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Package: AMR
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Version: 1.7.1.9061
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Date: 2021-12-05
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Version: 1.7.1.9062
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Date: 2021-12-06
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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4
NEWS.md
4
NEWS.md
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# `AMR` 1.7.1.9061
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## <small>Last updated: 5 December 2021</small>
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# `AMR` 1.7.1.9062
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## <small>Last updated: 6 December 2021</small>
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### Breaking changes
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* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
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@@ -200,10 +200,6 @@ reference:
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contents:
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- "`AMR-deprecated`"
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authors:
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Matthijs S. Berends:
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href: https://www.rug.nl/staff/m.s.berends/
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template:
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bootstrap: 3
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opengraph:
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
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<footer><div class="copyright">
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<p></p>
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<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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</div>
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<div class="pkgdown">
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
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</span>
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@@ -416,7 +416,7 @@ END OF TERMS AND CONDITIONS
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<footer><div class="copyright">
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<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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</div>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
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</header><script src="EUCAST_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
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</header><div class="row">
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<div class="col-md-9 contents">
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>How to apply EUCAST rules</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
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<div class="hidden name"><code>EUCAST.Rmd</code></div>
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<div id="introduction" class="section level2">
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<h2 class="hasAnchor">
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<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h2>
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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<p>What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Testing (EUCAST) states <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">on their website</a>:</p>
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<blockquote>
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<p><em>EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.</em></p>
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</blockquote>
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<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008" class="external-link">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and unusual phenotypes (v3.2, 2020).</p>
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<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008" class="external-link">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and unusual phenotypes (v3.3, 2021).</p>
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<p>Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
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</div>
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<div id="examples" class="section level2">
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<h2 class="hasAnchor">
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||||
<a href="#examples" class="anchor" aria-hidden="true"></a>Examples</h2>
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<div class="section level2">
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<h2 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a>
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</h2>
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<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
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<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<footer><div class="copyright">
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<p></p>
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||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
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<div class="pkgdown">
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<p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
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</div>
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</footer>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
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</span>
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</div>
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</header><script src="MDR_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
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</header><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
|
||||
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
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<div class="hidden name"><code>MDR.Rmd</code></div>
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</div>
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<p>With the function <code><a href="../reference/mdro.html">mdro()</a></code>, you can determine which micro-organisms are multi-drug resistant organisms (MDRO).</p>
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<div id="type-of-input" class="section level3">
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||||
<h3 class="hasAnchor">
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||||
<a href="#type-of-input" class="anchor" aria-hidden="true"></a>Type of input</h3>
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||||
<div class="section level3">
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||||
<h3 id="type-of-input">Type of input<a class="anchor" aria-label="anchor" href="#type-of-input"></a>
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||||
</h3>
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<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function takes a data set as input, such as a regular <code>data.frame</code>. It tries to automatically determine the right columns for info about your isolates, such as the name of the species and all columns with results of antimicrobial agents. See the help page for more info about how to set the right settings for your data with the command <code><a href="../reference/mdro.html">?mdro</a></code>.</p>
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<p>For WHONET data (and most other data), all settings are automatically set correctly.</p>
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</div>
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<div id="guidelines" class="section level3">
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<h3 class="hasAnchor">
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<a href="#guidelines" class="anchor" aria-hidden="true"></a>Guidelines</h3>
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<div class="section level3">
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<h3 id="guidelines">Guidelines<a class="anchor" aria-label="anchor" href="#guidelines"></a>
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</h3>
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<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function support multiple guidelines. You can select a guideline with the <code>guideline</code> parameter. Currently supported guidelines are (case-insensitive):</p>
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<ul>
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<li>
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@@ -236,15 +236,15 @@
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</li>
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</ul>
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<p>Please suggest your own (country-specific) guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="external-link uri">https://github.com/msberends/AMR/issues/new</a>.</p>
|
||||
<div id="custom-guidelines" class="section level4">
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||||
<h4 class="hasAnchor">
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||||
<a href="#custom-guidelines" class="anchor" aria-hidden="true"></a>Custom Guidelines</h4>
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||||
<div class="section level4">
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||||
<h4 id="custom-guidelines">Custom Guidelines<a class="anchor" aria-label="anchor" href="#custom-guidelines"></a>
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</h4>
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<p>You can also use your own custom guideline. Custom guidelines can be set with the <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.</p>
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<p>If you are familiar with <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when()</a></code> of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what R considers to be the ‘formula notation’:</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span class="va">custom</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mdro.html">custom_mdro_guideline</a></span><span class="op">(</span><span class="va">CIP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&</span> <span class="va">age</span> <span class="op">></span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type A"</span>,
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<span class="va">ERY</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&</span> <span class="va">age</span> <span class="op">></span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type B"</span><span class="op">)</span></code></pre></div>
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<p>If a row/an isolate matches the first rule, the value after the first <code><a href="https://rdrr.io/r/base/tilde.html" class="external-link">~</a></code> (in this case <em>‘Elderly Type A’</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The maximum number of rules is unlimited.</p>
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<p>If a row/an isolate matches the first rule, the value after the first <code>~</code> (in this case <em>‘Elderly Type A’</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The maximum number of rules is unlimited.</p>
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<p>You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.</p>
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<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span class="va">custom</span>
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@@ -269,17 +269,17 @@
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<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>
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||||
</div>
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||||
</div>
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||||
<div id="examples" class="section level3">
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||||
<h3 class="hasAnchor">
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||||
<a href="#examples" class="anchor" aria-hidden="true"></a>Examples</h3>
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||||
<div class="section level3">
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||||
<h3 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a>
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||||
</h3>
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||||
<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code> for predefined guidelines. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
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||||
<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains full antibiograms of 2,000 microbial isolates. It reflects reality and can be used to practise AMR data analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
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<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># to support pipes: %>%</span>
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||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
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<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
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||||
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%>%</span>
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<span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%>%</span>
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||||
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
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||||
<span class="fu"><a href="../reference/mdro.html">mdro</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>
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span>
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<span class="co"># ℹ Using column 'mo' as input for `col_mo`.</span>
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<span class="co"># Auto-guessing columns suitable for analysis... OK.</span>
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@@ -299,11 +299,12 @@
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<span class="co"># classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
|
||||
<p>Only results with ‘R’ are considered as resistance. Use <code>combine_SI = FALSE</code> to also consider ‘I’ as resistance.</p>
|
||||
<p>Determining multidrug-resistant organisms (MDRO), according to: Guideline: Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Author(s): Magiorakos AP, Srinivasan A, Carey RB, …, Vatopoulos A, Weber JT, Monnet DL Source: Clinical Microbiology and Infection 18:3, 2012; doi: 10.1111/j.1469-0691.2011.03570.x</p>
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<p>(16 isolates had no test results)</p>
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||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: factor > ordered (numeric)<br>
|
||||
Length: 2,000<br>
|
||||
Levels: 4: Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant …<br>
|
||||
Available: 1,745 (87.25%, NA: 255 = 12.75%)<br>
|
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Available: 1,729 (86.45%, NA: 271 = 13.55%)<br>
|
||||
Unique: 2</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
@@ -318,17 +319,17 @@ Unique: 2</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">1617</td>
|
||||
<td align="right">92.66%</td>
|
||||
<td align="right">1617</td>
|
||||
<td align="right">92.66%</td>
|
||||
<td align="right">1601</td>
|
||||
<td align="right">92.60%</td>
|
||||
<td align="right">1601</td>
|
||||
<td align="right">92.60%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Multi-drug-resistant (MDR)</td>
|
||||
<td align="right">128</td>
|
||||
<td align="right">7.34%</td>
|
||||
<td align="right">1745</td>
|
||||
<td align="right">7.40%</td>
|
||||
<td align="right">1729</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@@ -357,19 +358,19 @@ Unique: 2</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><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">my_TB_data</span><span class="op">)</span>
|
||||
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
|
||||
<span class="co"># 1 S S R R I I</span>
|
||||
<span class="co"># 2 S R R S I S</span>
|
||||
<span class="co"># 3 S I I S R I</span>
|
||||
<span class="co"># 4 I I R I S I</span>
|
||||
<span class="co"># 5 R I R R S S</span>
|
||||
<span class="co"># 6 I R S I I R</span>
|
||||
<span class="co"># 1 R I I R I I</span>
|
||||
<span class="co"># 2 S S S S I S</span>
|
||||
<span class="co"># 3 S I I S S I</span>
|
||||
<span class="co"># 4 R I S R R R</span>
|
||||
<span class="co"># 5 R S R R I I</span>
|
||||
<span class="co"># 6 I S R S I S</span>
|
||||
<span class="co"># kanamycin</span>
|
||||
<span class="co"># 1 I</span>
|
||||
<span class="co"># 2 S</span>
|
||||
<span class="co"># 3 S</span>
|
||||
<span class="co"># 4 I</span>
|
||||
<span class="co"># 2 I</span>
|
||||
<span class="co"># 3 R</span>
|
||||
<span class="co"># 4 R</span>
|
||||
<span class="co"># 5 R</span>
|
||||
<span class="co"># 6 S</span></code></pre></div>
|
||||
<span class="co"># 6 R</span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
|
||||
@@ -412,40 +413,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3194</td>
|
||||
<td align="right">63.88%</td>
|
||||
<td align="right">3194</td>
|
||||
<td align="right">63.88%</td>
|
||||
<td align="right">3230</td>
|
||||
<td align="right">64.60%</td>
|
||||
<td align="right">3230</td>
|
||||
<td align="right">64.60%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">964</td>
|
||||
<td align="right">19.28%</td>
|
||||
<td align="right">4158</td>
|
||||
<td align="right">83.16%</td>
|
||||
<td align="right">984</td>
|
||||
<td align="right">19.68%</td>
|
||||
<td align="right">4214</td>
|
||||
<td align="right">84.28%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">451</td>
|
||||
<td align="right">9.02%</td>
|
||||
<td align="right">4609</td>
|
||||
<td align="right">92.18%</td>
|
||||
<td align="right">445</td>
|
||||
<td align="right">8.90%</td>
|
||||
<td align="right">4659</td>
|
||||
<td align="right">93.18%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">253</td>
|
||||
<td align="right">5.06%</td>
|
||||
<td align="right">4862</td>
|
||||
<td align="right">97.24%</td>
|
||||
<td align="right">241</td>
|
||||
<td align="right">4.82%</td>
|
||||
<td align="right">4900</td>
|
||||
<td align="right">98.00%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">138</td>
|
||||
<td align="right">2.76%</td>
|
||||
<td align="right">100</td>
|
||||
<td align="right">2.00%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@@ -464,12 +465,12 @@ Unique: 5</p>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, Christian F. Luz.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -185,13 +185,13 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="PCA_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
|
||||
</header><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
|
||||
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>PCA.Rmd</code></div>
|
||||
|
||||
</div>
|
||||
@@ -199,93 +199,93 @@
|
||||
|
||||
|
||||
<p><strong>NOTE: This page will be updated soon, as the pca() function is currently being developed.</strong></p>
|
||||
<div id="introduction" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
|
||||
<div class="section level1">
|
||||
<h1 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
|
||||
</h1>
|
||||
</div>
|
||||
<div id="transforming" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#transforming" class="anchor" aria-hidden="true"></a>Transforming</h1>
|
||||
<div class="section level1">
|
||||
<h1 id="transforming">Transforming<a class="anchor" aria-label="anchor" href="#transforming"></a>
|
||||
</h1>
|
||||
<p>For PCA, we need to transform our AMR data first. This is what the <code>example_isolates</code> data set in this package looks like:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR" class="external-link">AMR</a></span><span class="op">)</span>
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
|
||||
<span class="co"># Rows: 2,000</span>
|
||||
<span class="co"># Columns: 49</span>
|
||||
<span class="co"># $ date <date> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
|
||||
<span class="co"># $ hospital_id <fct> D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B, …</span>
|
||||
<span class="co"># $ ward_icu <lgl> FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TR…</span>
|
||||
<span class="co"># $ ward_clinical <lgl> TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, FA…</span>
|
||||
<span class="co"># $ ward_outpatient <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE…</span>
|
||||
<span class="co"># $ age <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71…</span>
|
||||
<span class="co"># $ gender <chr> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M",…</span>
|
||||
<span class="co"># $ patient_id <chr> "A77334", "A77334", "067927", "067927", "067927", "067…</span>
|
||||
<span class="co"># $ mo <mo> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPH…</span>
|
||||
<span class="co"># $ PEN <rsi> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, …</span>
