"><span><span class="co"># See ?example_isolates</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 37 22 35 49 56 34 5 24 8 19 29 58 1 25 23 2 63 43 7 18 52 35 30 50 39</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 51 60 35 37 36 7 26 55 12 28 31 29 21 12 26 39 11 5 43 15 45 32 11 51 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 12 1 59 39 10 26 46 1 57 46 44 61 17 59 17 53 39 4 27 48 51 10 16 52 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 45 16 56 39 34 34 36 30 15 28 53 3 12 29 32 7 10 20 38 12 61 16 1 59 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 34 2 39 35 14 49 41 28 48 58 54 6 7 38 46 50 54 25 34 49 54 3 18 5 36</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 42 63 24 13 42 26 19 8 36 54 56 18 11 13 14 58 43 13 9 54 32 52 50 49 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 22 4 40 49 27 22 55 43 38 1 33 47 9 30 5 11 60 37 62 24 18 50 9 5 29</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 63 50 32 51 5 3 44 4 43 63 62 33 54 9 7 4 54 48 40 19 37 53 12 49 24</span>
|
||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 56 61 60 30 16 51 17 7 8 2 14 22 30 19 38 31 30 47 27 23 10 58 41 64 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 39 9 28 40 35 37 57 4 10 29 61 53 2 56 27 56 13 62 28 46 9 45 43 4 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 53 52 6 18 35 57 8 48 10 18 11 26 31 40 34 17 19 18 32 17 1 39 9 5 25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 5 51 52 33 45 14 4 12 6 38 62 7 9 9 45 49 40 33 30 12 13 4 47 39 60</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [101] 60 20 8 2 13 51 57 62 36 38 34 38 14 16 1 54 42 28 59 23 29 3 36 43 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [126] 27 9 48 1 40 9 24 57 22 59 33 7 30 7 60 32 37 36 13 35 10 32 49 41 62</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [151] 30 8 19 26 44 24 46 63 47 56 54 22 33 50 30 55 49 12 55 57 50 24 9 54 27</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [176] 30 40 26 58 39 9 58 25 13 60 21 44 39 26 28 41 29 35 10 18 3 46 38 61 20</span>
|
||||
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] TRUE TRUE FALSE FALSE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE FALSE FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [109] TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [121] TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [145] FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [157] FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [169] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [181] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [193] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospita…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-07-30 A TRUE TRUE FALSE 76 F 218912 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-07-30 A TRUE TRUE FALSE 76 F 218912 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-07-16 D FALSE FALSE TRUE 78 M 241328 B_STPHY_CONS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>, AMX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi>, and …</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-08-19 A49852 70 M Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-10-14 FCC668 54 F ICU B_STRPT_PNMN S NA NA S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># the functions also work for less than a day, e.g. to include one per hour:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fl">60</span> <span class="op">*</span> <span class="fl">60</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> episode_days <span class="op">=</span> <span class="fl">1</span><span class="op">/</span><span class="fl">24</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fl">60</span> <span class="op">*</span> <span class="fl">60</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span>episode_days <span class="op">=</span> <span class="fl">1</span> <span class="op">/</span> <span class="fl">24</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
@@ -231,51 +233,113 @@
|
||||
<span class="r-in"><span> <span class="co"># is_new_episode() can also be used in dplyr verbs to determine patient</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># episodes based on any (combination of) grouping variables:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>condition <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span>, </span></span>
|
||||
<span class="r-in"><span> size <span class="op">=</span> <span class="fl">2000</span>,</span></span>
|
||||
<span class="r-in"><span> replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>condition <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> size <span class="op">=</span> <span class="fl">200</span>,</span></span>
|
||||
<span class="r-in"><span> replace <span class="op">=</span> <span class="cn">TRUE</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">condition</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>new_episode <span class="op">=</span> <span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">365</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">patient_id</span>, <span class="va">date</span>, <span class="va">condition</span>, <span class="va">new_episode</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">date</span>, <span class="va">condition</span>, <span class="va">new_episode</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: condition [3]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 329C35 2016-04-02 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 694764 2017-03-30 A FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 4B1971 2017-01-13 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B65162 2008-12-29 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B338BC 2005-07-02 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> F67089 2014-10-24 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 969581 2005-10-18 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> F35553 2003-08-13 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 82C90B 2003-09-19 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> D10443 2002-04-26 C FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span>, <span class="va">patient_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">transmute</a></span><span class="op">(</span><span class="va">date</span>, </span></span>
|
||||
<span class="r-in"><span> <span class="va">patient_id</span>,</span></span>
|
||||
<span class="r-in"><span> new_index <span class="op">=</span> <span class="fu">get_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> new_logical <span class="op">=</span> <span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span>, <span class="va">patient</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">transmute</a></span><span class="op">(</span><span class="va">date</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="va">patient</span>,</span></span>
|
||||
<span class="r-in"><span> new_index <span class="op">=</span> <span class="fu">get_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> new_logical <span class="op">=</span> <span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [189]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2016-04-02 329C35 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2017-03-30 694764 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> ICU 2017-01-13 4B1971 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2008-12-29 B65162 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2005-07-02 B338BC 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2014-10-24 F67089 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2005-10-18 969581 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2003-08-13 F35553 2 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2003-09-19 82C90B 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2002-04-26 D10443 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>n_patients <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct</a></span><span class="op">(</span><span class="va">patient_id</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n_episodes_365 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">365</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n_episodes_60 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n_episodes_30 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">30</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> n_patients <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct</a></span><span class="op">(</span><span class="va">patient</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n_episodes_365 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">365</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n_episodes_60 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n_episodes_30 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">30</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 117 14 52 63</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 59 14 39 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 13 8 12 13</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">x</span> <span class="op"><-</span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="first_isolate.html">filter_first_isolate</a></span><span class="op">(</span>include_unknown <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
|
||||
<span class="r-in"><span> method <span class="op">=</span> <span class="st">"episode-based"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="first_isolate.html">filter_first_isolate</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> include_unknown <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
|
||||
<span class="r-in"><span> method <span class="op">=</span> <span class="st">"episode-based"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">y</span> <span class="op"><-</span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">patient_id</span>, <span class="va">mo</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">mo</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">365</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">ungroup</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] FALSE</span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># since you can now group on anything that seems relevant:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">patient_id</span>, <span class="va">mo</span>, <span class="va">hospital_id</span>, <span class="va">ward_icu</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">mo</span>, <span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>flag_episode <span class="op">=</span> <span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">365</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in mutate(., condition = sample(x = c("A", "B", "C"), size = 2000, replace = TRUE)):</span> Problem while computing `condition = sample(x = c("A", "B", "C"), size =</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> 2000, replace = TRUE)`.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="color: #BB0000;">✖</span> `condition` must be size 200 or 1, not 2000.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [191]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 329C35 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 694764 B_STPHY_HMNS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 4B1971 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B65162 B_STRPT_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B338BC B_ENTRC Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> F67089 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 969581 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> F35553 B_ENTRC_FCLS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 82C90B B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> D10443 B_KLBSL_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 190 more rows</span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -280,24 +280,26 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># calculate the resistance per group first </span></span></span>
|
||||
<span class="r-in"><span> <span class="va">resistance_data</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span>order <span class="op">=</span> <span class="fu"><a href="mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, <span class="co"># group on anything, like order</span></span></span>
|
||||
<span class="r-in"><span> genus <span class="op">=</span> <span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># and genus as we do here;</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span> <span class="op">>=</span> <span class="fl">30</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># filter on only 30 results per group</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="co"># then get resistance of all drugs</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># calculate the resistance per group first</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">resistance_data</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> order <span class="op">=</span> <span class="fu"><a href="mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, <span class="co"># group on anything, like order</span></span></span>
|
||||
<span class="r-in"><span> genus <span class="op">=</span> <span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># and genus as we do here;</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span> <span class="op">>=</span> <span class="fl">30</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># filter on only 30 results per group</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="co"># then get resistance of all drugs</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># now conduct PCA for certain antimicrobial agents</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">pca_result</span> <span class="op"><-</span> <span class="va">resistance_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="pca.html">pca</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>, <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span><span class="op">)</span> </span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">pca_result</span> <span class="op"><-</span> <span class="va">resistance_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="pca.html">pca</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>, <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># old base R plotting method:</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># new ggplot2 plotting method using this package:</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_pca</span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_pca</span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_viridis.html" class="external-link">scale_colour_viridis_d</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
@@ -455,7 +457,6 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> Groups (n=4, named as 'order'):</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Loading required package: ggplot2</span>
|
||||
<span class="r-plt img"><img src="ggplot_pca-1.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="ggplot_pca-2.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
|
||||
Binary file not shown.
