mirror of
https://github.com/msberends/AMR.git
synced 2025-07-27 17:07:54 +02:00
Built site for AMR: 1.8.2.9096@98e62c9
This commit is contained in:
github-actions
@ -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="">1.8.2.9095</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">
|
||||
@ -138,66 +138,66 @@
|
||||
|
||||
<div class="section level2">
|
||||
<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">ab_class</span><span class="op">(</span><span class="va">ab_class</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ab_class</span><span class="op">(</span><span class="va">ab_class</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">ab_selector</span><span class="op">(</span><span class="va">filter</span>, only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">ab_selector</span><span class="op">(</span><span class="va">filter</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">aminoglycosides</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">aminoglycosides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">aminopenicillins</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">aminopenicillins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">antifungals</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">antifungals</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">antimycobacterials</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">antimycobacterials</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">betalactams</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">betalactams</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">carbapenems</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">carbapenems</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">cephalosporins</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">cephalosporins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">cephalosporins_1st</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">cephalosporins_1st</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">cephalosporins_2nd</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">cephalosporins_2nd</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">cephalosporins_3rd</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">cephalosporins_3rd</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">cephalosporins_4th</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">cephalosporins_4th</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">cephalosporins_5th</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">cephalosporins_5th</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">fluoroquinolones</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">fluoroquinolones</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">glycopeptides</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">glycopeptides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">lincosamides</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">lincosamides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">lipoglycopeptides</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">lipoglycopeptides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">macrolides</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">macrolides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">oxazolidinones</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">oxazolidinones</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">penicillins</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">penicillins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">polymyxins</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">polymyxins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">streptogramins</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">streptogramins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">quinolones</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">quinolones</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">tetracyclines</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">tetracyclines</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">trimethoprims</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">trimethoprims</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">ureidopenicillins</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">ureidopenicillins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">administrable_per_os</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">administrable_per_os</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">administrable_iv</span><span class="op">(</span>only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span><span class="fu">administrable_iv</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||
<span></span>
|
||||
<span><span class="fu">not_intrinsic_resistant</span><span class="op">(</span></span>
|
||||
<span> only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
|
||||
<span> only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
|
||||
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||||
<span> version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
|
||||
<span> <span class="va">...</span></span>
|
||||
@ -210,8 +210,8 @@
|
||||
<dd><p>an antimicrobial class or a part of it, such as <code>"carba"</code> and <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href="antibiotics.html">antibiotics</a> data set will be searched (case-insensitive) for this value.</p></dd>
|
||||
|
||||
|
||||
<dt>only_rsi_columns</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns of class <code>rsi</code> must be selected (defaults to <code>FALSE</code>), see <code><a href="as.rsi.html">as.rsi()</a></code></p></dd>
|
||||
<dt>only_sir_columns</dt>
|
||||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns of class <code>sir</code> must be selected (defaults to <code>FALSE</code>), see <code><a href="as.sir.html">as.sir()</a></code></p></dd>
|
||||
|
||||
|
||||
<dt>only_treatable</dt>
|
||||
@ -285,7 +285,7 @@
|
||||
<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 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>
|
||||
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR 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">
|
||||
@ -295,7 +295,7 @@
|
||||
<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: #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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -306,13 +306,13 @@
|
||||
<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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <sir>, COL <sir>, MUP <sir>, RIF <sir></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>
|
||||
@ -321,7 +321,7 @@
|
||||
<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: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -340,7 +340,7 @@
|
||||
<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: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -366,7 +366,7 @@
|
||||
<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: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -377,16 +377,16 @@
|
||||
<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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 10 more variables: VAN <sir>, TCY <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, MTR <sir>, CHL <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, RIF <sir></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">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 × 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: #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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -397,18 +397,18 @@
|
||||
<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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 45 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, MUP <sir>, RIF <sir></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 × 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: #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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -419,21 +419,21 @@
|
||||
<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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 45 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, MUP <sir>, RIF <sir></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">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-msg co"><span class="r-pr">#></span> ℹ Filtering any of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"</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: #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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -444,19 +444,19 @@
|
||||
<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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 952 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, MUP <sir>, RIF <sir></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-msg co"><span class="r-pr">#></span> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"</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: #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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -467,13 +467,13 @@
|
||||
<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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 746 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, MUP <sir>, RIF <sir></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">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>
|
||||
@ -482,7 +482,7 @@
|
||||
<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: #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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -493,13 +493,13 @@
|
||||
<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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 16 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, MUP <sir>, RIF <sir></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">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>
|
||||
@ -510,7 +510,7 @@
|
||||
<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: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -544,7 +544,7 @@
|
||||
<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: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -568,7 +568,7 @@
|
||||
<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: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -621,7 +621,7 @@
|
||||
<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: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -786,7 +786,7 @@
|
||||
<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: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -808,7 +808,7 @@
|
||||
<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: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -835,7 +835,7 @@
|
||||
<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: #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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -846,13 +846,13 @@
|
||||
<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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 102 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, MUP <sir>, RIF <sir></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>
|
||||
@ -864,7 +864,7 @@
|
||||
<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: #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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -875,13 +875,13 @@
|
||||
<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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 521 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, MUP <sir>, RIF <sir></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>
|
||||
@ -894,7 +894,7 @@
|
||||
<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: #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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
@ -905,13 +905,13 @@
|
||||
<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-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 417 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, MUP <sir>, RIF <sir></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>
|
||||
@ -921,7 +921,7 @@
|
||||
<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: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></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>
|
||||
|
||||
Reference in New Issue
Block a user