|
||||
<span class="co"># $ OXA <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ FLC <rsi> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, …</span>
|
||||
<span class="co"># $ AMX <rsi> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …</span>
|
||||
<span class="co"># $ AMC <rsi> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, …</span>
|
||||
<span class="co"># $ AMP <rsi> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …</span>
|
||||
<span class="co"># $ TZP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ CZO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ FEP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ CXM <rsi> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R,…</span>
|
||||
<span class="co"># $ FOX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ CTX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
|
||||
<span class="co"># $ CAZ <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S…</span>
|
||||
<span class="co"># $ CRO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
|
||||
<span class="co"># $ GEN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ TOB <rsi> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA…</span>
|
||||
<span class="co"># $ AMK <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ KAN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ TMP <rsi> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R…</span>
|
||||
<span class="co"># $ SXT <rsi> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, …</span>
|
||||
<span class="co"># $ NIT <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ FOS <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ LNZ <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span>
|
||||
<span class="co"># $ CIP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, …</span>
|
||||
<span class="co"># $ MFX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ VAN <rsi> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S…</span>
|
||||
<span class="co"># $ TEC <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span>
|
||||
<span class="co"># $ TCY <rsi> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S…</span>
|
||||
<span class="co"># $ TGC <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …</span>
|
||||
<span class="co"># $ DOX <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …</span>
|
||||
<span class="co"># $ ERY <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …</span>
|
||||
<span class="co"># $ CLI <rsi> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, …</span>
|
||||
<span class="co"># $ AZM <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …</span>
|
||||
<span class="co"># $ IPM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
|
||||
<span class="co"># $ MEM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ MTR <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ CHL <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ COL <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R…</span>
|
||||
<span class="co"># $ MUP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ RIF <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span></code></pre></div>
|
||||
<span class="co"># $ date <span style="color: #949494; font-style: italic;"><date></span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
|
||||
<span class="co"># $ hospital_id <span style="color: #949494; font-style: italic;"><fct></span> D, D, B, B, B, B, D, D, B, B, D, D, D, D, D, B, B, B, …</span>
|
||||
<span class="co"># $ ward_icu <span style="color: #949494; font-style: italic;"><lgl></span> FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TR…</span>
|
||||
<span class="co"># $ ward_clinical <span style="color: #949494; font-style: italic;"><lgl></span> TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, FA…</span>
|
||||
<span class="co"># $ ward_outpatient <span style="color: #949494; font-style: italic;"><lgl></span> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE…</span>
|
||||
<span class="co"># $ age <span style="color: #949494; font-style: italic;"><dbl></span> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71…</span>
|
||||
<span class="co"># $ gender <span style="color: #949494; font-style: italic;"><chr></span> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M",…</span>
|
||||
<span class="co"># $ patient_id <span style="color: #949494; font-style: italic;"><chr></span> "A77334", "A77334", "067927", "067927", "067927", "067…</span>
|
||||
<span class="co"># $ mo <span style="color: #949494; font-style: italic;"><mo></span> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPH…</span>
|
||||
<span class="co"># $ PEN <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, …</span>
|
||||
<span class="co"># $ OXA <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ FLC <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, …</span>
|
||||
<span class="co"># $ AMX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …</span>
|
||||
<span class="co"># $ AMC <span style="color: #949494; font-style: italic;"><rsi></span> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, …</span>
|
||||
<span class="co"># $ AMP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, …</span>
|
||||
<span class="co"># $ TZP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ CZO <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ FEP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ CXM <span style="color: #949494; font-style: italic;"><rsi></span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R,…</span>
|
||||
<span class="co"># $ FOX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ CTX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
|
||||
<span class="co"># $ CAZ <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S…</span>
|
||||
<span class="co"># $ CRO <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
|
||||
<span class="co"># $ GEN <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ TOB <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA…</span>
|
||||
<span class="co"># $ AMK <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ KAN <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ TMP <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R…</span>
|
||||
<span class="co"># $ SXT <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, …</span>
|
||||
<span class="co"># $ NIT <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ FOS <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ LNZ <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span>
|
||||
<span class="co"># $ CIP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, …</span>
|
||||
<span class="co"># $ MFX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ VAN <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S…</span>
|
||||
<span class="co"># $ TEC <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span>
|
||||
<span class="co"># $ TCY <span style="color: #949494; font-style: italic;"><rsi></span> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S…</span>
|
||||
<span class="co"># $ TGC <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …</span>
|
||||
<span class="co"># $ DOX <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, …</span>
|
||||
<span class="co"># $ ERY <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …</span>
|
||||
<span class="co"># $ CLI <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, …</span>
|
||||
<span class="co"># $ AZM <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, …</span>
|
||||
<span class="co"># $ IPM <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, …</span>
|
||||
<span class="co"># $ MEM <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ MTR <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ CHL <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ COL <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R…</span>
|
||||
<span class="co"># $ MUP <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
|
||||
<span class="co"># $ RIF <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span></code></pre></div>
|
||||
<p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">resistance_data</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<code class="sourceCode R"><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 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="../reference/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>
|
||||
genus <span class="op">=</span> <span class="fu"><a href="../reference/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">%>%</span> <span class="co"># and genus as we do here</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="op">%>%</span> <span class="co"># then get resistance of all drugs</span>
|
||||
genus <span class="op">=</span> <span class="fu"><a href="../reference/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 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="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># then get resistance of all drugs</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">order</span>, <span class="va">genus</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 class="co"># and select only relevant columns</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">resistance_data</span><span class="op">)</span>
|
||||
<span class="co"># # A tibble: 6 x 10</span>
|
||||
<span class="co"># # Groups: order [5]</span>
|
||||
<span class="co"># order genus AMC CXM CTX CAZ GEN TOB TMP SXT</span>
|
||||
<span class="co"># <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl></span>
|
||||
<span class="co"># 1 (unknown order) (unknown gen… NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 2 Actinomycetales Schaalia NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 3 Bacteroidales Bacteroides NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 4 Campylobacteral… Campylobacter NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 5 Caryophanales Gemella NA NA NA NA NA NA NA NA</span>
|
||||
<span class="co"># 6 Caryophanales Listeria NA NA NA NA NA NA NA NA</span></code></pre></div>
|
||||
<span class="co"># <span style="color: #949494;"># A tibble: 6 × 10</span></span>
|
||||
<span class="co"># <span style="color: #949494;"># Groups: order [5]</span></span>
|
||||
<span class="co"># order genus AMC CXM CTX CAZ GEN TOB TMP SXT</span>
|
||||
<span class="co"># <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;"><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="co"># <span style="color: #BCBCBC;">1</span> (unknown order) (unknown ge… <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="co"># <span style="color: #BCBCBC;">2</span> Actinomycetales Schaalia <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="co"># <span style="color: #BCBCBC;">3</span> Bacteroidales Bacteroides <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="co"># <span style="color: #BCBCBC;">4</span> Campylobacterales Campylobact… <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="co"># <span style="color: #BCBCBC;">5</span> Caryophanales Gemella <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="co"># <span style="color: #BCBCBC;">6</span> Caryophanales Listeria <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></code></pre></div>
|
||||
</div>
|
||||
<div id="perform-principal-component-analysis" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#perform-principal-component-analysis" class="anchor" aria-hidden="true"></a>Perform principal component analysis</h1>
|
||||
<div class="section level1">
|
||||
<h1 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a>
|
||||
</h1>
|
||||
<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">pca_result</span> <span class="op"><-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
|
||||
@@ -301,13 +301,13 @@
|
||||
<span class="co"># Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 5.121e-17</span>
|
||||
<span class="co"># Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span>
|
||||
<span class="co"># Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></code></pre></div>
|
||||
<pre><code># Groups (n=4, named as 'order'):
|
||||
# [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</code></pre>
|
||||
<pre><code><span class="co"># Groups (n=4, named as 'order'):</span>
|
||||
<span class="co"># [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></code></pre>
|
||||
<p>Good news. The first two components explain a total of 93.3% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
|
||||
</div>
|
||||
<div id="plotting-the-results" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#plotting-the-results" class="anchor" aria-hidden="true"></a>Plotting the results</h1>
|
||||
<div class="section level1">
|
||||
<h1 id="plotting-the-results">Plotting the results<a class="anchor" aria-label="anchor" href="#plotting-the-results"></a>
|
||||
</h1>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><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></code></pre></div>
|
||||
<p><img src="PCA_files/figure-html/unnamed-chunk-5-1.png" width="750"></p>
|
||||
@@ -335,12 +335,12 @@
|
||||
|
||||
<footer><div class="copyright">
|
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<p></p>
|
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<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
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<div class="pkgdown">
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<p></p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
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@@ -30,6 +30,8 @@
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<![endif]-->
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
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Source Code
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@@ -183,34 +185,34 @@
|
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|
||||
</header><script src="SPSS_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
|
||||
</header><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
|
||||
|
||||
<h4 class="date">28 November 2021</h4>
|
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<h4 data-toc-skip class="date">06 December 2021</h4>
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|
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
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<div class="hidden name"><code>SPSS.Rmd</code></div>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<div id="spss-sas-stata" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#spss-sas-stata" class="anchor"></a>SPSS / SAS / Stata</h2>
|
||||
<div class="section level2">
|
||||
<h2 id="spss-sas-stata">SPSS / SAS / Stata<a class="anchor" aria-label="anchor" href="#spss-sas-stata"></a>
|
||||
</h2>
|
||||
<p>SPSS (Statistical Package for the Social Sciences) is probably the most well-known software package for statistical analysis. SPSS is easier to learn than R, because in SPSS you only have to click a menu to run parts of your analysis. Because of its user-friendliness, it is taught at universities and particularly useful for students who are new to statistics. From my experience, I would guess that pretty much all (bio)medical students know it at the time they graduate. SAS and Stata are comparable statistical packages popular in big industries.</p>
|
||||
</div>
|
||||
<div id="compared-to-r" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#compared-to-r" class="anchor"></a>Compared to R</h2>
|
||||
<div class="section level2">
|
||||
<h2 id="compared-to-r">Compared to R<a class="anchor" aria-label="anchor" href="#compared-to-r"></a>
|
||||
</h2>
|
||||
<p>As said, SPSS is easier to learn than R. But SPSS, SAS and Stata come with major downsides when comparing it with R:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<p><strong>R is highly modular.</strong></p>
|
||||
<p>The <a href="https://cran.r-project.org/">official R network (CRAN)</a> features more than 16,000 packages at the time of writing, our <code>AMR</code> package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitHub. So there may even be a lot more than 14,000 packages out there.</p>
|
||||
<p>The <a href="https://cran.r-project.org/" class="external-link">official R network (CRAN)</a> features more than 16,000 packages at the time of writing, our <code>AMR</code> package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitHub. So there may even be a lot more than 14,000 packages out there.</p>
|
||||
<p>Bottom line is, you can really extend it yourself or ask somebody to do this for you. Take for example our <code>AMR</code> package. Among other things, it adds reliable reference data to R to help you with the data cleaning and analysis. SPSS, SAS and Stata will never know what a valid MIC value is or what the Gram stain of <em>E. coli</em> is. Or that all species of <em>Klebiella</em> are resistant to amoxicillin and that Floxapen<sup>®</sup> is a trade name of flucloxacillin. These facts and properties are often needed to clean existing data, which would be very inconvenient in a software package without reliable reference data. See below for a demonstration.</p>
|
||||
</li>
|
||||
<li>
|
||||
@@ -219,27 +221,27 @@
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>R can be easily automated.</strong></p>
|
||||
<p>Over the last years, <a href="https://rmarkdown.rstudio.com/">R Markdown</a> has really made an interesting development. With R Markdown, you can very easily produce reports, whether the format has to be Word, PowerPoint, a website, a PDF document or just the raw data to Excel. It even allows the use of a reference file containing the layout style (e.g. fonts and colours) of your organisation. I use this a lot to generate weekly and monthly reports automatically. Just write the code once and enjoy the automatically updated reports at any interval you like.</p>
|
||||
<p>For an even more professional environment, you could create <a href="https://shiny.rstudio.com/">Shiny apps</a>: live manipulation of data using a custom made website. The webdesign knowledge needed (JavaScript, CSS, HTML) is almost <em>zero</em>.</p>
|
||||
<p>Over the last years, <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a> has really made an interesting development. With R Markdown, you can very easily produce reports, whether the format has to be Word, PowerPoint, a website, a PDF document or just the raw data to Excel. It even allows the use of a reference file containing the layout style (e.g. fonts and colours) of your organisation. I use this a lot to generate weekly and monthly reports automatically. Just write the code once and enjoy the automatically updated reports at any interval you like.</p>
|
||||
<p>For an even more professional environment, you could create <a href="https://shiny.rstudio.com/" class="external-link">Shiny apps</a>: live manipulation of data using a custom made website. The webdesign knowledge needed (JavaScript, CSS, HTML) is almost <em>zero</em>.</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>R has a huge community.</strong></p>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes">427,872 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
||||
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">428,733 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
|
||||
<p>And that’s not vice versa I’m afraid. You can import data from any source into R. For example from SPSS, SAS and Stata (<a href="https://haven.tidyverse.org/">link</a>), from Minitab, Epi Info and EpiData (<a href="https://cran.r-project.org/package=foreign">link</a>), from Excel (<a href="https://readxl.tidyverse.org/">link</a>), from flat files like CSV, TXT or TSV (<a href="https://readr.tidyverse.org/">link</a>), or directly from databases and datawarehouses from anywhere on the world (<a href="https://dbplyr.tidyverse.org/">link</a>). You can even scrape websites to download tables that are live on the internet (<a href="https://github.com/hadley/rvest">link</a>) or get the results of an API call and transform it into data in only one command (<a href="https://github.com/Rdatatable/data.table/wiki/Convenience-features-of-fread">link</a>).</p>
|
||||
<p>And that’s not vice versa I’m afraid. You can import data from any source into R. For example from SPSS, SAS and Stata (<a href="https://haven.tidyverse.org/" class="external-link">link</a>), from Minitab, Epi Info and EpiData (<a href="https://cran.r-project.org/package=foreign" class="external-link">link</a>), from Excel (<a href="https://readxl.tidyverse.org/" class="external-link">link</a>), from flat files like CSV, TXT or TSV (<a href="https://readr.tidyverse.org/" class="external-link">link</a>), or directly from databases and datawarehouses from anywhere on the world (<a href="https://dbplyr.tidyverse.org/" class="external-link">link</a>). You can even scrape websites to download tables that are live on the internet (<a href="https://github.com/hadley/rvest" class="external-link">link</a>) or get the results of an API call and transform it into data in only one command (<a href="https://github.com/Rdatatable/data.table/wiki/Convenience-features-of-fread" class="external-link">link</a>).</p>
|
||||
<p>And the best part - you can export from R to most data formats as well. So you can import an SPSS file, do your analysis neatly in R and export the resulting tables to Excel files for sharing.</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>R is completely free and open-source.</strong></p>
|
||||