|
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BIN
reference/ggplot_rsi-10.png
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reference/ggplot_rsi-10.png
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|
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reference/ggplot_rsi-2.png
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reference/ggplot_rsi-3.png
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|
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reference/ggplot_rsi-4.png
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reference/ggplot_rsi-5.png
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reference/ggplot_rsi-5.png
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|
After Width: | Height: | Size: 51 KiB |
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reference/ggplot_rsi-6.png
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reference/ggplot_rsi-6.png
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|
After Width: | Height: | Size: 34 KiB |
BIN
reference/ggplot_rsi-7.png
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reference/ggplot_rsi-7.png
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|
After Width: | Height: | Size: 21 KiB |
BIN
reference/ggplot_rsi-8.png
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BIN
reference/ggplot_rsi-8.png
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|
After Width: | Height: | Size: 37 KiB |
BIN
reference/ggplot_rsi-9.png
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BIN
reference/ggplot_rsi-9.png
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Binary file not shown.
|
After Width: | Height: | Size: 48 KiB |
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -311,12 +311,15 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># get antimicrobial results for drugs against a UTI:</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">NIT</span>, <span class="va">FOS</span>, <span class="va">TMP</span>, <span class="va">CIP</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">geom_rsi</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-1.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># prettify the plot using some additional functions:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">NIT</span>, <span class="va">FOS</span>, <span class="va">TMP</span>, <span class="va">CIP</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
@@ -325,74 +328,105 @@
|
||||
<span class="r-in"><span> <span class="fu">scale_rsi_colours</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">labels_rsi_count</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">theme_rsi</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-2.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># or better yet, simplify this using the wrapper function - a single command:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">NIT</span>, <span class="va">FOS</span>, <span class="va">TMP</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-3.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># get only proportions and no counts:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">NIT</span>, <span class="va">FOS</span>, <span class="va">TMP</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span>datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-4.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># add other ggplot2 arguments as you like:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">NIT</span>, <span class="va">FOS</span>, <span class="va">TMP</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span>width <span class="op">=</span> <span class="fl">0.5</span>,</span></span>
|
||||
<span class="r-in"><span> colour <span class="op">=</span> <span class="st">"black"</span>,</span></span>
|
||||
<span class="r-in"><span> size <span class="op">=</span> <span class="fl">1</span>,</span></span>
|
||||
<span class="r-in"><span> linetype <span class="op">=</span> <span class="fl">2</span>,</span></span>
|
||||
<span class="r-in"><span> alpha <span class="op">=</span> <span class="fl">0.25</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> width <span class="op">=</span> <span class="fl">0.5</span>,</span></span>
|
||||
<span class="r-in"><span> colour <span class="op">=</span> <span class="st">"black"</span>,</span></span>
|
||||
<span class="r-in"><span> size <span class="op">=</span> <span class="fl">1</span>,</span></span>
|
||||
<span class="r-in"><span> linetype <span class="op">=</span> <span class="fl">2</span>,</span></span>
|
||||
<span class="r-in"><span> alpha <span class="op">=</span> <span class="fl">0.25</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-5.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># you can alter the colours with colour names:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span>colours <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>SI <span class="op">=</span> <span class="st">"yellow"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-6.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># but you can also use the built-in colour-blind friendly colours for</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># your plots, where "S" is green, "I" is yellow and "R" is red:</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Value1"</span>, <span class="st">"Value2"</span>, <span class="st">"Value3"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> z <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Value4"</span>, <span class="st">"Value5"</span>, <span class="st">"Value6"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Value1"</span>, <span class="st">"Value2"</span>, <span class="st">"Value3"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> z <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Value4"</span>, <span class="st">"Value5"</span>, <span class="st">"Value6"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">x</span>, y <span class="op">=</span> <span class="va">y</span>, fill <span class="op">=</span> <span class="va">z</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">scale_rsi_colours</span><span class="op">(</span>Value4 <span class="op">=</span> <span class="st">"S"</span>, Value5 <span class="op">=</span> <span class="st">"I"</span>, Value6 <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-7.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># resistance of ciprofloxacine per age group</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first_isolate <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first_isolate</span> <span class="op">==</span> <span class="cn">TRUE</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="va">mo</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">first_isolate</span> <span class="op">==</span> <span class="cn">TRUE</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="va">mo</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># age_groups() is also a function in this AMR package:</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span>age_group <span class="op">=</span> <span class="fu"><a href="age_groups.html">age_groups</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">age_group</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"age_group"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Removed 6 rows containing missing values (position_stack).</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Removed 6 rows containing missing values (position_stack).</span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-8.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># a shorter version which also adjusts data label colours:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">NIT</span>, <span class="va">FOS</span>, <span class="va">TMP</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span>colours <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-9.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># it also supports groups (don't forget to use the group var on `x` or `facet`):</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">ward</span> <span class="op">!=</span> <span class="st">"Outpatient"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># select only UTI-specific drugs</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">hospital_id</span>, <span class="va">AMX</span>, <span class="va">NIT</span>, <span class="va">FOS</span>, <span class="va">TMP</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"hospital_id"</span>,</span></span>
|
||||
<span class="r-in"><span> facet <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
|
||||
<span class="r-in"><span> nrow <span class="op">=</span> <span class="fl">1</span>,</span></span>
|
||||
<span class="r-in"><span> title <span class="op">=</span> <span class="st">"AMR of Anti-UTI Drugs Per Hospital"</span>,</span></span>
|
||||
<span class="r-in"><span> x.title <span class="op">=</span> <span class="st">"Hospital"</span>,</span></span>
|
||||
<span class="r-in"><span> datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">ward</span>, <span class="va">AMX</span>, <span class="va">NIT</span>, <span class="va">FOS</span>, <span class="va">TMP</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">ggplot_rsi</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="st">"ward"</span>,</span></span>
|
||||
<span class="r-in"><span> facet <span class="op">=</span> <span class="st">"antibiotic"</span>,</span></span>
|
||||
<span class="r-in"><span> nrow <span class="op">=</span> <span class="fl">1</span>,</span></span>
|
||||
<span class="r-in"><span> title <span class="op">=</span> <span class="st">"AMR of Anti-UTI Drugs Per Ward"</span>,</span></span>
|
||||
<span class="r-in"><span> x.title <span class="op">=</span> <span class="st">"Ward"</span>,</span></span>
|
||||
<span class="r-in"><span> datalabels <span class="op">=</span> <span class="cn">FALSE</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_is_gram_negative()`</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Removed 6 rows containing missing values (position_stack).</span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-1.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-plt img"><img src="ggplot_rsi-10.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -172,8 +172,10 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>amox <span class="op">=</span> <span class="st">"S"</span>,</span></span>
|
||||
<span class="r-in"><span> tetr <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span></span></span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> amox <span class="op">=</span> <span class="st">"S"</span>,</span></span>
|
||||