<p>No strings attached. It was created and is being maintained by volunteers who believe that (data) science should be open and publicly available to everybody. SPSS, SAS and Stata are quite expensive. IBM SPSS Staticstics only comes with subscriptions nowadays, varying <a href="https://www.ibm.com/products/spss-statistics/pricing">between USD 1,300 and USD 8,500</a> per user <em>per year</em>. SAS Analytics Pro costs <a href="https://www.sas.com/store/products-solutions/sas-analytics-pro/prodPERSANL.html">around USD 10,000</a> per computer. Stata also has a business model with subscription fees, varying <a href="https://www.stata.com/order/new/bus/single-user-licenses/dl/">between USD 600 and USD 2,800</a> per computer per year, but lower prices come with a limitation of the number of variables you can work with. And still they do not offer the above benefits of R.</p>
|
||||
<p>No strings attached. It was created and is being maintained by volunteers who believe that (data) science should be open and publicly available to everybody. SPSS, SAS and Stata are quite expensive. IBM SPSS Staticstics only comes with subscriptions nowadays, varying <a href="https://www.ibm.com/products/spss-statistics/pricing" class="external-link">between USD 1,300 and USD 8,500</a> per user <em>per year</em>. SAS Analytics Pro costs <a href="https://www.sas.com/store/products-solutions/sas-analytics-pro/prodPERSANL.html" class="external-link">around USD 10,000</a> per computer. Stata also has a business model with subscription fees, varying <a href="https://www.stata.com/order/new/bus/single-user-licenses/dl/" class="external-link">between USD 600 and USD 2,800</a> per computer per year, but lower prices come with a limitation of the number of variables you can work with. And still they do not offer the above benefits of R.</p>
|
||||
<p>If you are working at a midsized or small company, you can save it tens of thousands of dollars by using R instead of e.g. SPSS - gaining even more functions and flexibility. And all R enthousiasts can do as much PR as they want (like I do here), because nobody is officially associated with or affiliated by R. It is really free.</p>
|
||||
</li>
|
||||
<li>
|
||||
<p><strong>R is (nowadays) the preferred analysis software in academic papers.</strong></p>
|
||||
<p>At present, R is among the world most powerful statistical languages, and it is generally very popular in science (Bollmann <em>et al.</em>, 2017). For all the above reasons, the number of references to R as an analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/">is rising continuously</a> and has even surpassed SPSS for academic use (Muenchen, 2014).</p>
|
||||
<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2021, I don’t see any reason why SPSS would be of any better use than R.</p>
|
||||
<p>At present, R is among the world most powerful statistical languages, and it is generally very popular in science (Bollmann <em>et al.</em>, 2017). For all the above reasons, the number of references to R as an analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/" class="external-link">is rising continuously</a> and has even surpassed SPSS for academic use (Muenchen, 2014).</p>
|
||||
<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2021, I don’t see any reason why SPSS would be of any better use than R.</p>
|
||||
</li>
|
||||
</ul>
|
||||
<p>To demonstrate the first point:</p>
|
||||
@@ -251,11 +253,13 @@
|
||||
<span class="fu"><a href="../reference/as.mic.html">as.mic</a></span><span class="op">(</span><span class="st">"testvalue"</span><span class="op">)</span>
|
||||
<span class="co"># Class <mic></span>
|
||||
<span class="co"># [1] <NA></span>
|
||||
|
||||
<span class="co"># the Gram stain is available for all bacteria:</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
|
||||
<span class="co"># [1] "Gram-negative"</span>
|
||||
|
||||
<span class="co"># Klebsiella is intrinsic resistant to amoxicillin, according to EUCAST:</span>
|
||||
<span class="va">klebsiella_test</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="st">"klebsiella"</span>,
|
||||
<span class="va">klebsiella_test</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="st">"klebsiella"</span>,
|
||||
amox <span class="op">=</span> <span class="st">"S"</span>,
|
||||
stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
|
||||
<span class="va">klebsiella_test</span> <span class="co"># (our original data)</span>
|
||||
@@ -263,7 +267,8 @@
|
||||
<span class="co"># 1 klebsiella S</span>
|
||||
<span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">klebsiella_test</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="co"># (the edited data by EUCAST rules)</span>
|
||||
<span class="co"># mo amox</span>
|
||||
<span class="co"># 1 klebsiella S</span>
|
||||
<span class="co"># 1 klebsiella R</span>
|
||||
|
||||
<span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span>
|
||||
<span class="co"># [1] "Flucloxacillin"</span>
|
||||
@@ -274,19 +279,19 @@
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"floxapen"</span><span class="op">)</span>
|
||||
<span class="co"># [1] "J01CF05"</span></code></pre></div>
|
||||
</div>
|
||||
<div id="import-data-from-spsssasstata" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#import-data-from-spsssasstata" class="anchor"></a>Import data from SPSS/SAS/Stata</h2>
|
||||
<div id="rstudio" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#rstudio" class="anchor"></a>RStudio</h3>
|
||||
<p>To work with R, probably the best option is to use <a href="https://www.rstudio.com/products/rstudio/">RStudio</a>. It is an open-source and free desktop environment which not only allows you to run R code, but also supports project management, version management, package management and convenient import menus to work with other data sources. You can also install <a href="https://www.rstudio.com/products/rstudio/">RStudio Server</a> on a private or corporate server, which brings nothing less than the complete RStudio software to you as a website (at home or at work).</p>
|
||||
<div class="section level2">
|
||||
<h2 id="import-data-from-spsssasstata">Import data from SPSS/SAS/Stata<a class="anchor" aria-label="anchor" href="#import-data-from-spsssasstata"></a>
|
||||
</h2>
|
||||
<div class="section level3">
|
||||
<h3 id="rstudio">RStudio<a class="anchor" aria-label="anchor" href="#rstudio"></a>
|
||||
</h3>
|
||||
<p>To work with R, probably the best option is to use <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio</a>. It is an open-source and free desktop environment which not only allows you to run R code, but also supports project management, version management, package management and convenient import menus to work with other data sources. You can also install <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio Server</a> on a private or corporate server, which brings nothing less than the complete RStudio software to you as a website (at home or at work).</p>
|
||||
<p>To import a data file, just click <em>Import Dataset</em> in the Environment tab:</p>
|
||||
<p><img src="https://github.com/msberends/AMR/raw/main/docs/import1.png"></p>
|
||||
<p>If additional packages are needed, RStudio will ask you if they should be installed on beforehand.</p>
|
||||
<p>In the the window that opens, you can define all options (parameters) that should be used for import and you’re ready to go:</p>
|
||||
<p><img src="https://github.com/msberends/AMR/raw/main/docs/import2.png"></p>
|
||||
<p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>.</p>
|
||||
<p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html" class="external-link">as_factor()</a></code>.</p>
|
||||
<p>The difference is this:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">SPSS_data</span>
|
||||
@@ -321,72 +326,72 @@
|
||||
<span class="co"># 10 10018 Female alive 66.6</span>
|
||||
<span class="co"># # … with 4,193 more rows</span></code></pre></div>
|
||||
</div>
|
||||
<div id="base-r" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#base-r" class="anchor"></a>Base R</h3>
|
||||
<p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/">great <code>haven</code> package</a> yourself:</p>
|
||||
<div class="section level3">
|
||||
<h3 id="base-r">Base R<a class="anchor" aria-label="anchor" href="#base-r"></a>
|
||||
</h3>
|
||||
<p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/" class="external-link">great <code>haven</code> package</a> yourself:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># download and install the latest version:</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"haven"</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"haven"</span><span class="op">)</span>
|
||||
<span class="co"># load the package you just installed:</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://haven.tidyverse.org">haven</a></span><span class="op">)</span> </code></pre></div>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://haven.tidyverse.org" class="external-link">haven</a></span><span class="op">)</span> </code></pre></div>
|
||||
<p>You can now import files as follows:</p>
|
||||
<div id="spss" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#spss" class="anchor"></a>SPSS</h4>
|
||||
<div class="section level4">
|
||||
<h4 id="spss">SPSS<a class="anchor" aria-label="anchor" href="#spss"></a>
|
||||
</h4>
|
||||
<p>To read files from SPSS into R:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># read any SPSS file based on file extension (best way):</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_spss</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">read_spss</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># read .sav or .zsav file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_sav</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">read_sav</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># read .por file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">read_por</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
|
||||
<p>Do not forget about <code><a href="https://haven.tidyverse.org/reference/as_factor.html">as_factor()</a></code>, as mentioned above.</p>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">read_por</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
|
||||
<p>Do not forget about <code><a href="https://haven.tidyverse.org/reference/as_factor.html" class="external-link">as_factor()</a></code>, as mentioned above.</p>
|
||||
<p>To export your R objects to the SPSS file format:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># save as .sav file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># save as compressed .zsav file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, compress <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_spss.html" class="external-link">write_sav</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, compress <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
|
||||
</div>
|
||||
<div id="sas" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#sas" class="anchor"></a>SAS</h4>
|
||||
<div class="section level4">
|
||||
<h4 id="sas">SAS<a class="anchor" aria-label="anchor" href="#sas"></a>
|
||||
</h4>
|
||||
<p>To read files from SAS into R:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># read .sas7bdat + .sas7bcat files:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">read_sas</a></span><span class="op">(</span>data_file <span class="op">=</span> <span class="st">"path/to/file"</span>, catalog_file <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html" class="external-link">read_sas</a></span><span class="op">(</span>data_file <span class="op">=</span> <span class="st">"path/to/file"</span>, catalog_file <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># read SAS transport files (version 5 and version 8):</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">read_xpt</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html" class="external-link">read_xpt</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span></code></pre></div>
|
||||
<p>To export your R objects to the SAS file format:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># save as regular SAS file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html">write_sas</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_sas.html" class="external-link">write_sas</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># the SAS transport format is an open format </span>
|
||||
<span class="co"># (required for submission of the data to the FDA)</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html">write_xpt</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, version <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html" class="external-link">write_xpt</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"path/to/file"</span>, version <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></code></pre></div>
|
||||
</div>
|
||||
<div id="stata" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#stata" class="anchor"></a>Stata</h4>
|
||||
<div class="section level4">
|
||||
<h4 id="stata">Stata<a class="anchor" aria-label="anchor" href="#stata"></a>
|
||||
</h4>
|
||||
<p>To read files from Stata into R:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># read .dta file:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_stata</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html" class="external-link">read_stata</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># works exactly the same:</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">read_dta</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html" class="external-link">read_dta</a></span><span class="op">(</span>file <span class="op">=</span> <span class="st">"/path/to/file"</span><span class="op">)</span></code></pre></div>
|
||||
<p>To export your R objects to the Stata file format:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># save as .dta file, Stata version 14:</span>
|
||||
<span class="co"># (supports Stata v8 until v15 at the time of writing)</span>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html">write_dta</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"/path/to/file"</span>, version <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://haven.tidyverse.org/reference/read_dta.html" class="external-link">write_dta</a></span><span class="op">(</span>data <span class="op">=</span> <span class="va">yourdata</span>, path <span class="op">=</span> <span class="st">"/path/to/file"</span>, version <span class="op">=</span> <span class="fl">14</span><span class="op">)</span></code></pre></div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
@@ -403,11 +408,13 @@
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
@@ -416,5 +423,7 @@
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
|
||||
@@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -185,22 +185,22 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="WHONET_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
|
||||
</header><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to work with WHONET data</h1>
|
||||
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/WHONET.Rmd" class="external-link"><code>vignettes/WHONET.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/WHONET.Rmd" class="external-link"><code>vignettes/WHONET.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>WHONET.Rmd</code></div>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<div id="import-of-data" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#import-of-data" class="anchor" aria-hidden="true"></a>Import of data</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="import-of-data">Import of data<a class="anchor" aria-label="anchor" href="#import-of-data"></a>
|
||||
</h3>
|
||||
<p>This tutorial assumes you already imported the WHONET data with e.g. the <a href="https://readxl.tidyverse.org/" class="external-link"><code>readxl</code> package</a>. In RStudio, this can be done using the menu button ‘Import Dataset’ in the tab ‘Environment’. Choose the option ‘From Excel’ and select your exported file. Make sure date fields are imported correctly.</p>
|
||||
<p>An example syntax could look like this:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
@@ -208,14 +208,14 @@
|
||||
<span class="va">data</span> <span class="op"><-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html" class="external-link">read_excel</a></span><span class="op">(</span>path <span class="op">=</span> <span class="st">"path/to/your/file.xlsx"</span><span class="op">)</span></code></pre></div>
|
||||
<p>This package comes with an <a href="https://msberends.github.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
|
||||
</div>
|
||||
<div id="preparation" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#preparation" class="anchor" aria-hidden="true"></a>Preparation</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="preparation">Preparation<a class="anchor" aria-label="anchor" href="#preparation"></a>
|
||||
</h3>
|
||||
<p>First, load the relevant packages if you did not yet did this. I use the tidyverse for all of my analyses. All of them. If you don’t know it yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="external-link uri">https://www.tidyverse.org/</a>.</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR" class="external-link">AMR</a></span><span class="op">)</span> <span class="co"># this package</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span> <span class="co"># this package</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
|
||||
<p>We will have to transform some variables to simplify and automate the analysis:</p>
|
||||
<ul>
|
||||
@@ -224,9 +224,9 @@
|
||||
</ul>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># transform variables</span>
|
||||
<span class="va">data</span> <span class="op"><-</span> <span class="va">WHONET</span> <span class="op">%>%</span>
|
||||
<span class="va">data</span> <span class="op"><-</span> <span class="va">WHONET</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="co"># get microbial ID based on given organism</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">Organism</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">Organism</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"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</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_ND10</span><span class="op">:</span><span class="va">CIP_EE</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></code></pre></div>
|
||||
<p>No errors or warnings, so all values are transformed succesfully.</p>
|
||||
@@ -234,7 +234,7 @@
|
||||
<p>So let’s check our data, with a couple of frequency tables:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># our newly created `mo` variable, put in the mo_name() function</span>
|
||||
<span class="va">data</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, nmax <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></code></pre></div>
|
||||
<span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, nmax <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 500<br>
|
||||
@@ -338,7 +338,7 @@ Longest: 40</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># our transformed antibiotic columns</span>
|
||||
<span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span>
|
||||
<span class="va">data</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></code></pre></div>
|
||||
<span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: factor > ordered > rsi (numeric)<br>
|
||||
Length: 500<br>
|
||||
@@ -385,14 +385,14 @@ Drug group: Beta-lactams/penicillins<br>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div id="a-first-glimpse-at-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#a-first-glimpse-at-results" class="anchor" aria-hidden="true"></a>A first glimpse at results</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="a-first-glimpse-at-results">A first glimpse at results<a class="anchor" aria-label="anchor" href="#a-first-glimpse-at-results"></a>
|
||||
</h3>
|
||||
<p>An easy <code>ggplot</code> will already give a lot of information, using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data</span> <span class="op">%>%</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">Country</span><span class="op">)</span> <span class="op">%>%</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">Country</span>, <span class="va">AMP_ND2</span>, <span class="va">AMC_ED20</span>, <span class="va">CAZ_ED10</span>, <span class="va">CIP_ED5</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<code class="sourceCode R"><span class="va">data</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/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">Country</span><span class="op">)</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">Country</span>, <span class="va">AMP_ND2</span>, <span class="va">AMC_ED20</span>, <span class="va">CAZ_ED10</span>, <span class="va">CIP_ED5</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">'ab'</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
|
||||
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
|
||||
</div>
|
||||
@@ -408,12 +408,12 @@ Drug group: Beta-lactams/penicillins<br>
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -185,13 +185,13 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="benchmarks_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
|
||||
</header><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Benchmarks</h1>
|
||||
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/benchmarks.Rmd" class="external-link"><code>vignettes/benchmarks.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/benchmarks.Rmd" class="external-link"><code>vignettes/benchmarks.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>benchmarks.Rmd</code></div>
|
||||
|
||||
</div>
|
||||
@@ -202,7 +202,7 @@
|
||||
<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/joshuaulrich/microbenchmark/" class="external-link">microbenchmark</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR" class="external-link">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></code></pre></div>
|
||||
<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
|
||||
<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, its taxonomic kingdom).</p>
|
||||
@@ -224,42 +224,42 @@
|
||||
times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># as.mo("sau") 12.0 13.0 15.0 14.0 15.0 48 25</span>
|
||||
<span class="co"># as.mo("stau") 54.0 57.0 73.0 62.0 92.0 99 25</span>
|
||||
<span class="co"># as.mo("STAU") 54.0 58.0 73.0 63.0 91.0 98 25</span>
|
||||
<span class="co"># as.mo("staaur") 13.0 13.0 20.0 14.0 15.0 52 25</span>
|
||||
<span class="co"># as.mo("STAAUR") 11.0 13.0 18.0 14.0 16.0 47 25</span>
|
||||
<span class="co"># as.mo("S. aureus") 27.0 30.0 38.0 31.0 36.0 63 25</span>
|
||||
<span class="co"># as.mo("S aureus") 27.0 29.0 42.0 33.0 60.0 66 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 3.8 4.1 6.8 4.2 4.6 36 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 240.0 250.0 280.0 270.0 300.0 320 25</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 160.0 190.0 200.0 200.0 210.0 340 25</span>
|
||||
<span class="co"># as.mo("MRSA") 13.0 13.0 17.0 14.0 15.0 46 25</span>
|
||||
<span class="co"># as.mo("VISA") 20.0 23.0 34.0 25.0 52.0 59 25</span></code></pre></div>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># as.mo("sau") 12.0 13 18.0 14.0 15.0 45.0 25</span>
|
||||
<span class="co"># as.mo("stau") 55.0 61 79.0 87.0 91.0 99.0 25</span>
|
||||
<span class="co"># as.mo("STAU") 55.0 58 71.0 61.0 91.0 100.0 25</span>
|
||||
<span class="co"># as.mo("staaur") 11.0 12 20.0 14.0 25.0 46.0 25</span>
|
||||
<span class="co"># as.mo("STAAUR") 12.0 12 13.0 13.0 14.0 15.0 25</span>
|
||||
<span class="co"># as.mo("S. aureus") 27.0 30 43.0 34.0 58.0 62.0 25</span>
|
||||
<span class="co"># as.mo("S aureus") 26.0 28 43.0 32.0 59.0 66.0 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 3.7 4 4.3 4.1 4.6 5.3 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 250.0 250 280.0 280.0 290.0 390.0 25</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 190.0 200 210.0 210.0 220.0 230.0 25</span>
|
||||
<span class="co"># as.mo("MRSA") 10.0 12 18.0 14.0 14.0 43.0 25</span>
|
||||
<span class="co"># as.mo("VISA") 19.0 22 29.0 24.0 26.0 55.0 25</span></code></pre></div>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 200 times slower to determine.</p>
|
||||
<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
|
||||
<div id="repetitive-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#repetitive-results" class="anchor" aria-hidden="true"></a>Repetitive results</h3>
|
||||
<p>Repetitive results are values that are present more than once in a vector. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. So running <code><a href="../reference/as.mo.html">as.mo(c("E. coli", "E. coli"))</a></code> will check the value <code>"E. coli"</code> only once.</p>
|
||||
<div class="section level3">
|
||||
<h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
|
||||
</h3>
|
||||
<p>Repetitive results are values that are present more than once in a vector. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. So running <code>as.mo(c("E. coli", "E. coli"))</code> will check the value <code>"E. coli"</code> only once.</p>
|
||||
<p>To prove this, we will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for testing - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># start with the example_isolates data set</span>
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="va">x</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="co"># take all MO codes from the 'mo' column</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">mo</span><span class="op">)</span> <span class="op">%>%</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">mo</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 copy them a thousand times</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="fl">1000</span><span class="op">)</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="fl">1000</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"># then scramble them</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="op">)</span>
|
||||
|
||||
<span class="co"># what do these values look like? They are of class <mo>:</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 class="co"># Class <mo></span>
|
||||
<span class="co"># [1] B_STRPT_PNMN B_KLBSL_PNMN B_ESCHR_COLI B_SERRT_MRCS B_STPHY_CONS</span>
|
||||
<span class="co"># [6] B_ESCHR_COLI</span>
|
||||
<span class="co"># [1] B_STPHY_CONS B_STPHY_EPDR B_STPHY_CONS B_STRPT_PNMN B_STRPT_EQNS</span>
|
||||
<span class="co"># [6] B_STPHY_AURS</span>
|
||||
|
||||
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
@@ -275,12 +275,12 @@
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># mo_name(x) 188 202 260 233 335 408 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.233 seconds. That is 116 nanoseconds on average. You only lose time on your unique input values.</p>
|
||||
<span class="co"># mo_name(x) 190 204 271 259 346 372 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.259 seconds. That is 130 nanoseconds on average. You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div id="precalculated-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#precalculated-results" class="anchor" aria-hidden="true"></a>Precalculated results</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
|
||||
</h3>
|
||||
<p>What about precalculated results? If the input is an already precalculated result of a helper function such as <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all. In other words, if you run <code><a href="../reference/mo_property.html">mo_name()</a></code> on a valid taxonomic name, it will return the results immediately (see ‘C’ below):</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"STAAUR"</span><span class="op">)</span>,
|
||||
@@ -290,10 +290,10 @@
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 8.09 8.18 8.94 8.69 9.47 10.50 10</span>
|
||||
<span class="co"># B 23.40 24.90 31.90 27.90 28.20 80.70 10</span>
|
||||
<span class="co"># C 2.03 2.20 2.35 2.35 2.48 2.66 10</span></code></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0023 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<span class="co"># A 8.16 8.77 9.77 10.10 10.60 10.90 10</span>
|
||||
<span class="co"># B 23.20 26.60 32.00 27.50 28.90 76.30 10</span>
|
||||
<span class="co"># C 2.01 2.24 2.44 2.44 2.67 2.91 10</span></code></pre></div>
|
||||
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0024 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">run_it</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
|
||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
|
||||
@@ -307,19 +307,19 @@
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 1.68 1.72 1.88 1.88 1.97 2.32 10</span>
|
||||
<span class="co"># B 1.64 1.80 1.90 1.95 1.98 2.14 10</span>
|
||||
<span class="co"># C 1.71 1.74 1.88 1.80 2.08 2.21 10</span>
|
||||
<span class="co"># D 1.70 1.79 1.86 1.87 1.96 1.99 10</span>
|
||||
<span class="co"># E 1.73 1.85 1.94 1.91 2.03 2.20 10</span>
|
||||
<span class="co"># F 1.71 1.78 1.91 1.89 2.00 2.25 10</span>
|
||||
<span class="co"># G 1.66 1.78 1.87 1.88 1.98 2.04 10</span>
|
||||
<span class="co"># H 1.73 1.82 2.06 1.98 2.07 2.80 10</span></code></pre></div>
|
||||
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
|
||||
<span class="co"># A 1.57 1.61 1.69 1.65 1.77 1.91 10</span>
|
||||
<span class="co"># B 1.54 1.59 1.73 1.64 1.84 2.19 10</span>
|
||||
<span class="co"># C 1.56 1.63 1.76 1.75 1.77 2.11 10</span>
|
||||
<span class="co"># D 1.58 1.59 1.73 1.65 1.66 2.62 10</span>
|
||||
<span class="co"># E 1.55 1.62 1.70 1.66 1.72 2.13 10</span>
|
||||
<span class="co"># F 1.58 1.62 1.81 1.72 1.81 2.61 10</span>
|
||||
<span class="co"># G 1.54 1.65 1.73 1.69 1.71 2.32 10</span>
|
||||
<span class="co"># H 1.58 1.65 1.80 1.74 1.84 2.24 10</span></code></pre></div>
|
||||
<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
|
||||
</div>
|
||||
<div id="results-in-other-languages" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#results-in-other-languages" class="anchor" aria-hidden="true"></a>Results in other languages</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="results-in-other-languages">Results in other languages<a class="anchor" aria-label="anchor" href="#results-in-other-languages"></a>
|
||||
</h3>
|
||||
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on an English system</span>
|
||||
@@ -342,13 +342,13 @@
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># en 19.64 20.10 28.32 20.72 22.65 104.80 100</span>
|
||||
<span class="co"># de 30.76 31.59 37.06 32.27 33.87 95.10 100</span>
|
||||
<span class="co"># nl 34.88 35.58 43.87 36.41 38.73 94.00 100</span>
|
||||
<span class="co"># es 34.62 35.22 44.72 36.04 37.88 97.92 100</span>
|
||||
<span class="co"># it 24.03 24.59 28.09 25.19 26.12 79.32 100</span>
|
||||
<span class="co"># fr 23.79 24.37 30.37 24.89 26.29 194.10 100</span>
|
||||
<span class="co"># pt 23.85 24.42 28.21 24.90 26.22 83.14 100</span></code></pre></div>
|
||||
<span class="co"># en 19.38 19.92 23.08 20.50 21.40 67.58 100</span>
|
||||
<span class="co"># de 30.74 31.50 39.35 32.08 33.43 201.20 100</span>
|
||||
<span class="co"># nl 34.89 35.54 43.82 36.15 37.79 86.27 100</span>
|
||||
<span class="co"># es 34.62 35.30 42.36 35.99 37.61 90.39 100</span>
|
||||
<span class="co"># it 33.42 34.36 41.50 35.13 36.40 84.45 100</span>
|
||||
<span class="co"># fr 32.86 33.35 38.69 34.20 35.26 82.96 100</span>
|
||||
<span class="co"># pt 30.76 31.42 37.89 32.17 33.33 84.66 100</span></code></pre></div>
|
||||
<p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
||||
</div>
|
||||
</div>
|
||||
@@ -363,12 +363,12 @@
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
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||||
</footer>
|
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|
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Binary file not shown.
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@@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9061</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -190,7 +190,7 @@
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">05 December 2021</h4>
|
||||
<h4 data-toc-skip class="date">06 December 2021</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>datasets.Rmd</code></div>
|
||||
@@ -1256,7 +1256,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -185,7 +185,7 @@
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -44,7 +44,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -185,35 +185,35 @@
|
||||
|
||||
|
||||
|
||||
</header><script src="resistance_predict_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
|
||||
</header><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>How to predict antimicrobial resistance</h1>
|
||||
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/resistance_predict.Rmd" class="external-link"><code>vignettes/resistance_predict.Rmd</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/resistance_predict.Rmd" class="external-link"><code>vignettes/resistance_predict.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>resistance_predict.Rmd</code></div>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
<div id="needed-r-packages" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#needed-r-packages" class="anchor" aria-hidden="true"></a>Needed R packages</h2>
|
||||
<div class="section level2">
|
||||
<h2 id="needed-r-packages">Needed R packages<a class="anchor" aria-label="anchor" href="#needed-r-packages"></a>
|
||||
</h2>
|
||||
<p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
|
||||
<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR" class="external-link">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
|
||||
|
||||
<span class="co"># (if not yet installed, install with:)</span>
|
||||
<span class="co"># install.packages(c("tidyverse", "AMR"))</span></code></pre></div>
|
||||
</div>
|
||||
<div id="prediction-analysis" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#prediction-analysis" class="anchor" aria-hidden="true"></a>Prediction analysis</h2>
|
||||
<div class="section level2">
|
||||
<h2 id="prediction-analysis">Prediction analysis<a class="anchor" aria-label="anchor" href="#prediction-analysis"></a>
|
||||
</h2>
|
||||
<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR data analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
|
||||
<p>It is basically as easy as:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
|
||||
@@ -229,8 +229,8 @@
|
||||
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
|
||||
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a> <span class="at">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
|
||||
<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
|
||||
<p>When running any of these commands, a summary of the regression model will be printed unless using <code><a href="../reference/resistance_predict.html">resistance_predict(..., info = FALSE)</a></code>.</p>
|
||||
<pre><code># ℹ Using column 'date' as input for `col_date`.</code></pre>
|
||||
<p>When running any of these commands, a summary of the regression model will be printed unless using <code>resistance_predict(..., info = FALSE)</code>.</p>
|
||||
<pre><code><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre>
|
||||
<p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">predict_TZP</span>
|
||||
@@ -279,14 +279,14 @@
|
||||
<span class="co"># choose for error bars instead of a ribbon</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span>, ribbon <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-2.png" width="720"></p>
|
||||
<div id="choosing-the-right-model" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#choosing-the-right-model" class="anchor" aria-hidden="true"></a>Choosing the right model</h3>
|
||||
<div class="section level3">
|
||||
<h3 id="choosing-the-right-model">Choosing the right model<a class="anchor" aria-label="anchor" href="#choosing-the-right-model"></a>
|
||||
</h3>
|
||||
<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram-positive bacteria, the spread (i.e. standard error) is enormous:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%>%</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="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<code class="sourceCode R"><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="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
|
||||
@@ -309,14 +309,14 @@
|
||||
<td>
|
||||
<code>"binomial"</code> or <code>"binom"</code> or <code>"logit"</code>
|
||||
</td>
|
||||
<td><code><a href="https://rdrr.io/r/stats/glm.html" class="external-link">glm(..., family = binomial)</a></code></td>
|
||||
<td><code>glm(..., family = binomial)</code></td>
|
||||
<td>Generalised linear model with binomial distribution</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>
|
||||
<code>"loglin"</code> or <code>"poisson"</code>
|
||||
</td>
|
||||
<td><code><a href="https://rdrr.io/r/stats/glm.html" class="external-link">glm(..., family = poisson)</a></code></td>
|
||||
<td><code>glm(..., family = poisson)</code></td>
|
||||
<td>Generalised linear model with poisson distribution</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
@@ -330,9 +330,9 @@
|
||||
</table>
|
||||
<p>For the vancomycin resistance in Gram-positive bacteria, a linear model might be more appropriate since no binomial distribution is to be expected based on the observed years:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%>%</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="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<code class="sourceCode R"><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="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
|
||||
@@ -366,12 +366,12 @@
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p></p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
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|
||||
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|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -202,7 +202,7 @@
|
||||
<hr>
|
||||
<p><code>AMR</code> is a free, open-source and independent R package (see <a href="https://msberends.github.io/AMR/#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
|
||||
<p>After installing this package, R knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.</p>
|
||||
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. Since its first public release in early 2018, this package has been downloaded from more than 160 countries.</p>
|
||||
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.</p>
|
||||
<p>This package can be used for:</p>
|
||||
<ul>
|
||||
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</li>
|
||||
@@ -236,7 +236,7 @@
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -158,7 +158,7 @@
|
||||
|
||||
|
||||
<ul class="list-unstyled"><li>
|
||||
<p><strong><a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a></strong>. Author, maintainer. <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
<p><strong>Matthijs S. Berends</strong>. Author, maintainer. <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
|
||||
</p>
|
||||
</li>
|
||||
<li>
|
||||
@@ -269,7 +269,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -38,6 +38,9 @@
|
||||
#r4ds .img {
|
||||
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|
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|
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#r4ds .img img {
|
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}
|
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|
||||
/* class for footer */
|
||||
.footer_logo {
|
||||
@@ -52,7 +55,7 @@
|
||||
.countries_map {
|
||||
float: left;
|
||||
padding: 0 10px 10px 0;
|
||||
max-width: 35%;
|
||||
max-width: 35% !important;
|
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}
|
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@media only screen and (max-width: 992px) {
|
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.footer_logo {
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footer p {
|
||||
display: inline-block;
|
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}
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footer {
|
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padding: 15px 0 20px !important;
|
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}
|
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/* Supports icons for brand using font-awesome */
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.fab {
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kbd {
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box-shadow: 1px 1px 1px #2c3e50;
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box-shadow: 1px 1px 1px slategrey;
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margin: 1px;
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font-size: small;
|
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vertical-align: text-bottom;
|
||||
color: #2c3e50;
|
||||
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|
||||
font-weight: bold;
|
||||
}
|
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li, p {
|
||||
@@ -134,6 +138,9 @@ li p {
|
||||
.template-news li p {
|
||||
margin: 0;
|
||||
}
|
||||
.template-news h3 {
|
||||
padding-top: 10px;
|
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}
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/* slightly smaller blockquote */
|
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blockquote {
|
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@@ -258,16 +265,9 @@ table a:not(.btn):hover {
|
||||
font-size: 16px;
|
||||
}
|
||||
|
||||
/* logos on index page */
|
||||
.logo_img {
|
||||
display: inline-block;
|
||||
}
|
||||
.logo_txt {
|
||||
display: inline;
|
||||
font-size: 125%;
|
||||
vertical-align: middle;
|
||||
color: black;
|
||||
font-weight: bold;
|
||||
/* AMR logo on index page */
|
||||
.template-home h1 img {
|
||||
height: 120px;
|
||||
}
|
||||
|
||||
.btn.btn-info.btn-amr {
|
||||
|
||||
@@ -85,11 +85,9 @@ $(document).ready(function() {
|
||||
// edit footer
|
||||
$('footer').html(
|
||||
'<div>' +
|
||||
'<p><code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>.</p>' +
|
||||
'<a href="https://www.rug.nl"><img src="https://github.com/msberends/AMR/raw/main/docs/logo_rug.png" class="footer_logo"></a>' +
|
||||
'<p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl">University Medical Center Groningen</a>.</p>' +
|
||||
'<a target="_blank" href="https://www.rug.nl"><img src="https://github.com/msberends/AMR/raw/main/docs/logo_rug.png" class="footer_logo"></a>' +
|
||||
'</div>');
|
||||
// all links should open in new tab/window
|
||||
$('footer').html($('footer').html().replace(/href/g, 'target="_blank" href'));
|
||||
|
||||
// doctoral titles of authors
|
||||
function doct_tit(x) {
|
||||
|
||||
@@ -47,7 +47,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -202,7 +202,7 @@
|
||||
</h3>
|
||||
<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
|
||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~560 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.</p>
|
||||
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.177417131</a>) but is <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
|
||||
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.177417131</a>) but is <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
|
||||
<div class="main-content" style="display: inline-block;">
|
||||
<p>
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 175 countries</strong><br> Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.