<span class="r-in"><span> tetr <span class="op">=</span> <span class="st">"R"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">guess_ab_col</span><span class="op">(</span><span class="va">df</span>, <span class="st">"amoxicillin"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "amox"</span>
|
||||
@@ -194,8 +196,10 @@
|
||||
<span class="r-in"><span><span class="co"># [1] "tetr"</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># WHONET codes</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>AMP_ND10 <span class="op">=</span> <span class="st">"R"</span>,</span></span>
|
||||
<span class="r-in"><span> AMC_ED20 <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> AMP_ND10 <span class="op">=</span> <span class="st">"R"</span>,</span></span>
|
||||
<span class="r-in"><span> AMC_ED20 <span class="op">=</span> <span class="st">"S"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">guess_ab_col</span><span class="op">(</span><span class="va">df</span>, <span class="st">"ampicillin"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "AMP_ND10"</span>
|
||||
<span class="r-in"><span><span class="co"># [1] "AMP_ND10"</span></span></span>
|
||||
@@ -207,8 +211,10 @@
|
||||
<span class="r-in"><span><span class="co"># [1] "AMC_ED20"</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Longer names take precendence:</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>AMP_ED2 <span class="op">=</span> <span class="st">"S"</span>,</span></span>
|
||||
<span class="r-in"><span> AMP_ED20 <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> AMP_ED2 <span class="op">=</span> <span class="st">"S"</span>,</span></span>
|
||||
<span class="r-in"><span> AMP_ED20 <span class="op">=</span> <span class="st">"S"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">guess_ab_col</span><span class="op">(</span><span class="va">df</span>, <span class="st">"ampicillin"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "AMP_ED2"</span>
|
||||
<span class="r-in"><span><span class="co"># [1] "AMP_ED20"</span></span></span>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -138,31 +138,38 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 134,956 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID</p></li>
|
||||
<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 134,956 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID</p></li>
|
||||
<li><p><code>ab</code><br> Antibiotic ID</p></li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p>The repository of this <code>AMR</code> package contains a file comprising this data set with full taxonomic and antibiotic names: <a href="https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt</a>. This file <strong>allows for machine reading EUCAST guidelines about intrinsic resistance</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.</p>
|
||||
<p>This data set is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021).</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
<p>This data set is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021).</p><div class="section">
|
||||
<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
|
||||
|
||||
|
||||
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
<p>They <strong>allow for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI.</p>
|
||||
</div>
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">intrinsic_resistant</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo ab</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 B_GRAMP ATM</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B_GRAMP COL</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 B_GRAMP NAL</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 B_GRAMP PLB</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 B_GRAMP TEM</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 B_ABTRP ATM</span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">intrinsic_resistant</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 134,956 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo ab </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_GRAMP ATM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_GRAMP COL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_GRAMP NAL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B_GRAMP PLB </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B_GRAMP TEM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B_ABTRP ATM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B_ABTRP COL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B_ABTRP NAL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_ABTRP PLB </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B_ABTRP TEM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 134,946 more rows</span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -183,48 +183,67 @@
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "K. pneumoniae" (assuming</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Klebsiella pneumoniae). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname kingdom phylum</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 B_KLBSL_PNMN Klebsiella pneumoniae Bacteria Proteobacteria</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> class order family genus species</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Gammaproteobacteria Enterobacterales Enterobacteriaceae Klebsiella pneumoniae</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> subspecies rank ref species_id source prevalence</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 species Trevisan, 1887 777151 LPSN 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> snomed</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1098101000112102, 446870005, 1098201000112108, 409801009, 56415008, 714315002</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 16</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname kingdom phylum class order family genus species subsp…¹</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> B_KLBSL_PNMN Klebsiel… Bacter… Prote… Gamm… Ente… Enter… Kleb… pneumo… <span style="color: #949494;">""</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 6 more variables: rank <chr>, ref <chr>, species_id <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># source <chr>, prevalence <dbl>, snomed <list>, and abbreviated variable</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># name ¹subspecies</span></span>
|
||||
<span class="r-in"><span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="st">"B_KLBSL_PNMN"</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname kingdom phylum</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 B_KLBSL_PNMN Klebsiella pneumoniae Bacteria Proteobacteria</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> class order family genus species</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Gammaproteobacteria Enterobacterales Enterobacteriaceae Klebsiella pneumoniae</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> subspecies rank ref species_id source prevalence</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 species Trevisan, 1887 777151 LPSN 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> snomed</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1098101000112102, 446870005, 1098201000112108, 409801009, 56415008, 714315002</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 1 × 16</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname kingdom phylum class order family genus species subsp…¹</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> B_KLBSL_PNMN Klebsiel… Bacter… Prote… Gamm… Ente… Enter… Kleb… pneumo… <span style="color: #949494;">""</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 6 more variables: rank <chr>, ref <chr>, species_id <dbl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># source <chr>, prevalence <dbl>, snomed <list>, and abbreviated variable</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># name ¹subspecies</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span>from <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-01-01"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-01-07"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> by <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> bacteria <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S. aureus"</span>, <span class="st">"MRSA"</span>, <span class="st">"MSSA"</span>, <span class="st">"STAAUR"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"E. coli"</span>, <span class="st">"E. coli"</span>, <span class="st">"E. coli"</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df_joined</span> <span class="op"><-</span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="va">df</span>, <span class="st">"bacteria"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df_joined</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Joining, by = "mo"</span>
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> from <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-01-01"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-01-07"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> by <span class="op">=</span> <span class="fl">1</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> bacteria <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="st">"S. aureus"</span>, <span class="st">"MRSA"</span>, <span class="st">"MSSA"</span>, <span class="st">"STAAUR"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="st">"E. coli"</span>, <span class="st">"E. coli"</span>, <span class="st">"E. coli"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli) and "S. aureus" (assuming Staphylococcus aureus). Run</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> `mo_uncertainties()` to review these uncertainties.</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "bacteria"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">df_joined</span> <span class="op"><-</span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="va">df</span>, <span class="st">"bacteria"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df_joined</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "bacteria" "fullname" "kingdom" "phylum" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] "class" "order" "family" "genus" "species" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] "subspecies" "rank" "ref" "species_id" "source" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [16] "prevalence" "snomed" </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Joining, by = "mo"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "patient" "age" "gender" "ward" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [6] "mo" "PEN" "OXA" "FLC" "AMX" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] "AMC" "AMP" "TZP" "CZO" "FEP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [16] "CXM" "FOX" "CTX" "CAZ" "CRO" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] "GEN" "TOB" "AMK" "KAN" "TMP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] "SXT" "NIT" "FOS" "LNZ" "CIP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [31] "MFX" "VAN" "TEC" "TCY" "TGC" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [36] "DOX" "ERY" "CLI" "AZM" "IPM" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [41] "MEM" "MTR" "CHL" "COL" "MUP" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [46] "RIF" "fullname" "kingdom" "phylum" "class" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] "order" "family" "genus" "species" "subspecies"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [56] "rank" "ref" "species_id" "source" "prevalence"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] "snomed" </span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -274,11 +274,13 @@