|
||||
@@ -539,8 +539,7 @@
|
||||
<div class="developers">
|
||||
<h2 data-toc-skip>Developers</h2>
|
||||
<ul class="list-unstyled">
|
||||
<li>
|
||||
<a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>Matthijs S. Berends <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>Christian F. Luz <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>Dennis Souverein <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0003-0455-0336" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
|
||||
<li>Erwin E. A. Hassing <br><small class="roles"> Author, contributor </small> </li>
|
||||
@@ -556,7 +555,7 @@
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p>
|
||||
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9061</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -157,19 +157,19 @@
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="page-header" data-toc-text="1.7.1.9061" id="amr-1719061">
|
||||
<code>AMR</code> 1.7.1.9061<a class="anchor" aria-label="anchor" href="#amr-1719061"></a></h2>
|
||||
<h2 class="page-header" data-toc-text="1.7.1.9062" id="amr-1719062">
|
||||
<code>AMR</code> 1.7.1.9062<a class="anchor" aria-label="anchor" href="#amr-1719062"></a></h2>
|
||||
<div class="section level3">
|
||||
<h3 id="last-updated-december-1-7-1-9061"><small>Last updated: 5 December 2021</small><a class="anchor" aria-label="anchor" href="#last-updated-december-1-7-1-9061"></a></h3>
|
||||
<h3 id="last-updated-december-1-7-1-9062"><small>Last updated: 6 December 2021</small><a class="anchor" aria-label="anchor" href="#last-updated-december-1-7-1-9062"></a></h3>
|
||||
<div class="section level4">
|
||||
<h4 id="breaking-changes-1-7-1-9061">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-1-7-1-9061"></a></h4>
|
||||
<h4 id="breaking-changes-1-7-1-9062">Breaking changes<a class="anchor" aria-label="anchor" href="#breaking-changes-1-7-1-9062"></a></h4>
|
||||
<ul><li>Removed <code>p_symbol()</code> and all <code>filter_*()</code> functions (except for <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>), which were all deprecated in a previous package version</li>
|
||||
<li>Removed the <code>key_antibiotics()</code> and <code>key_antibiotics_equal()</code> functions, which were deprecated and superseded by <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> and <code><a href="../reference/key_antimicrobials.html">antimicrobials_equal()</a></code>
|
||||
</li>
|
||||
<li>Removed all previously implemented <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot2::ggplot()</a></code> generics for classes <code><mic></code>, <code><disk></code>, <code><rsi></code> and <code><resistance_predict></code> as they did not follow the <code>ggplot2</code> logic. They were replaced with <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> generics.</li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="new-1-7-1-9061">New<a class="anchor" aria-label="anchor" href="#new-1-7-1-9061"></a></h4>
|
||||
<h4 id="new-1-7-1-9062">New<a class="anchor" aria-label="anchor" href="#new-1-7-1-9062"></a></h4>
|
||||
<ul><li><p>Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021), effective in the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function. This is now the default guideline (all other guidelines are still available).</p></li>
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/ab_property.html">set_ab_names()</a></code> to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. Its second argument can be a tidyverse way of selecting:</p>
|
||||
@@ -181,7 +181,7 @@
|
||||
<li><p>Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese</p></li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="changed-1-7-1-9061">Changed<a class="anchor" aria-label="anchor" href="#changed-1-7-1-9061"></a></h4>
|
||||
<h4 id="changed-1-7-1-9062">Changed<a class="anchor" aria-label="anchor" href="#changed-1-7-1-9062"></a></h4>
|
||||
<ul><li>Updated the bacterial taxonomy to 5 October 2021 (according to <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a>), including all 11 new staphylococcal species named since 1 January last year</li>
|
||||
<li>The <code>antibiotics</code> data set now contains <strong>all ATC codes</strong> that are available through the <a href="https://www.whocc.no" class="external-link">WHOCC website</a>, regardless of drugs being present in more than one ATC group. This means that:
|
||||
<ul><li>Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)</li>
|
||||
@@ -235,7 +235,7 @@
|
||||
</li>
|
||||
<li>Improved plot legends for MICs and disk diffusion values</li>
|
||||
<li>Improved speed of <code><a href="../reference/as.ab.html">as.ab()</a></code> and all <code>ab_*()</code> functions</li>
|
||||
<li>Added <code>fortify()</code> extensions for plotting methods</li>
|
||||
<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify()</a></code> extensions for plotting methods</li>
|
||||
<li>
|
||||
<code>NA</code> values of the classes <code><mic></code>, <code><disk></code> and <code><rsi></code> are now exported objects of this package, e.g. <code>NA_mic_</code> is an <code>NA</code> of class <code>mic</code> (just like the base R <code>NA_character_</code> is an <code>NA</code> of class <code>character</code>)</li>
|
||||
<li>The <code><a href="../reference/proportion.html">proportion_df()</a></code>, <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/proportion.html">rsi_df()</a></code> functions now return with the additional S3 class ‘rsi_df’ so they can be extended by other packages</li>
|
||||
@@ -247,7 +247,7 @@
|
||||
<code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> can now cope with <code>NA</code>s</li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
<h4 id="other-1-7-1-9061">Other<a class="anchor" aria-label="anchor" href="#other-1-7-1-9061"></a></h4>
|
||||
<h4 id="other-1-7-1-9062">Other<a class="anchor" aria-label="anchor" href="#other-1-7-1-9062"></a></h4>
|
||||
<ul><li>This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.</li>
|
||||
</ul></div>
|
||||
</div>
|
||||
@@ -293,7 +293,7 @@
|
||||
<li>The documentation of the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> functions has been completely rewritten.</li>
|
||||
</ul></li>
|
||||
<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code>filter_betalactams()</code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
|
||||
<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
|
||||
<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
|
||||
</li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
@@ -376,7 +376,7 @@
|
||||
<span class="co">#> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
|
||||
<li><p><code>ggplot()</code> generics for classes <code><mic></code> and <code><disk></code></p></li>
|
||||
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> generics for classes <code><mic></code> and <code><disk></code></p></li>
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
@@ -427,7 +427,7 @@
|
||||
<ul><li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
|
||||
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
|
||||
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
|
||||
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
|
||||
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
|
||||
</ul></li>
|
||||
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
|
||||
<li>
|
||||
@@ -443,7 +443,7 @@
|
||||
<code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
|
||||
<li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
|
||||
<li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
|
||||
<li>Functions <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">dplyr::group_by()</a></code>
|
||||
<li>Functions <code><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">dplyr::group_by()</a></code>
|
||||
</li>
|
||||
<li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
|
||||
<li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
|
||||
@@ -722,7 +722,7 @@
|
||||
<p>Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.</p>
|
||||
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
|
||||
<p>Negative effects of this change are:</p>
|
||||
<ul><li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner" class="external-link">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
|
||||
<ul><li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner" class="external-link">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>.</li>
|
||||
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code><ord></code>, not <code><rsi></code> anymore. This is purely a visual effect.</del></li>
|
||||
<li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
|
||||
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
|
||||
@@ -985,7 +985,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<span class="co">#> invalid microorganism code, NA generated</span></code></pre></div>
|
||||
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
|
||||
</li>
|
||||
<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean" class="external-link"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean" class="external-link">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
|
||||
<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean" class="external-link"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean" class="external-link">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
|
||||
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
|
||||
</ul></div>
|
||||
<div class="section level4">
|
||||
@@ -1214,7 +1214,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
|
||||
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
|
||||
</li>
|
||||
<li>Frequency tables (<code>freq()</code>):
|
||||
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>):
|
||||
<ul><li><p>speed improvement for microbial IDs</p></li>
|
||||
<li><p>fixed factor level names for R Markdown</p></li>
|
||||
<li><p>when all values are unique it now shows a message instead of a warning</p></li>
|
||||
@@ -1223,12 +1223,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># grouped boxplots:</span>
|
||||
<span class="va">septic_patients</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/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 class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
</ul></li>
|
||||
@@ -1237,7 +1237,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
|
||||
</li>
|
||||
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
|
||||
<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
|
||||
<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> for when all values are <code>NA</code>
|
||||
</li>
|
||||
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
|
||||
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
|
||||
@@ -1448,7 +1448,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Now accepts high and low resistance: <code>"HIGH S"</code> will return <code>S</code>
|
||||
</li>
|
||||
</ul></li>
|
||||
<li>Frequency tables (<code>freq()</code> function):
|
||||
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> function):
|
||||
<ul><li>
|
||||
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
||||
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
|
||||
@@ -1457,15 +1457,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<span class="co"># OLD WAY</span>
|
||||
<span class="va">septic_patients</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>genus <span class="op">=</span> <span class="fu"><a href="../reference/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="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||
<span class="co"># NEW WAY</span>
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/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="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/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="co"># Even supports grouping variables:</span>
|
||||
<span class="va">septic_patients</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/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
|
||||
<li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
|
||||
@@ -1534,21 +1534,21 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
|
||||
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
|
||||
<li>
|
||||
<p>Frequency tables - <code>freq()</code>:</p>
|
||||
<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>:</p>
|
||||
<ul><li>
|
||||
<p>Support for grouping variables, test with:</p>
|
||||
<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</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/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 class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for (un)selecting columns:</p>
|
||||
<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</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 class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</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 class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html" class="external-link">hms::is.hms</a></code></p></li>
|
||||
@@ -1565,7 +1565,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
|
||||
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
|
||||
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
|
||||
<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
|
||||
<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">top_freq()</a></code></p></li>
|
||||
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
|
||||
<li>
|
||||
<p>AI improvements for <code>as.mo</code>:</p>
|
||||
@@ -1714,13 +1714,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html" class="external-link">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</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="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
|
||||
<p>For lists, subsetting is possible:</p>
|
||||
<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
</ul></div>
|
||||
<div class="section level5">
|
||||
@@ -1902,7 +1902,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -12,7 +12,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2021-12-05T21:06Z
|
||||
last_built: 2021-12-06T10:09Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
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@@ -1,88 +1,12 @@
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<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>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<meta property="og:description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)." />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<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>
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<!--[if lt IE 9]>
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<!-- 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=1.0"><title>Deprecated Functions — AMR-deprecated • 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"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- 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"><!-- 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><!-- 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><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Deprecated Functions — AMR-deprecated"><meta property="og:description" content="These functions are so-called 'Deprecated'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one)."><meta property="og:image" content="https://msberends.github.io/AMR/logo.png"><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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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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<![endif]-->
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|
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</head>
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<body data-spy="scroll" data-target="#toc">
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<![endif]--></head><body data-spy="scroll" data-target="#toc">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
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@@ -114,8 +37,7 @@
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@@ -192,8 +114,7 @@
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Other: benchmarks
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<a href="../reference/index.html">
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<span class="fa fa-book-open"></span>
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@@ -215,78 +136,68 @@
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<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Deprecated Functions</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/deprecated.R'><code>R/deprecated.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/deprecated.R" class="external-link"><code>R/deprecated.R</code></a></small>
|
||||
<div class="hidden name"><code>AMR-deprecated.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>These functions are so-called '<a href='https://rdrr.io/r/base/Deprecated.html'>Deprecated</a>'. <strong>They will be removed in a future release.</strong> Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
|
||||
<p>These functions are so-called '<a href="https://rdrr.io/r/base/Deprecated.html" class="external-link">Deprecated</a>'. <strong>They will be removed in a future release.</strong> Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
|
||||
</div>
|
||||
|
||||
<div id="ref-usage">Usage,NULL</div>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="retired-lifecycle"><a class="anchor" href="#retired-lifecycle"></a>Retired Lifecycle</h2>
|
||||
|
||||
<div id="retired-lifecycle">
|
||||
<h2>Retired Lifecycle</h2>
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_retired.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.</p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
|
||||
|
||||
<p><img src="figures/lifecycle_retired.svg" style="margin-bottom:5px"><br>
|
||||
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.</p>
|
||||
</div>
|
||||
<div id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<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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|
||||
|
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
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Other: benchmarks
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<div class="col-md-9 contents">
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<div class="page-header">
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||||
<h1>The <code>AMR</code> Package</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/amr.R" class="external-link"><code>R/amr.R</code></a></small>
|
||||
<div class="hidden name"><code>AMR.Rd</code></div>
|
||||
</div>
|
||||
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||||
@@ -238,15 +161,14 @@
|
||||
<p>Welcome to the <code>AMR</code> package.</p>
|
||||
</div>
|
||||
|
||||
<div id="ref-usage">Usage,NULL</div>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<div id="details">
|
||||
<h2>Details</h2>
|
||||
<p><code>AMR</code> is a free, open-source and independent <span style="R">R</span> package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
|
||||
<p>After installing this package, <span style="R">R</span> knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
|
||||
<p>This package is fully independent of any other <span style="R">R</span> package and works on Windows, macOS and Linux with all versions of <span style="R">R</span> since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This <span style="R">R</span> package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
|
||||
<p>This package can be used for:</p><ul>
|
||||
<li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</p></li>
|
||||
<p>This package can be used for:</p><ul><li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</p></li>
|
||||
<li><p>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</p></li>
|
||||
<li><p>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</p></li>
|
||||
<li><p>Determining first isolates to be used for AMR data analysis</p></li>
|
||||
@@ -262,60 +184,57 @@
|
||||
<li><p>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code</p></li>
|
||||
<li><p>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI</p></li>
|
||||
<li><p>Principal component analysis for AMR</p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
||||
|
||||
</ul></div>
|
||||
<div id="reference-data-publicly-available">
|
||||
<h2>Reference Data Publicly Available</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 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</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 id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="contact-us"><a class="anchor" href="#contact-us"></a>Contact Us</h2>
|
||||
|
||||
<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>
|
||||
</div>
|
||||
<div id="contact-us">
|
||||
<h2>Contact Us</h2>
|
||||
|
||||
|
||||
<p>For suggestions, comments or questions, please contact us at:</p>
|
||||
<p>Matthijs S. Berends <br />
|
||||
m.s.berends [at] umcg [dot] nl <br />
|
||||
<p>Matthijs S. Berends <br>
|
||||
m.s.berends [at] umcg [dot] nl <br>
|
||||
University of Groningen
|
||||
Department of Medical Microbiology and Infection Prevention <br />
|
||||
University Medical Center Groningen <br />
|
||||
Post Office Box 30001 <br />
|
||||
9700 RB Groningen <br />
|
||||
Department of Medical Microbiology and Infection Prevention <br>
|
||||
University Medical Center Groningen <br>
|
||||
Post Office Box 30001 <br>
|
||||
9700 RB Groningen <br>
|
||||
The Netherlands
|
||||
<a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a></p>
|
||||
<p>If you have found a bug, please file a new issue at: <br />
|
||||
<a href='https://github.com/msberends/AMR/issues'>https://github.com/msberends/AMR/issues</a></p>
|
||||
<a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a></p>
|
||||
<p>If you have found a bug, please file a new issue at: <br><a href="https://github.com/msberends/AMR/issues" class="external-link">https://github.com/msberends/AMR/issues</a></p>
|
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<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
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||||
<h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/whocc.R'><code>R/whocc.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/whocc.R" class="external-link"><code>R/whocc.R</code></a></small>
|
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<div class="hidden name"><code>WHOCC.Rd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -246,56 +161,54 @@
|
||||
<p>All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.</p>
|
||||
</div>
|
||||
|
||||
<div id="ref-usage">Usage,NULL</div>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
|
||||
|
||||
<div id="whocc">
|
||||
<h2>WHOCC</h2>
|
||||
|
||||
|
||||
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
|
||||
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm'>https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
|
||||
<p><img src="figures/logo_who.png" height="60px" style="margin-bottom:5px"><br>
|
||||
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link">https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
|
||||
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
|
||||
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href='https://www.whocc.no/copyright_disclaimer/.'>https://www.whocc.no/copyright_disclaimer/.</a></p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
|
||||
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href="https://www.whocc.no/copyright_disclaimer/." class="external-link">https://www.whocc.no/copyright_disclaimer/.</a></p>
|
||||
</div>
|
||||
<div id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<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>
|
||||
</div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'><a href='as.ab.html'>as.ab</a></span><span class='op'>(</span><span class='st'>"meropenem"</span><span class='op'>)</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span><span class='op'>(</span><span class='st'>"J01DH02"</span><span class='op'>)</span>
|
||||
<div id="ref-examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"meropenem"</span><span class="op">)</span>
|
||||
<span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01DH02"</span><span class="op">)</span>
|
||||
|
||||
<span class='fu'><a href='ab_property.html'>ab_tradenames</a></span><span class='op'>(</span><span class='st'>"flucloxacillin"</span><span class='op'>)</span>
|
||||
<span class="fu"><a href="ab_property.html">ab_tradenames</a></span><span class="op">(</span><span class="st">"flucloxacillin"</span><span class="op">)</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
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|
||||
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<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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@@ -1,88 +1,12 @@
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<!-- Generated by pkgdown: do not edit by hand -->
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<title>Data Set with 500 Isolates - WHONET Example — WHONET • AMR (for R)</title>
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<div class="page-header">
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<h1>Data Set with 500 Isolates - WHONET Example</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
|
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<div class="hidden name"><code>WHONET.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our <a href='example_isolates.html'>example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
|
||||
<p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our <a href="example_isolates.html">example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
|
||||
</div>
|
||||
|
||||
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>WHONET</span></code></pre></div>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 500 observations and 53 variables:</p><ul>
|
||||
<li><p><code>Identification number</code><br /> ID of the sample</p></li>
|
||||
<li><p><code>Specimen number</code><br /> ID of the specimen</p></li>
|
||||
<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>
|
||||
<li><p><code>Country</code><br /> Country of origin</p></li>
|
||||
<li><p><code>Laboratory</code><br /> Name of laboratory</p></li>
|
||||
<li><p><code>Last name</code><br /> Fictitious last name of patient</p></li>
|
||||
<li><p><code>First name</code><br /> Fictitious initial of patient</p></li>
|
||||
<li><p><code>Sex</code><br /> Fictitious gender of patient</p></li>
|
||||
<li><p><code>Age</code><br /> Fictitious age of patient</p></li>
|
||||
<li><p><code>Age category</code><br /> Age group, can also be looked up using <code><a href='age_groups.html'>age_groups()</a></code></p></li>
|
||||
<li><p><code>Date of admission</code><br /> <a href='https://rdrr.io/r/base/Dates.html'>Date</a> of hospital admission</p></li>
|
||||
<li><p><code>Specimen date</code><br /> <a href='https://rdrr.io/r/base/Dates.html'>Date</a> when specimen was received at laboratory</p></li>
|
||||
<li><p><code>Specimen type</code><br /> Specimen type or group</p></li>
|
||||
<li><p><code>Specimen type (Numeric)</code><br /> Translation of <code>"Specimen type"</code></p></li>
|
||||
<li><p><code>Reason</code><br /> Reason of request with Differential Diagnosis</p></li>
|
||||
<li><p><code>Isolate number</code><br /> ID of isolate</p></li>
|
||||
<li><p><code>Organism type</code><br /> Type of microorganism, can also be looked up using <code><a href='mo_property.html'>mo_type()</a></code></p></li>
|
||||
<li><p><code>Serotype</code><br /> Serotype of microorganism</p></li>
|
||||
<li><p><code>Beta-lactamase</code><br /> Microorganism produces beta-lactamase?</p></li>
|
||||
<li><p><code>ESBL</code><br /> Microorganism produces extended spectrum beta-lactamase?</p></li>
|
||||
<li><p><code>Carbapenemase</code><br /> Microorganism produces carbapenemase?</p></li>
|
||||
<li><p><code>MRSA screening test</code><br /> Microorganism is possible MRSA?</p></li>
|
||||
<li><p><code>Inducible clindamycin resistance</code><br /> Clindamycin can be induced?</p></li>
|
||||
<li><p><code>Comment</code><br /> Other comments</p></li>
|
||||
<li><p><code>Date of data entry</code><br /> <a href='https://rdrr.io/r/base/Dates.html'>Date</a> this data was entered in WHONET</p></li>
|
||||
<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>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">WHONET</span></code></pre></div></div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</h2>
|
||||
<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>
|
||||
<li><p><code>Specimen number</code><br> ID of the specimen</p></li>
|
||||
<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>
|
||||
<li><p><code>Country</code><br> Country of origin</p></li>
|
||||
<li><p><code>Laboratory</code><br> Name of laboratory</p></li>
|
||||
<li><p><code>Last name</code><br> Fictitious last name of patient</p></li>
|
||||
<li><p><code>First name</code><br> Fictitious initial of patient</p></li>
|
||||
<li><p><code>Sex</code><br> Fictitious gender of patient</p></li>
|
||||
<li><p><code>Age</code><br> Fictitious age of patient</p></li>
|
||||
<li><p><code>Age category</code><br> Age group, can also be looked up using <code><a href="age_groups.html">age_groups()</a></code></p></li>
|
||||
<li><p><code>Date of admission</code><br><a href="https://rdrr.io/r/base/Dates.html" class="external-link">Date</a> of hospital admission</p></li>
|
||||
<li><p><code>Specimen date</code><br><a href="https://rdrr.io/r/base/Dates.html" class="external-link">Date</a> when specimen was received at laboratory</p></li>
|
||||
<li><p><code>Specimen type</code><br> Specimen type or group</p></li>
|
||||
<li><p><code>Specimen type (Numeric)</code><br> Translation of <code>"Specimen type"</code></p></li>
|
||||
<li><p><code>Reason</code><br> Reason of request with Differential Diagnosis</p></li>
|
||||
<li><p><code>Isolate number</code><br> ID of isolate</p></li>
|
||||
<li><p><code>Organism type</code><br> Type of microorganism, can also be looked up using <code><a href="mo_property.html">mo_type()</a></code></p></li>
|
||||
<li><p><code>Serotype</code><br> Serotype of microorganism</p></li>
|
||||
<li><p><code>Beta-lactamase</code><br> Microorganism produces beta-lactamase?</p></li>
|
||||
<li><p><code>ESBL</code><br> Microorganism produces extended spectrum beta-lactamase?</p></li>
|
||||
<li><p><code>Carbapenemase</code><br> Microorganism produces carbapenemase?</p></li>
|
||||
<li><p><code>MRSA screening test</code><br> Microorganism is possible MRSA?</p></li>
|
||||
<li><p><code>Inducible clindamycin resistance</code><br> Clindamycin can be induced?</p></li>
|
||||
<li><p><code>Comment</code><br> Other comments</p></li>
|
||||
<li><p><code>Date of data entry</code><br><a href="https://rdrr.io/r/base/Dates.html" class="external-link">Date</a> this data was entered in WHONET</p></li>
|
||||
<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>
|
||||
</ul></div>
|
||||
<div id="reference-data-publicly-available">
|
||||
<h2>Reference Data Publicly Available</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 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</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 id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<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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@@ -273,7 +273,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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@@ -343,7 +343,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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@@ -224,7 +224,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
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|
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@@ -248,7 +248,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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@@ -410,7 +410,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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<meta property="og:description" content="Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes." />
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||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
||||
|
||||
|
||||
</header>
|
||||
|
||||
<div class="row">
|
||||
</header><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Data Sets with 558 Antimicrobial Drugs</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
|
||||
<div class="hidden name"><code>antibiotics.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><a href='as.ab.html'>as.ab()</a></code> or one of the <code><a href='ab_property.html'>ab_*</a></code> functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.</p>
|
||||
<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><a href="as.ab.html">as.ab()</a></code> or one of the <code><a href="ab_property.html">ab_*</a></code> functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='va'>antibiotics</span>
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">antibiotics</span>
|
||||
|
||||
<span class='va'>antivirals</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
<span class="va">antivirals</span></code></pre></div></div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</h2>
|
||||
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
|
||||
<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 456 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>
|
||||
|
||||
<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>
|
||||
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
|
||||
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
|
||||
<li><p><code>atc</code><br /> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
|
||||
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
|
||||
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
|
||||
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
|
||||
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
|
||||
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs</p></li>
|
||||
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
|
||||
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs</p></li>
|
||||
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
|
||||
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
|
||||
</ul>
|
||||
<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>
|
||||
<li><p><code>name</code><br> Official name as used by WHONET/EARS-Net or the WHO</p></li>
|
||||
<li><p><code>group</code><br> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
|
||||
<li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
|
||||
<li><p><code>atc_group1</code><br> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
|
||||
<li><p><code>atc_group2</code><br> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
|
||||
<li><p><code>abbr</code><br> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
|
||||
<li><p><code>synonyms</code><br> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
|
||||
<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs</p></li>
|
||||
<li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
|
||||
<li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs</p></li>
|
||||
<li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
|
||||
<li><p><code>loinc</code><br> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href="ab_property.html">ab_loinc()</a></code> to retrieve them quickly, see <code><a href="ab_property.html">ab_property()</a></code>.</p></li>
|
||||
</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 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</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>
|
||||
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
|
||||
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
|
||||
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
|
||||
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
|
||||
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
|
||||
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
|
||||
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
|
||||
</ul>
|
||||
|
||||
<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>
|
||||
<li><p><code>name</code><br> Official name as used by WHONET/EARS-Net or the WHO</p></li>
|
||||
<li><p><code>atc_group</code><br> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
|
||||
<li><p><code>synonyms</code><br> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
|
||||
<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment</p></li>
|
||||
<li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
|
||||
<li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral treatment</p></li>
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
|
||||
<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
|
||||
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm'>https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
</div>
|
||||
<div id="source">
|
||||
<h2>Source</h2>
|
||||
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href="https://www.whocc.no/atc_ddd_index/" class="external-link">https://www.whocc.no/atc_ddd_index/</a></p>
|
||||
<p>WHONET 2019 software: <a href="http://www.whonet.org/software.html" class="external-link">http://www.whonet.org/software.html</a></p>
|
||||
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
|
||||
</div>
|
||||
<div id="details">
|
||||
<h2>Details</h2>
|
||||
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
|
||||
<p>Synonyms (i.e. trade names) were derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</h3>
|
||||
<p>Synonyms (i.e. trade names) were derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><div class="section">
|
||||
<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'>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'>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'>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'>https://github.com/msberends/AMR/raw/main/data/antivirals.rda</a></p></li>
|
||||
</ul>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
||||
<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>
|
||||
|
||||
</div>
|
||||
<div id="reference-data-publicly-available">
|
||||
<h2>Reference Data Publicly Available</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 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</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 id="whocc">
|
||||
<h2>WHOCC</h2>
|
||||
|
||||
|
||||
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
|
||||
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm'>https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
|
||||
<p><img src="figures/logo_who.png" height="60px" style="margin-bottom:5px"><br>
|
||||
This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link">https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
|
||||
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
|
||||
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href='https://www.whocc.no/copyright_disclaimer/.'>https://www.whocc.no/copyright_disclaimer/.</a></p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
|
||||
|
||||
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href="https://www.whocc.no/copyright_disclaimer/." class="external-link">https://www.whocc.no/copyright_disclaimer/.</a></p>
|
||||
</div>
|
||||
<div id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a>, <a href='intrinsic_resistant.html'>intrinsic_resistant</a></p></div>
|
||||
<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>
|
||||
</div>
|
||||
<div id="see-also">
|
||||
<h2>See also</h2>
|
||||
<div class="dont-index"><p><a href="microorganisms.html">microorganisms</a>, <a href="intrinsic_resistant.html">intrinsic_resistant</a></p></div>
|
||||
</div>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
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<nav id="toc" data-toggle="toc" class="sticky-top">
|
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<h2 data-toc-skip>Contents</h2>
|
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|
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|
||||
<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
|
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|
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|
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|
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|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
|
||||
<footer><div class="copyright">
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||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
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|
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@@ -279,7 +279,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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@@ -237,7 +237,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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||||
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||||
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||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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@@ -271,7 +271,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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<footer><div class="copyright">
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<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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@@ -374,7 +374,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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||||
|
||||
|
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<footer><div class="copyright">
|
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<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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@@ -421,7 +421,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
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|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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@@ -255,7 +255,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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||||
@@ -214,7 +214,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
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||||
@@ -263,7 +263,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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||||
<div class="pkgdown">
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@@ -1,80 +1,12 @@
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|
||||
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||||
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<title>The Catalogue of Life — catalogue_of_life • AMR (for R)</title>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<script src="../extra.js"></script>
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<meta property="og:title" content="The Catalogue of Life — catalogue_of_life" />
|
||||
<meta property="og:description" content="This package contains the complete taxonomic tree (last updated: 5 October 2021) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN)." />