|
||||
<span class="r-in"><span> <span class="co"># and first WEIGHTED isolates</span></span></span>
|
||||
<span class="r-in"><span> first_weighted <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="st">"keyab"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># Check the difference in this data set, 'weighted' results in more isolates:</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1395</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -167,9 +167,9 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2.964037</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2.879763</span>
|
||||
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.06905028</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.01332259</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -192,7 +192,7 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># also supports multiple patterns</span></span></span>
|
||||
<span class="r-in"><span><span class="va">a</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Test case"</span>, <span class="st">"Something different"</span>, <span class="st">"Yet another thing"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span> <span class="st">"case"</span>, <span class="st">"diff"</span>, <span class="st">"yet"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"case"</span>, <span class="st">"diff"</span>, <span class="st">"yet"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">a</span> <span class="op">%like%</span> <span class="va">b</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE TRUE</span>
|
||||
<span class="r-in"><span><span class="va">a</span> <span class="op">%unlike%</span> <span class="va">b</span></span></span>
|
||||
@@ -203,78 +203,56 @@
|
||||
<span class="r-in"><span><span class="va">a</span> <span class="op">%like%</span> <span class="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE FALSE FALSE</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># get isolates whose name start with 'Ent' or 'ent'</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 106 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospi…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 C FALSE TRUE FALSE 69 M 4FC193 B_ENTRC_FACM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-04-08 A TRUE TRUE FALSE 78 M 130252 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-06-23 D FALSE TRUE FALSE 82 M 798871 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-06-23 D FALSE TRUE FALSE 82 M 798871 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2003-04-20 D TRUE TRUE FALSE 62 M 6BC362 B_ENTRC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2003-04-21 D TRUE TRUE FALSE 62 M 6BC362 B_ENTRC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2003-08-13 B TRUE FALSE FALSE 52 M F35553 B_ENTRBC_CLOC</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2003-08-13 B TRUE FALSE FALSE 52 M F35553 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2003-09-05 B TRUE FALSE FALSE 52 M F35553 B_ENTRC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2003-09-05 B TRUE FALSE FALSE 52 M F35553 B_ENTRBC_CLOC</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 96 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># faster way, since mo_name() is context-aware:</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># get isolates whose name start with 'Entero' (case-insensitive)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^entero"</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_name()`</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 106 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospi…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 C FALSE TRUE FALSE 69 M 4FC193 B_ENTRC_FACM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-04-08 A TRUE TRUE FALSE 78 M 130252 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-06-23 D FALSE TRUE FALSE 82 M 798871 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-06-23 D FALSE TRUE FALSE 82 M 798871 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2003-04-20 D TRUE TRUE FALSE 62 M 6BC362 B_ENTRC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2003-04-21 D TRUE TRUE FALSE 62 M 6BC362 B_ENTRC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2003-08-13 B TRUE FALSE FALSE 52 M F35553 B_ENTRBC_CLOC</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2003-08-13 B TRUE FALSE FALSE 52 M F35553 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2003-09-05 B TRUE FALSE FALSE 52 M F35553 B_ENTRC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2003-09-05 B TRUE FALSE FALSE 52 M F35553 B_ENTRBC_CLOC</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 96 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 4FC193 69 M Clinic… B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-04-08 130252 78 M ICU B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-06-23 798871 82 M Clinic… B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-06-23 798871 82 M Clinic… B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2003-04-20 6BC362 62 M ICU B_ENTRC NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2003-04-21 6BC362 62 M ICU B_ENTRC NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2003-08-13 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2003-08-13 F35553 52 M ICU B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2003-09-05 F35553 52 M ICU B_ENTRC NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2003-09-05 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 96 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_name()`</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 106 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospi…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 C FALSE TRUE FALSE 69 M 4FC193 B_ENTRC_FACM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-04-08 A TRUE TRUE FALSE 78 M 130252 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-06-23 D FALSE TRUE FALSE 82 M 798871 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-06-23 D FALSE TRUE FALSE 82 M 798871 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2003-04-20 D TRUE TRUE FALSE 62 M 6BC362 B_ENTRC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2003-04-21 D TRUE TRUE FALSE 62 M 6BC362 B_ENTRC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2003-08-13 B TRUE FALSE FALSE 52 M F35553 B_ENTRBC_CLOC</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2003-08-13 B TRUE FALSE FALSE 52 M F35553 B_ENTRC_FCLS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2003-09-05 B TRUE FALSE FALSE 52 M F35553 B_ENTRC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2003-09-05 B TRUE FALSE FALSE 52 M F35553 B_ENTRBC_CLOC</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 96 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-02-21 4FC193 69 M Clinic… B_ENTRC_FACM NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-04-08 130252 78 M ICU B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-06-23 798871 82 M Clinic… B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-06-23 798871 82 M Clinic… B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2003-04-20 6BC362 62 M ICU B_ENTRC NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2003-04-21 6BC362 62 M ICU B_ENTRC NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2003-08-13 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2003-08-13 F35553 52 M ICU B_ENTRC_FCLS NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2003-09-05 F35553 52 M ICU B_ENTRC NA NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2003-09-05 F35553 52 M ICU B_ENTRBC_CLOC R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 96 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -260,7 +260,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> 1. CIP is "R" and age is higher than 60 -> Elderly Type A</span></span>
|
||||
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#> 2. ERY is "R" and age is higher than 60 -> Elderly Type B</span></span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> 3. Otherwise -> Negative</span></span>
|
||||
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span></span>
|
||||
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#></span></span>
|
||||
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="co">#> Unmatched rows will return NA.</span></span></code></pre><p></p></div>
|
||||
<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code>mdro()</code> function:</p>
|
||||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>x <span class="ot"><-</span> <span class="fu">mdro</span>(example_isolates,</span>
|
||||
@@ -270,10 +270,10 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> 1070 198 732</span></span></code></pre><p></p></div>
|
||||
<p>Rules can also be combined with other custom rules by using <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code>:</p>
|
||||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>x <span class="ot"><-</span> <span class="fu">mdro</span>(example_isolates,</span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="at">guideline =</span> <span class="fu">c</span>(custom, </span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="at">guideline =</span> <span class="fu">c</span>(custom,</span>
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">custom_mdro_guideline</span>(ERY <span class="sc">==</span> <span class="st">"R"</span> <span class="sc">&</span> age <span class="sc">></span> <span class="dv">50</span> <span class="sc">~</span> <span class="st">"Elderly Type C"</span>)))</span>
|
||||
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">table</span>(x)</span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> Negative Elderly Type A Elderly Type B Elderly Type C </span></span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> Negative Elderly Type A Elderly Type B Elderly Type C</span></span>
|
||||
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#> 961 198 732 109</span></span></code></pre><p></p></div>
|
||||
<p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>.</p>
|
||||
</div>
|
||||
@@ -310,8 +310,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1978 0 6 </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">out</span> <span class="op"><-</span> <span class="fu">mdro</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="fu">custom_mdro_guideline</span><span class="op">(</span><span class="va">AMX</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="st">"Custom MDRO 1"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="va">VAN</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="st">"Custom MDRO 2"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="fu">custom_mdro_guideline</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">AMX</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="st">"Custom MDRO 1"</span>,</span></span>
|
||||
<span class="r-in"><span> <span class="va">VAN</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">~</span> <span class="st">"Custom MDRO 2"</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> out</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Negative Custom MDRO 1 Custom MDRO 2 </span>
|
||||
@@ -322,13 +325,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">mdro</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># no need to define `x` when used inside dplyr verbs:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>MDRO <span class="op">=</span> <span class="fu">mdro</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html" class="external-link">pull</a></span><span class="op">(</span><span class="va">MDRO</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (16 isolates had no test results)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `mdro()`: NA introduced for isolates where the available percentage of</span>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -138,14 +138,12 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 5,604 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
|
||||
<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 5,604 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
|
||||
<li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
|
||||
@@ -162,14 +160,21 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">microorganisms.codes</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> code mo</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 _FAM_A- B_GRAMN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 _FAM_A+ B_GRAMP</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 _FAM_AC B_GRAMP</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 _FAM_AE B_GRAMN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 _FAM_AN B_GRAMN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 _FAM_AO B_GRAMP</span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms.codes</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 5,604 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> code mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> _FAM_A- B_GRAMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> _FAM_A+ B_GRAMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> _FAM_AC B_GRAMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> _FAM_AE B_GRAMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> _FAM_AN B_GRAMN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> _FAM_AO B_GRAMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> _FAM_AP UNKNOWN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> _FAM_AS F_FUNGUS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> _FAM_AT UNKNOWN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> _FAM_AV UNKNOWN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 5,594 more rows</span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -138,7 +138,7 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 70,764 observations and 16 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
|
||||
<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 70,764 observations and 16 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
|
||||
<li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code></p></li>
|
||||
<li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism</p></li>
|
||||
<li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></li>
|
||||
@@ -181,8 +181,7 @@
|
||||
<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
|
||||
|
||||
|
||||
<p>This data set is available as 'flat file' for use even without <span style="R">R</span> - you can find the file here: <a href="https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt" class="external-link">https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt</a>.</p>
|
||||
<p>The file in <span style="R">R</span> format (with preserved data structure) can be found here: <a href="https://github.com/msberends/AMR/raw/main/data/microorganisms.rda" class="external-link">https://github.com/msberends/AMR/raw/main/data/microorganisms.rda</a>.</p>
|
||||
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
|
||||
</div>
|
||||
@@ -200,12 +199,6 @@
|
||||
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
|
||||
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
|
||||
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
@@ -214,35 +207,22 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">microorganisms</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname kingdom phylum</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 F_FUNGUS (unknown fungus) Fungi (unknown phylum)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 B_GRAMN (unknown Gram-negatives) Bacteria (unknown phylum)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 B_GRAMP (unknown Gram-positives) Bacteria (unknown phylum)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 UNKNOWN (unknown name) (unknown kingdom) (unknown phylum)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 F_YEAST (unknown yeast) Fungi (unknown phylum)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 B_[FAM]_ABDTBCTR Abditibacteriaceae Bacteria Abditibacteriota</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> class order family genus</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 (unknown class) (unknown order) (unknown family) (unknown genus)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 (unknown class) (unknown order) (unknown family) (unknown Gram-negatives)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 (unknown class) (unknown order) (unknown family) (unknown Gram-positives)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 (unknown class) (unknown order) (unknown family) (unknown genus)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 (unknown class) (unknown order) (unknown family) (unknown genus)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Abditibacteria Abditibacteriales Abditibacteriaceae </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> species subspecies rank ref species_id</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 (unknown species) (unknown subspecies) species <NA> NA</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 (unknown species) (unknown subspecies) species <NA> NA</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 (unknown species) (unknown subspecies) species <NA> NA</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 (unknown species) (unknown subspecies) (unknown rank) <NA> NA</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 (unknown species) (unknown subspecies) species <NA> NA</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 family <NA> NA</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> source prevalence snomed</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 manually added 3 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 manually added 3 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 manually added 3 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 manually added 3 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 manually added 3 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 CoL 2 </span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 70,764 × 16</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo fullname kingdom phylum class order family genus species</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> F_FUNGUS (unknown fu… Fungi (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_GRAMN (unknown Gr… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_GRAMP (unknown Gr… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> UNKNOWN (unknown na… (unkno… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> F_YEAST (unknown ye… Fungi (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B_[FAM]_ABDTBCTR Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B_[ORD]_ABDTBCTR Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B_ABDTB Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_ABDTB_UTST Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>utste…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> C_ABDTD Abditodentr… Chromi… Foram… Glob… Rota… <span style="color: #949494;">"</span>Boli… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 70,754 more rows, and 7 more variables: subspecies <chr>, rank <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ref <chr>, species_id <dbl>, source <chr>, prevalence <dbl>, snomed <list></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -138,7 +138,7 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 14,338 observations and 4 variables:</p><ul><li><p><code>fullname</code><br> Old full taxonomic name of the microorganism</p></li>
|
||||
<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 14,338 observations and 4 variables:</p><ul><li><p><code>fullname</code><br> Old full taxonomic name of the microorganism</p></li>
|
||||
<li><p><code>fullname_new</code><br> New full taxonomic name of the microorganism</p></li>
|
||||
<li><p><code>ref</code><br> Author(s) and year of concerning scientific publication</p></li>
|
||||
<li><p><code>prevalence</code><br> Prevalence of the microorganism, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
|
||||
@@ -147,6 +147,10 @@
|
||||
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
|
||||
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a> (check included annual version with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>).</p>
|
||||
<p>Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">doi:10.1099/ijsem.0.002786</a></p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