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<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<!-- 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=1.0"><title>The Catalogue of Life — catalogue_of_life • 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"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- 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"><!-- 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><!-- 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><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="The Catalogue of Life — catalogue_of_life"><meta property="og:description" content="This package contains the complete taxonomic tree (last updated: 5 October 2021) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN)."><meta property="og:image" content="https://msberends.github.io/AMR/logo.png"><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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|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
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@@ -184,8 +114,7 @@
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@@ -207,30 +136,24 @@
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||||
</div><!--/.nav-collapse -->
|
||||
</ul></div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
||||
|
||||
|
||||
</header>
|
||||
|
||||
<div class="row">
|
||||
</header><div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>The Catalogue of Life</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/catalogue_of_life.R" class="external-link"><code>R/catalogue_of_life.R</code></a></small>
|
||||
<div class="hidden name"><code>catalogue_of_life.Rd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -238,95 +161,94 @@
|
||||
<p>This package contains the complete taxonomic tree (last updated: 5 October 2021) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN).</p>
|
||||
</div>
|
||||
|
||||
<div id="ref-usage">Usage,NULL</div>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
|
||||
|
||||
<div id="catalogue-of-life">
|
||||
<h2>Catalogue of Life</h2>
|
||||
|
||||
|
||||
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <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'>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'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
|
||||
<p>Click here 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>
|
||||
<h2 class="hasAnchor" id="included-taxa"><a class="anchor" href="#included-taxa"></a>Included Taxa</h2>
|
||||
|
||||
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><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>Click here 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 id="included-taxa">
|
||||
<h2>Included Taxa</h2>
|
||||
|
||||
|
||||
<p>Included are:</p><ul>
|
||||
<li><p>All ~58,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa</p></li>
|
||||
<p>Included are:</p><ul><li><p>All ~58,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa</p></li>
|
||||
<li><p>All ~5,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Microascales, Mucorales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales, as well as ~4,600 other fungal (sub)species. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
|
||||
<li><p>All ~2,200 (sub)species from ~50 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
|
||||
<li><p>All ~14,000 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
|
||||
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
|
||||
<li><p>The responsible author(s) and year of scientific publication</p></li>
|
||||
</ul>
|
||||
|
||||
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
|
||||
<p>The syntax used to transform the original data to a cleansed <span style="R">R</span> format, can be found here: <a href='https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R'>https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R</a>.</p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
|
||||
|
||||
</ul><p>The Catalogue of Life (<a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
|
||||
<p>The syntax used to transform the original data to a cleansed <span style="R">R</span> format, can be found here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R</a>.</p>
|
||||
</div>
|
||||
<div id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
<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>
|
||||
</div>
|
||||
<div id="see-also">
|
||||
<h2>See also</h2>
|
||||
<div class="dont-index"><p>Data set <a href="microorganisms.html">microorganisms</a> for the actual data. <br>
|
||||
Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intelligent determination of microorganisms.</p></div>
|
||||
</div>
|
||||
|
||||
<div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a> for the actual data. <br />
|
||||
Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intelligent determination of microorganisms.</p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># Get version info of included data set</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>
|
||||
<div id="ref-examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># Get version info of included data set</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 class='co'># Get a note when a species was renamed</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_shortname</a></span><span class='op'>(</span><span class='st'>"Chlamydophila psittaci"</span><span class='op'>)</span>
|
||||
<span class='co'># Note: 'Chlamydophila psittaci' (Everett et al., 1999) was renamed back to</span>
|
||||
<span class='co'># 'Chlamydia psittaci' (Page, 1968)</span>
|
||||
<span class='co'>#> [1] "C. psittaci"</span>
|
||||
<span class="co"># Get a note when a species was renamed</span>
|
||||
<span class="fu"><a href="mo_property.html">mo_shortname</a></span><span class="op">(</span><span class="st">"Chlamydophila psittaci"</span><span class="op">)</span>
|
||||
<span class="co"># Note: 'Chlamydophila psittaci' (Everett et al., 1999) was renamed back to</span>
|
||||
<span class="co"># 'Chlamydia psittaci' (Page, 1968)</span>
|
||||
<span class="co">#> [1] "C. psittaci"</span>
|
||||
|
||||
<span class='co'># Get any property from the entire taxonomic tree for all included species</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 class='co'>#> [1] "Gammaproteobacteria"</span>
|
||||
<span class="co"># Get any property from the entire taxonomic tree for all included species</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 class="co">#> [1] "Gammaproteobacteria"</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 class='co'>#> [1] "Enterobacteriaceae"</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 class="co">#> [1] "Enterobacteriaceae"</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 class='co'>#> [1] "Gram-negative"</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 class="co">#> [1] "Gram-negative"</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 class='co'>#> [1] "Castellani et al., 1919"</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 class="co">#> [1] "Castellani et al., 1919"</span>
|
||||
|
||||
<span class='co'># Do not get mistaken - this package is about microorganisms</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_kingdom</a></span><span class='op'>(</span><span class='st'>"C. elegans"</span><span class='op'>)</span>
|
||||
<span class='co'>#> [1] "Fungi" # Fungi?!</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"C. elegans"</span><span class='op'>)</span>
|
||||
<span class='co'>#> [1] "Cladosporium elegans" # Because a microorganism was found</span>
|
||||
</pre>
|
||||
<span class="co"># Do not get mistaken - this package is about microorganisms</span>
|
||||
<span class="fu"><a href="mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"C. elegans"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Fungi" # Fungi?!</span>
|
||||
<span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"C. elegans"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Cladosporium elegans" # Because a microorganism was found</span>
|
||||
</code></pre></div>
|
||||
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|
||||
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|
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<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
|
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
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<h1>Version info of included Catalogue of Life</h1>
|
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/catalogue_of_life.R" class="external-link"><code>R/catalogue_of_life.R</code></a></small>
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<div class="hidden name"><code>catalogue_of_life_version.Rd</code></div>
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@@ -238,56 +161,56 @@
|
||||
<p>This function returns information about the included data from the Catalogue of Life.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>catalogue_of_life_version</span><span class='op'>(</span><span class='op'>)</span></pre>
|
||||
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||||
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||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>a <a href='https://rdrr.io/r/base/list.html'>list</a>, which prints in pretty format</p>
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>For LPSN, see <a href='microorganisms.html'>microorganisms</a>.</p>
|
||||
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">catalogue_of_life_version</span><span class="op">(</span><span class="op">)</span></code></pre></div></div>
|
||||
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<div id="value">
|
||||
<h2>Value</h2>
|
||||
<p>a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>, which prints in pretty format</p>
|
||||
</div>
|
||||
<div id="details">
|
||||
<h2>Details</h2>
|
||||
<p>For LPSN, see <a href="microorganisms.html">microorganisms</a>.</p>
|
||||
</div>
|
||||
<div id="catalogue-of-life">
|
||||
<h2>Catalogue of Life</h2>
|
||||
|
||||
|
||||
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <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'>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'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>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>catalogue_of_life_version()</code>.</p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
|
||||
|
||||
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><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>catalogue_of_life_version()</code>.</p>
|
||||
</div>
|
||||
<div id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
|
||||
<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>
|
||||
</div>
|
||||
<div id="see-also">
|
||||
<h2>See also</h2>
|
||||
<div class="dont-index"><p><a href="microorganisms.html">microorganisms</a></p></div>
|
||||
</div>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
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@@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
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@@ -356,7 +356,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
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@@ -299,7 +299,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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<h1>Data Set with Treatment Dosages as Defined by EUCAST</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="hidden name"><code>dosage.Rd</code></div>
|
||||
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|
||||
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||||
<div class="ref-description">
|
||||
<p>EUCAST breakpoints used in this package are based on the dosages in this data set. They can be retrieved with <code><a href='eucast_rules.html'>eucast_dosage()</a></code>.</p>
|
||||
<p>EUCAST breakpoints used in this package are based on the dosages in this data set. They can be retrieved with <code><a href="eucast_rules.html">eucast_dosage()</a></code>.</p>
|
||||
</div>
|
||||
|
||||
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>dosage</span></code></pre></div>
|
||||
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||||
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||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>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>
|
||||
<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>
|
||||
<li><p><code>dose_times</code><br /> Number of times a dose must be administered</p></li>
|
||||
<li><p><code>administration</code><br /> Route of administration, either "im", "iv" or "oral"</p></li>
|
||||
<li><p><code>notes</code><br /> Additional dosage notes</p></li>
|
||||
<li><p><code>original_txt</code><br /> Original text in the PDF file of EUCAST</p></li>
|
||||
<li><p><code>eucast_version</code><br /> Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply</p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p><a href='https://www.eucast.org/clinical_breakpoints/'>'EUCAST Clinical Breakpoint Tables' v11.0</a> (2021) are based on the dosages in this data set.</p>
|
||||
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">dosage</span></code></pre></div></div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</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>
|
||||
<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>
|
||||
<li><p><code>dose_times</code><br> Number of times a dose must be administered</p></li>
|
||||
<li><p><code>administration</code><br> Route of administration, either "im", "iv" or "oral"</p></li>
|
||||
<li><p><code>notes</code><br> Additional dosage notes</p></li>
|
||||
<li><p><code>original_txt</code><br> Original text in the PDF file of EUCAST</p></li>
|
||||
<li><p><code>eucast_version</code><br> Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply</p></li>
|
||||
</ul></div>
|
||||
<div id="details">
|
||||
<h2>Details</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 id="reference-data-publicly-available">
|
||||
<h2>Reference Data Publicly Available</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 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</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>Read more on Our Website!</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>
|
||||
<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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<div class="page-header">
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<h1>Data Set with 2,000 Example Isolates</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
|
||||
<div class="hidden name"><code>example_isolates.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<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. 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>
|
||||
</div>
|
||||
|
||||
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>example_isolates</span></code></pre></div>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>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'>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'>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'>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>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">example_isolates</span></code></pre></div></div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</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>
|
||||
</ul></div>
|
||||
<div id="reference-data-publicly-available">
|
||||
<h2>Reference Data Publicly Available</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 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</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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|
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<div id="read-more-on-our-website-">
|
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<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<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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<div class="col-md-9 contents">
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<div class="page-header">
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<h1>Data Set with Unclean Data</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
|
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
|
||||
<div class="hidden name"><code>example_isolates_unclean.Rd</code></div>
|
||||
</div>
|
||||
|
||||
@@ -246,57 +161,50 @@
|
||||
<p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.</p>
|
||||
</div>
|
||||
|
||||
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>example_isolates_unclean</span></code></pre></div>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>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>
|
||||
<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>
|
||||
|
||||
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">example_isolates_unclean</span></code></pre></div></div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</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>
|
||||
<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 id="reference-data-publicly-available">
|
||||
<h2>Reference Data Publicly Available</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 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</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 id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</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>
|
||||
<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></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<div class="page-header">
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<h1><em>G</em>-test for Count Data</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/g.test.R'><code>R/g.test.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/g.test.R" class="external-link"><code>R/g.test.R</code></a></small>
|
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<div class="hidden name"><code>g.test.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p><code>g.test()</code> performs chi-squared contingency table tests and goodness-of-fit tests, just like <code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code> but is more reliable (1). A <em>G</em>-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a <strong><em>G</em>-test of goodness-of-fit</strong>), or to see whether the proportions of one variable are different for different values of the other variable (called a <strong><em>G</em>-test of independence</strong>).</p>
|
||||
<p><code>g.test()</code> performs chi-squared contingency table tests and goodness-of-fit tests, just like <code><a href="https://rdrr.io/r/stats/chisq.test.html" class="external-link">chisq.test()</a></code> but is more reliable (1). A <em>G</em>-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a <strong><em>G</em>-test of goodness-of-fit</strong>), or to see whether the proportions of one variable are different for different values of the other variable (called a <strong><em>G</em>-test of independence</strong>).</p>
|
||||
</div>
|
||||
|
||||
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>g.test</span><span class='op'>(</span><span class='va'>x</span>, y <span class='op'>=</span> <span class='cn'>NULL</span>, p <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>/</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>, rescale.p <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></code></pre></div>
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">g.test</span><span class="op">(</span><span class="va">x</span>, y <span class="op">=</span> <span class="cn">NULL</span>, p <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="fl">1</span><span class="op">/</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, rescale.p <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div></div>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>a numeric vector or matrix. <code>x</code> and <code>y</code> can also
|
||||
both be factors.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>y</th>
|
||||
<td><p>a numeric vector; ignored if <code>x</code> is a matrix. If
|
||||
<code>x</code> is a factor, <code>y</code> should be a factor of the same length.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>p</th>
|
||||
<td><p>a vector of probabilities of the same length of <code>x</code>.
|
||||
An error is given if any entry of <code>p</code> is negative.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>rescale.p</th>
|
||||
<td><p>a logical scalar; if TRUE then <code>p</code> is rescaled
|
||||
(if necessary) to sum to 1. If <code>rescale.p</code> is FALSE, and
|
||||
<code>p</code> does not sum to 1, an error is given.</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
<p>The code for this function is identical to that of <code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>, except that:</p><ul>
|
||||
<li><p>The calculation of the statistic was changed to \(2 * sum(x * log(x / E))\)</p></li>
|
||||
<div id="source">
|
||||
<h2>Source</h2>
|
||||
<p>The code for this function is identical to that of <code><a href="https://rdrr.io/r/stats/chisq.test.html" class="external-link">chisq.test()</a></code>, except that:</p><ul><li><p>The calculation of the statistic was changed to \(2 * sum(x * log(x / E))\)</p></li>
|
||||
<li><p>Yates' continuity correction was removed as it does not apply to a <em>G</em>-test</p></li>
|
||||
<li><p>The possibility to simulate p values with <code>simulate.p.value</code> was removed</p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
</ul></div>
|
||||
<div id="arguments">
|
||||
<h2>Arguments</h2>
|
||||
<dl><dt>x</dt>
|
||||
<dd><p>a numeric vector or matrix. <code>x</code> and <code>y</code> can also
|
||||
both be factors.</p></dd>
|
||||
<dt>y</dt>
|
||||
<dd><p>a numeric vector; ignored if <code>x</code> is a matrix. If
|
||||
<code>x</code> is a factor, <code>y</code> should be a factor of the same length.</p></dd>
|
||||
<dt>p</dt>
|
||||
<dd><p>a vector of probabilities of the same length of <code>x</code>.