|
||||
@@ -155,12 +159,6 @@
|
||||
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
|
||||
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
|
||||
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
@@ -169,21 +167,21 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">microorganisms.old</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> fullname fullname_new</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Abaphospora petrucciana Nectria petrucciana</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 Abathostoma stercoris Echinocyclidium stercoris</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 Abbottina tannerbankensis Nonion tannerbankensis</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 Abditodentrix rhomboidalis Tortoplectella rhomboidalis</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Abiotrophia adiacens Granulicatella adiacens</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Abiotrophia balaenopterae Granulicatella balaenopterae</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ref prevalence</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Kirschst, 1939 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 Berger in Corliss, 1979 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 McCulloch, 1977 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 Millett, 1899 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 Kawamura et al., 1995 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 Lawson et al., 1999 2</span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms.old</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 14,338 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> fullname fullname_new ref preva…¹</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Abaphospora petrucciana Nectria petrucciana Kirschst, 19… 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Abathostoma stercoris Echinocyclidium stercoris Berger in Co… 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Abbottina tannerbankensis Nonion tannerbankensis McCulloch, 1… 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Abditodentrix rhomboidalis Tortoplectella rhomboidalis Millett, 1899 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Abiotrophia adiacens Granulicatella adiacens Kawamura et … 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Abiotrophia balaenopterae Granulicatella balaenopterae Lawson et al… 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Abiotrophia elegans Granulicatella elegans Roggenkamp e… 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Absidia blakesleeana Lichtheimia blakesleeana Lendn, 1924 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Absidia butleri Gongronella butleri Lendn, 1926 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Absidia corymbifera Lichtheimia corymbifera Sacc et al.,… 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 14,328 more rows, and abbreviated variable name ¹prevalence</span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -167,11 +167,11 @@
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
|
||||
<p>Dr Matthijs Berends</p>
|
||||
<p>Dr. Matthijs Berends</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
@@ -189,8 +189,10 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> Also matched: Entamoeba coli (0.079)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_matching_score</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_matching_score</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> n <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.68750000 0.07936508</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -283,7 +283,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
@@ -421,12 +421,14 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,</span></span>
|
||||
<span class="r-in"><span> Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
|
||||
<span class="r-in"><span> language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
|
||||
<span class="r-in"><span> language <span class="op">=</span> <span class="st">"de"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Streptococcus Gruppe A"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>,</span></span>
|
||||
<span class="r-in"><span> Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
|
||||
<span class="r-in"><span> language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> Lancefield <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
|
||||
<span class="r-in"><span> language <span class="op">=</span> <span class="st">"nl"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Streptococcus groep A"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@@ -439,32 +441,32 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_is_gram_positive()`</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 709 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospit…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-19 D FALSE TRUE FALSE 71 M 738003 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-19 D FALSE TRUE FALSE 71 M 738003 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-21 D FALSE TRUE FALSE 75 F 462081 B_CTRBC_FRND</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-22 B TRUE FALSE FALSE 50 M F35553 B_PROTS_MRBL</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-22 B TRUE FALSE FALSE 50 M F35553 B_PROTS_MRBL</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-02-05 B TRUE FALSE FALSE 45 F 067927 B_SERRT_MRCS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-02-05 B TRUE FALSE FALSE 45 F 067927 B_SERRT_MRCS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-05 B TRUE FALSE FALSE 45 F 067927 B_SERRT_MRCS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 699 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 709 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-21 462081 75 F Clinical B_CTRBC_FRND R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-02-05 067927 45 F ICU B_SERRT_MRCS R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 699 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>, TZP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span></span></span>
|
||||
|
||||
@@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -177,7 +177,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p>
|
||||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">set_mo_source</span>(<span class="st">"home/me/ourcodes.xlsx"</span>)</span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from</span></span>
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns </span></span>
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span></span>
|
||||
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#> "Organisation XYZ" and "mo"</span></span></code></pre><p></p></div>
|
||||
<p>It has now created a file <code>"~/mo_source.rds"</code> with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.</p>
|
||||
<p>And now we can use it in our functions:</p>
|
||||
@@ -204,7 +204,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="dv">5</span> <span class="sc">|</span> <span class="er">|</span> <span class="er">|</span></span></code></pre><p></p></div>
|
||||
<p>...any new usage of an MO function in this package will update your data file:</p>
|
||||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">as.mo</span>(<span class="st">"lab_mo_ecoli"</span>)</span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from </span></span>
|
||||
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from</span></span>
|
||||
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span></span>
|
||||
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#> "Organisation XYZ" and "mo"</span></span>
|
||||
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> Class <mo></span></span>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -214,25 +214,27 @@
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># calculate the resistance per group first </span></span></span>
|
||||
<span class="r-in"><span> <span class="va">resistance_data</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span>order <span class="op">=</span> <span class="fu"><a href="mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, <span class="co"># group on anything, like order</span></span></span>
|
||||
<span class="r-in"><span> genus <span class="op">=</span> <span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># and genus as we do here;</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span> <span class="op">>=</span> <span class="fl">30</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># filter on only 30 results per group</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="co"># then get resistance of all drugs</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="co"># calculate the resistance per group first</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">resistance_data</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> order <span class="op">=</span> <span class="fu"><a href="mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, <span class="co"># group on anything, like order</span></span></span>
|
||||
<span class="r-in"><span> genus <span class="op">=</span> <span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># and genus as we do here;</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span> <span class="op">>=</span> <span class="fl">30</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># filter on only 30 results per group</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="co"># then get resistance of all drugs</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># now conduct PCA for certain antimicrobial agents</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">pca_result</span> <span class="op"><-</span> <span class="va">resistance_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu">pca</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>, <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span><span class="op">)</span> </span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">pca_result</span> <span class="op"><-</span> <span class="va">resistance_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">pca</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>, <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">pca_result</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># old base R plotting method:</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># new ggplot2 plotting method using this package:</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_viridis.html" class="external-link">scale_colour_viridis_d</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
|
||||
|
||||
Binary file not shown.
|
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|
Before Width: | Height: | Size: 26 KiB After Width: | Height: | Size: 27 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 38 KiB After Width: | Height: | Size: 37 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 37 KiB After Width: | Height: | Size: 38 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 36 KiB After Width: | Height: | Size: 37 KiB |
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -278,7 +278,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span><span class="co"># run ?example_isolates for more info.</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># base R ------------------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">resistance</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># determines %R</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">resistance</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># determines %R</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.5955556</span>
|
||||
<span class="r-in"><span><span class="fu">susceptibility</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># determines %S+I</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.4044444</span>
|
||||
@@ -299,80 +299,88 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>r <span class="op">=</span> <span class="fu">resistance</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n <span class="op">=</span> <span class="fu"><a href="count.html">n_rsi</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span><span class="op">)</span> <span class="co"># n_rsi works like n_distinct in dplyr, see ?n_rsi</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> r <span class="op">=</span> <span class="fu">resistance</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n <span class="op">=</span> <span class="fu"><a href="count.html">n_rsi</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="co"># n_rsi works like n_distinct in dplyr, see ?n_rsi</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>R <span class="op">=</span> <span class="fu">resistance</span><span class="op">(</span><span class="va">CIP</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> SI <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n1 <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># the actual total; sum of all three</span></span></span>
|
||||
<span class="r-in"><span> n2 <span class="op">=</span> <span class="fu"><a href="count.html">n_rsi</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># same - analogous to n_distinct</span></span></span>
|
||||
<span class="r-in"><span> total <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># NOT the number of tested isolates!</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> R <span class="op">=</span> <span class="fu">resistance</span><span class="op">(</span><span class="va">CIP</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> SI <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> n1 <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># the actual total; sum of all three</span></span></span>
|
||||
<span class="r-in"><span> n2 <span class="op">=</span> <span class="fu"><a href="count.html">n_rsi</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># same - analogous to n_distinct</span></span></span>
|
||||
<span class="r-in"><span> total <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span> <span class="co"># NOT the number of tested isolates!</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># so we can see that combination therapy does a lot more than mono therapy:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># %SI = 76.3%</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># n = 1879</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># %SI = 75.4%</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># n = 1855</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># %SI = 76.3%</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># n = 1879</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># %SI = 75.4%</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># n = 1855</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># %SI = 94.1%</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># n = 1939</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># n = 1939</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># See Details on how `only_all_tested` works. Example:</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>numerator <span class="op">=</span> <span class="fu"><a href="count.html">count_susceptible</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> denominator <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> proportion <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> numerator <span class="op">=</span> <span class="fu"><a href="count.html">count_susceptible</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> denominator <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> proportion <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>numerator <span class="op">=</span> <span class="fu"><a href="count.html">count_susceptible</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> denominator <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> proportion <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> numerator <span class="op">=</span> <span class="fu"><a href="count.html">count_susceptible</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> denominator <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> proportion <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span>, only_all_tested <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>cipro_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> cipro_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> genta_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">GEN</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> genta_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> combination_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, <span class="va">GEN</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> combination_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span>, <span class="va">GEN</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> cipro_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> cipro_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> genta_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">GEN</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> genta_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> combination_p <span class="op">=</span> <span class="fu">susceptibility</span><span class="op">(</span><span class="va">CIP</span>, <span class="va">GEN</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> combination_n <span class="op">=</span> <span class="fu"><a href="count.html">count_all</a></span><span class="op">(</span><span class="va">CIP</span>, <span class="va">GEN</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># Get proportions S/I/R immediately of all rsi columns</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">proportion_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># It also supports grouping variables</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># (use rsi_df to also include the count)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">hospital_id</span>, <span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">ward</span>, <span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">rsi_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> hospital_id antibiotic interpretation value isolates</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 A AMX SI 0.3932584 70</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 A AMX R 0.6067416 108</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 A CIP SI 0.8743961 181</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 A CIP R 0.1256039 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 B AMX SI 0.3854875 170</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 B AMX R 0.6145125 271</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 B CIP SI 0.8296593 414</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 B CIP R 0.1703407 85</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 C AMX SI 0.3714286 65</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 C AMX R 0.6285714 110</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 11 C CIP SI 0.7970297 161</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 12 C CIP R 0.2029703 41</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 13 D AMX SI 0.4334532 241</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 14 D AMX R 0.5665468 315</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 15 D CIP SI 0.8483034 425</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 16 D CIP R 0.1516966 76</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 12 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward antibiotic interpretation value isolates</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ord></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical AMX SI 0.423 357</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical AMX R 0.577 487</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical CIP SI 0.853 741</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical CIP R 0.147 128</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU AMX SI 0.369 158</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU AMX R 0.631 270</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU CIP SI 0.810 362</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU CIP R 0.190 85</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Outpatient AMX SI 0.397 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Outpatient AMX R 0.603 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Outpatient CIP SI 0.839 78</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Outpatient CIP R 0.161 15</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -178,43 +178,41 @@
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625 0.5 4 16 4 0.0625 8 0.002 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 0.25 64 64 0.5 <=0.001 0.5 <=0.001 8 1 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 2 0.01 0.5 0.0625 0.125 >=256 0.025 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.005 0.002 0.025 128 1 0.002 0.0625 0.25 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 64 2 0.5 0.0625 128 128 >=256 32 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 4 0.002 32 8 8 8 <=0.001</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 39 16 46 31 49 28 18 41 45 40 42 49 22 47 40 6 49 25 12 43 43 36 7 16 10</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 35 28 42 31 7 47 45 37 17 44 17 26 25 47 40 22 10 32 36 50 50 24 46 40 10</span>
|
||||
<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] S I S S R S S I S R R S S S S R S R I R R R R S R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R I S R I R R S S S S I S I I R I I I S I I I I R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 8 0.002 <=0.001 0.005 0.125 256 4 32 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] <=0.001 0.25 1 0.025 0.125 32 32 16 0.005 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.5 <=0.001 0.0625 0.5 256 2 64 </span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 0.0625 0.25 0.001 8 0.0625 32 8 0.001 1 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 32 >=64 >=64 8 32 0.0625 0.125 0.5 0.25 0.002 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 1 1 0.5 16 0.0625</span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 32 <=0.25 16 0.5 8 <=0.25 8 16 8 32 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 32 0.5 <=0.25 32 32 32 0.5 4 8 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] <=0.25 32 16 16 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 64 1 8 16 16 16 8 64 16 32 1 64 8 16 2 2 32 32 32 4 32 1 8 2 4 </span>
|
||||
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <mic></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 0.25 <=0.025 >=16 0.0625 0.5 8 0.25 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 4 0.125 1 0.5 0.125 8 >=16 0.0625 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] 0.25 >=16 2 >=16 1 1 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625 1 4 2 1 0.0625 0.025 0.025 0.125 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 4 0.025 0.25 0.25 0.025 0.25 1 2 0.25 0.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 4 1 1 0.025 4 </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 47 15 40 39 45 10 36 40 47 22 12 11 44 14 45 21 17 49 24 14 11 22 44 45 11</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 8 24 37 27 23 31 14 9 18 27 42 22 44 41 22 24 22 42 25 49 27 30 30 8 46</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 16 14 13 11 11 14 12 14 15 14 14 16 15 11 14 12 13 17 11 17 13 11 15 11 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 12 13 14 12 12 13 14 12 16 13 14 15 11 16 17 12 12 17 11 13 15 11 13 17 16</span>
|
||||
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <disk></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 17 25 23 21 19 21 15 15 25 22 22 16 16 18 16 25 23 24 17 23 15 25 22 23 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 24 26 22 26 25 20 24 22 26 20 19 20 27 19 15 15 17 15 22 27 18 15 27 16 25</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -283,10 +283,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu">resistance_predict</span><span class="op">(</span><span class="va">example_isolates</span>, </span></span>
|
||||
<span class="r-in"><span> col_ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
|
||||
<span class="r-in"><span> year_min <span class="op">=</span> <span class="fl">2010</span>,</span></span>
|
||||
<span class="r-in"><span> model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span></span></span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu">resistance_predict</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||||
<span class="r-in"><span> col_ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
|
||||
<span class="r-in"><span> year_min <span class="op">=</span> <span class="fl">2010</span>,</span></span>
|
||||
<span class="r-in"><span> model <span class="op">=</span> <span class="st">"binomial"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'date' as input for `col_date`.</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
|
||||
<span class="r-plt img"><img src="resistance_predict-1.png" alt="" width="700" height="433"></span>
|
||||
@@ -302,14 +303,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span> <span class="fu"><a href="first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Staphylococcus"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">resistance_predict</span><span class="op">(</span><span class="st">"PEN"</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># get the model from the object</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">mymodel</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html" class="external-link">attributes</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">$</span><span class="va">model</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mymodel</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Including isolates from ICU.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'date' as input for `col_date`.</span>
|
||||
<span class="r-plt img"><img src="resistance_predict-3.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> NULL</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Call:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> glm(formula = df_matrix ~ year, family = binomial)</span>
|
||||
@@ -333,15 +336,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># create nice plots with ggplot2 yourself</span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span> <span class="op">&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span> <span class="op">&&</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">data</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">mo</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">resistance_predict</span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
|
||||
<span class="r-in"><span> col_date <span class="op">=</span> <span class="st">"date"</span>,</span></span>
|
||||
<span class="r-in"><span> model <span class="op">=</span> <span class="st">"binomial"</span>,</span></span>
|
||||
<span class="r-in"><span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
|
||||
<span class="r-in"><span> minimum <span class="op">=</span> <span class="fl">15</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">resistance_predict</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> col_ab <span class="op">=</span> <span class="st">"AMX"</span>,</span></span>
|
||||
<span class="r-in"><span> col_date <span class="op">=</span> <span class="st">"date"</span>,</span></span>
|
||||
<span class="r-in"><span> model <span class="op">=</span> <span class="st">"binomial"</span>,</span></span>
|
||||
<span class="r-in"><span> info <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
|
||||
<span class="r-in"><span> minimum <span class="op">=</span> <span class="fl">15</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -138,7 +138,7 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 20,369 observations and 11 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
|
||||
<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 20,369 observations and 11 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
|
||||
<li><p><code>method</code><br> Either "DISK" or "MIC"</p></li>
|
||||
<li><p><code>site</code><br> Body site, e.g. "Oral" or "Respiratory"</p></li>
|
||||
<li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
|
||||
@@ -152,13 +152,8 @@
|
||||
</ul></div>
|
||||
<div class="section level2">
|
||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||||
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt</a>. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the <code>mo</code> and <code>ab</code> columns have been transformed to contain the full official names instead of codes.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
|
||||
|
||||
|
||||
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
|
||||
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
|
||||
<p>They <strong>allow for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI.</p>
|
||||
</div>
|
||||
<div class="section level2">
|
||||
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
|
||||
@@ -167,21 +162,22 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">rsi_translation</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> guideline method site mo rank_index ab ref_tbl disk_dose</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 EUCAST 2022 MIC <NA> F_ASPRG_MGTS 2 AMB Aspergillus <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 EUCAST 2022 MIC <NA> F_ASPRG_NIGR 2 AMB Aspergillus <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 EUCAST 2022 MIC <NA> F_CANDD 3 AMB Candida <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 EUCAST 2022 MIC <NA> F_CANDD_ALBC 2 AMB Candida <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 EUCAST 2022 MIC <NA> F_CANDD_DBLN 2 AMB Candida <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 EUCAST 2022 MIC <NA> F_CANDD_KRUS 2 AMB Candida <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> breakpoint_S breakpoint_R uti</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1 1 FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1 1 FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1 1 FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1 1 FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1 1 FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1 1 FALSE</span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rsi_translation</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 20,369 × 11</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> guideline method site mo rank_in…¹ ab ref_tbl disk_…² break…³</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_ASPRG_MGTS 2 AMB Aspergi… <span style="color: #BB0000;">NA</span> 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_ASPRG_NIGR 2 AMB Aspergi… <span style="color: #BB0000;">NA</span> 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD 3 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD_ALBC 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD_DBLN 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD_KRUS 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD_PRPS 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CANDD_TRPC 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_CRYPT_NFRM 2 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> EUCAST 2022 MIC <span style="color: #BB0000;">NA</span> F_PICHI 3 AMB Candida <span style="color: #BB0000;">NA</span> 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 20,359 more rows, 2 more variables: breakpoint_R <dbl>, uti <lgl>, and</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable names ¹rank_index, ²disk_dose, ³breakpoint_S</span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.06729828</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.001278582</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@@ -10,7 +10,7 @@
|
||||
|
||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@@ -135,7 +135,7 @@
|
||||
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_AMR_locale</span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="va">lang</span><span class="op">)</span></span>
|
||||
<span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="va">language</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">reset_AMR_locale</span><span class="op">(</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
@@ -144,7 +144,7 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
|
||||
<dl><dt>lang</dt>
|
||||
<dl><dt>language</dt>
|
||||
<dd><p>language to choose. Use one of these supported language names or ISO-639-1 codes: "English" ("en"), "Chinese" ("zh"), "Danish" ("da"), "Dutch" ("nl"), "French" ("fr"), "German" ("de"), "Greek" ("el"), "Italian" ("it"), "Japanese" ("ja"), "Polish" ("pl"), "Portuguese" ("pt"), "Russian" ("ru"), "Spanish" ("es"), "Swedish" ("sv"), "Turkish" ("tr"), "Ukrainian" ("uk").</p></dd>
|
||||
|
||||
|
||||
@@ -159,7 +159,7 @@
|
||||
<h3 id="changing-the-default-language">Changing the Default Language<a class="anchor" aria-label="anchor" href="#changing-the-default-language"></a></h3>
|
||||
|
||||
|
||||
<p>The system language will be used at default (as returned by <code>Sys.getenv("LANG")</code> or, if <code>LANG</code> is not set, Sys.getlocale("LC_COLLATE")), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol><li><p>Setting the R option <code>AMR_locale</code>, either by using <code>set_AMR_locale()</code> or by running e.g. <code>options(AMR_locale = "de")</code>.</p>
|
||||
<p>The system language will be used at default (as returned by <code>Sys.getenv("LANG")</code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html" class="external-link">Sys.getlocale("LC_COLLATE")</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol><li><p>Setting the R option <code>AMR_locale</code>, either by using <code>set_AMR_locale()</code> or by running e.g. <code>options(AMR_locale = "de")</code>.</p>
|
||||
<p>Note that setting an <span style="R">R</span> option only works in the same session. Save the command <code>options(AMR_locale = "(your language)")</code> to your <code>.Rprofile</code> file to apply it for every session.</p></li>
|
||||
<li><p>Setting the system variable <code>LANGUAGE</code> or <code>LANG</code>, e.g. by adding <code>LANGUAGE="de_DE.utf8"</code> to your <code>.Renviron</code> file in your home directory.</p></li>
|
||||
</ol><p>Thus, if the R option <code>AMR_locale</code> is set, the system variables <code>LANGUAGE</code> and <code>LANG</code> will be ignored.</p>
|
||||
|
||||
Reference in New Issue
Block a user