|
||||
An error is given if any entry of <code>p</code> is negative.</p></dd>
|
||||
<dt>rescale.p</dt>
|
||||
<dd><p>a logical scalar; if TRUE then <code>p</code> is rescaled
|
||||
(if necessary) to sum to 1. If <code>rescale.p</code> is FALSE, and
|
||||
<code>p</code> does not sum to 1, an error is given.</p></dd>
|
||||
</dl></div>
|
||||
<div id="value">
|
||||
<h2>Value</h2>
|
||||
<p>A list with class <code>"htest"</code> containing the following
|
||||
components:</p>
|
||||
<dt>statistic</dt><dd><p>the value the chi-squared test statistic.</p></dd>
|
||||
<dt>parameter</dt><dd><p>the degrees of freedom of the approximate
|
||||
<dl><dt>statistic</dt>
|
||||
<dd><p>the value the chi-squared test statistic.</p></dd>
|
||||
<dt>parameter</dt>
|
||||
<dd><p>the degrees of freedom of the approximate
|
||||
chi-squared distribution of the test statistic, <code>NA</code> if the
|
||||
p-value is computed by Monte Carlo simulation.</p></dd>
|
||||
<dt>p.value</dt><dd><p>the p-value for the test.</p></dd>
|
||||
<dt>method</dt><dd><p>a character string indicating the type of test
|
||||
<dt>p.value</dt>
|
||||
<dd><p>the p-value for the test.</p></dd>
|
||||
<dt>method</dt>
|
||||
<dd><p>a character string indicating the type of test
|
||||
performed, and whether Monte Carlo simulation or continuity
|
||||
correction was used.</p></dd>
|
||||
<dt>data.name</dt><dd><p>a character string giving the name(s) of the data.</p></dd>
|
||||
<dt>observed</dt><dd><p>the observed counts.</p></dd>
|
||||
<dt>expected</dt><dd><p>the expected counts under the null hypothesis.</p></dd>
|
||||
<dt>residuals</dt><dd><p>the Pearson residuals,
|
||||
<dt>data.name</dt>
|
||||
<dd><p>a character string giving the name(s) of the data.</p></dd>
|
||||
<dt>observed</dt>
|
||||
<dd><p>the observed counts.</p></dd>
|
||||
<dt>expected</dt>
|
||||
<dd><p>the expected counts under the null hypothesis.</p></dd>
|
||||
<dt>residuals</dt>
|
||||
<dd><p>the Pearson residuals,
|
||||
<code>(observed - expected) / sqrt(expected)</code>.</p></dd>
|
||||
<dt>stdres</dt><dd><p>standardized residuals,
|
||||
<dt>stdres</dt>
|
||||
<dd><p>standardized residuals,
|
||||
<code>(observed - expected) / sqrt(V)</code>, where <code>V</code> is the residual cell variance (Agresti, 2007,
|
||||
section 2.4.5 for the case where <code>x</code> is a matrix, <code>n * p * (1 - p)</code> otherwise).</p></dd>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>If <code>x</code> is a <a href='https://rdrr.io/r/base/matrix.html'>matrix</a> with one row or column, or if <code>x</code> is a vector and <code>y</code> is not given, then a <em>goodness-of-fit test</em> is performed (<code>x</code> is treated as a one-dimensional contingency table). The entries of <code>x</code> must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in <code>p</code>, or are all equal if <code>p</code> is not given.</p>
|
||||
<p>If <code>x</code> is a <a href='https://rdrr.io/r/base/matrix.html'>matrix</a> with at least two rows and columns, it is taken as a two-dimensional contingency table: the entries of <code>x</code> must be non-negative integers. Otherwise, <code>x</code> and <code>y</code> must be vectors or factors of the same length; cases with missing values are removed, the objects are coerced to factors, and the contingency table is computed from these. Then Pearson's chi-squared test is performed of the null hypothesis that the joint distribution of the cell counts in a 2-dimensional contingency table is the product of the row and column marginals.</p>
|
||||
</dl></div>
|
||||
<div id="details">
|
||||
<h2>Details</h2>
|
||||
<p>If <code>x</code> is a <a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a> with one row or column, or if <code>x</code> is a vector and <code>y</code> is not given, then a <em>goodness-of-fit test</em> is performed (<code>x</code> is treated as a one-dimensional contingency table). The entries of <code>x</code> must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in <code>p</code>, or are all equal if <code>p</code> is not given.</p>
|
||||
<p>If <code>x</code> is a <a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a> with at least two rows and columns, it is taken as a two-dimensional contingency table: the entries of <code>x</code> must be non-negative integers. Otherwise, <code>x</code> and <code>y</code> must be vectors or factors of the same length; cases with missing values are removed, the objects are coerced to factors, and the contingency table is computed from these. Then Pearson's chi-squared test is performed of the null hypothesis that the joint distribution of the cell counts in a 2-dimensional contingency table is the product of the row and column marginals.</p>
|
||||
<p>The p-value is computed from the asymptotic chi-squared distribution of the test statistic.</p>
|
||||
<p>In the contingency table case simulation is done by random sampling from the set of all contingency tables with given marginals, and works only if the marginals are strictly positive. Note that this is not the usual sampling situation assumed for a chi-squared test (such as the <em>G</em>-test) but rather that for Fisher's exact test.</p>
|
||||
<p>In the goodness-of-fit case simulation is done by random sampling from the discrete distribution specified by <code>p</code>, each sample being of size <code>n = sum(x)</code>. This simulation is done in <span style="R">R</span> and may be slow.</p><h3 class='hasAnchor' id='list-g-'><a class='anchor' aria-hidden='true' href='#list-g-'></a><em>G</em>-test Of Goodness-of-Fit (Likelihood Ratio Test)</h3>
|
||||
<p>In the goodness-of-fit case simulation is done by random sampling from the discrete distribution specified by <code>p</code>, each sample being of size <code>n = sum(x)</code>. This simulation is done in <span style="R">R</span> and may be slow.</p><div class="section">
|
||||
<h3 id="g-test-of-goodness-of-fit-likelihood-ratio-test-"><em>G</em>-test Of Goodness-of-Fit (Likelihood Ratio Test)<a class="anchor" aria-label="anchor" href="#g-test-of-goodness-of-fit-likelihood-ratio-test-"></a></h3>
|
||||
|
||||
|
||||
<p>Use the <em>G</em>-test of goodness-of-fit when you have one nominal variable with two or more values (such as male and female, or red, pink and white flowers). You compare the observed counts of numbers of observations in each category with the expected counts, which you calculate using some kind of theoretical expectation (such as a 1:1 sex ratio or a 1:2:1 ratio in a genetic cross).</p>
|
||||
<p>If the expected number of observations in any category is too small, the <em>G</em>-test may give inaccurate results, and you should use an exact test instead (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>).</p>
|
||||
<p>The <em>G</em>-test of goodness-of-fit is an alternative to the chi-square test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>); each of these tests has some advantages and some disadvantages, and the results of the two tests are usually very similar.</p><h3 class='hasAnchor' id='-test-of-goodness-of-fit-likelihood-ratio-test-'><a class='anchor' aria-hidden='true' href='#-test-of-goodness-of-fit-likelihood-ratio-test-'></a><em>G</em>-test Of Goodness-of-Fit (Likelihood Ratio Test)</h3>
|
||||
<p>If the expected number of observations in any category is too small, the <em>G</em>-test may give inaccurate results, and you should use an exact test instead (<code><a href="https://rdrr.io/r/stats/fisher.test.html" class="external-link">fisher.test()</a></code>).</p>
|
||||
<p>The <em>G</em>-test of goodness-of-fit is an alternative to the chi-square test of goodness-of-fit (<code><a href="https://rdrr.io/r/stats/chisq.test.html" class="external-link">chisq.test()</a></code>); each of these tests has some advantages and some disadvantages, and the results of the two tests are usually very similar.</p>
|
||||
</div>
|
||||
|
||||
|
||||
<p>Use the <em>G</em>-test of goodness-of-fit when you have one nominal variable with two or more values (such as male and female, or red, pink and white flowers). You compare the observed counts of numbers of observations in each category with the expected counts, which you calculate using some kind of theoretical expectation (such as a 1:1 sex ratio or a 1:2:1 ratio in a genetic cross).</p>
|
||||
<p>If the expected number of observations in any category is too small, the <em>G</em>-test may give inaccurate results, and you should use an exact test instead (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>).</p>
|
||||
<p>The <em>G</em>-test of goodness-of-fit is an alternative to the chi-square test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>); each of these tests has some advantages and some disadvantages, and the results of the two tests are usually very similar.</p>
|
||||
|
||||
<h3 class='hasAnchor' id='list-g-'><a class='anchor' aria-hidden='true' href='#list-g-'></a><em>G</em>-test of Independence</h3>
|
||||
<div class="section">
|
||||
<h3 id="g-test-of-independence"><em>G</em>-test of Independence<a class="anchor" aria-label="anchor" href="#g-test-of-independence"></a></h3>
|
||||
|
||||
|
||||
<p>Use the <em>G</em>-test of independence when you have two nominal variables, each with two or more possible values. You want to know whether the proportions for one variable are different among values of the other variable.</p>
|
||||
<p>It is also possible to do a <em>G</em>-test of independence with more than two nominal variables. For example, Jackson et al. (2013) also had data for children under 3, so you could do an analysis of old vs. young, thigh vs. arm, and reaction vs. no reaction, all analyzed together.</p>
|
||||
<p>Fisher's exact test (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>) is an <strong>exact</strong> test, where the <em>G</em>-test is still only an <strong>approximation</strong>. For any 2x2 table, Fisher's Exact test may be slower but will still run in seconds, even if the sum of your observations is multiple millions.</p>
|
||||
<p>The <em>G</em>-test of independence is an alternative to the chi-square test of independence (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>), and they will give approximately the same results.</p><h3 class='hasAnchor' id='-test-of-independence'><a class='anchor' aria-hidden='true' href='#-test-of-independence'></a><em>G</em>-test of Independence</h3>
|
||||
<p>Fisher's exact test (<code><a href="https://rdrr.io/r/stats/fisher.test.html" class="external-link">fisher.test()</a></code>) is an <strong>exact</strong> test, where the <em>G</em>-test is still only an <strong>approximation</strong>. For any 2x2 table, Fisher's Exact test may be slower but will still run in seconds, even if the sum of your observations is multiple millions.</p>
|
||||
<p>The <em>G</em>-test of independence is an alternative to the chi-square test of independence (<code><a href="https://rdrr.io/r/stats/chisq.test.html" class="external-link">chisq.test()</a></code>), and they will give approximately the same results.</p>
|
||||
</div>
|
||||
|
||||
<div class="section">
|
||||
<h3 id="how-the-test-works">How the Test Works<a class="anchor" aria-label="anchor" href="#how-the-test-works"></a></h3>
|
||||
|
||||
|
||||
<p>Use the <em>G</em>-test of independence when you have two nominal variables, each with two or more possible values. You want to know whether the proportions for one variable are different among values of the other variable.</p>
|
||||
<p>It is also possible to do a <em>G</em>-test of independence with more than two nominal variables. For example, Jackson et al. (2013) also had data for children under 3, so you could do an analysis of old vs. young, thigh vs. arm, and reaction vs. no reaction, all analyzed together.</p>
|
||||
<p>Fisher's exact test (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>) is an <strong>exact</strong> test, where the <em>G</em>-test is still only an <strong>approximation</strong>. For any 2x2 table, Fisher's Exact test may be slower but will still run in seconds, even if the sum of your observations is multiple millions.</p>
|
||||
<p>The <em>G</em>-test of independence is an alternative to the chi-square test of independence (<code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code>), and they will give approximately the same results.</p>
|
||||
|
||||
<h3 class='hasAnchor' id='how-the-test-works'><a class='anchor' aria-hidden='true' href='#how-the-test-works'></a>How the Test Works</h3>
|
||||
|
||||
|
||||
<p>Unlike the exact test of goodness-of-fit (<code><a href='https://rdrr.io/r/stats/fisher.test.html'>fisher.test()</a></code>), the <em>G</em>-test does not directly calculate the probability of obtaining the observed results or something more extreme. Instead, like almost all statistical tests, the <em>G</em>-test has an intermediate step; it uses the data to calculate a test statistic that measures how far the observed data are from the null expectation. You then use a mathematical relationship, in this case the chi-square distribution, to estimate the probability of obtaining that value of the test statistic.</p>
|
||||
<p>Unlike the exact test of goodness-of-fit (<code><a href="https://rdrr.io/r/stats/fisher.test.html" class="external-link">fisher.test()</a></code>), the <em>G</em>-test does not directly calculate the probability of obtaining the observed results or something more extreme. Instead, like almost all statistical tests, the <em>G</em>-test has an intermediate step; it uses the data to calculate a test statistic that measures how far the observed data are from the null expectation. You then use a mathematical relationship, in this case the chi-square distribution, to estimate the probability of obtaining that value of the test statistic.</p>
|
||||
<p>The <em>G</em>-test uses the log of the ratio of two likelihoods as the test statistic, which is why it is also called a likelihood ratio test or log-likelihood ratio test. The formula to calculate a <em>G</em>-statistic is:</p>
|
||||
<p>\(G = 2 * sum(x * log(x / E))\)</p>
|
||||
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><pre class='sourceCode r'><code><span class='va'>p</span> <span class='op'><-</span> <span class='fu'>stats</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/stats/Chisquare.html'>pchisq</a></span><span class='op'>(</span><span class='va'>G</span>, <span class='va'>df</span>, lower.tail <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
||||
</code></pre>
|
||||
<p>where <code>E</code> are the expected values. Since this is chi-square distributed, the p value can be calculated in <span style="R">R</span> with:</p><div class="sourceCode"><pre><code><span class="va">p</span> <span class="op"><-</span> <span class="fu">stats</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/stats/Chisquare.html" class="external-link">pchisq</a></span><span class="op">(</span><span class="va">G</span>, <span class="va">df</span>, lower.tail <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
|
||||
|
||||
<p>where <code>df</code> are the degrees of freedom.</p>
|
||||
<p>If there are more than two categories and you want to find out which ones are significantly different from their null expectation, you can use the same method of testing each category vs. the sum of all categories, with the Bonferroni correction. You use <em>G</em>-tests for each category, of course.</p>
|
||||
</div>
|
||||
|
||||
<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning Lifecycle</h2>
|
||||
|
||||
</div>
|
||||
<div id="questioning-lifecycle">
|
||||
<h2>Questioning Lifecycle</h2>
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
|
||||
|
||||
<p><img src="figures/lifecycle_questioning.svg" style="margin-bottom:5px"><br>
|
||||
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
|
||||
</div>
|
||||
<div id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
|
||||
|
||||
<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>
|
||||
</div>
|
||||
<div id="references">
|
||||
<h2>References</h2>
|
||||
|
||||
<ol>
|
||||
<li><p>McDonald, J.H. 2014. <strong>Handbook of Biological Statistics (3rd ed.)</strong>. Sparky House Publishing, Baltimore, Maryland. <a href='http://www.biostathandbook.com/gtestgof.html'>http://www.biostathandbook.com/gtestgof.html</a>.</p></li>
|
||||
</ol>
|
||||
<ol><li><p>McDonald, J.H. 2014. <strong>Handbook of Biological Statistics (3rd ed.)</strong>. Sparky House Publishing, Baltimore, Maryland. <a href="http://www.biostathandbook.com/gtestgof.html" class="external-link">http://www.biostathandbook.com/gtestgof.html</a>.</p></li>
|
||||
</ol></div>
|
||||
<div id="see-also">
|
||||
<h2>See also</h2>
|
||||
<div class="dont-index"><p><code><a href="https://rdrr.io/r/stats/chisq.test.html" class="external-link">chisq.test()</a></code></p></div>
|
||||
</div>
|
||||
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
<div id="ref-examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># = EXAMPLE 1 =</span>
|
||||
<span class="co"># Shivrain et al. (2006) crossed clearfield rice (which are resistant</span>
|
||||
<span class="co"># to the herbicide imazethapyr) with red rice (which are susceptible to</span>
|
||||
<span class="co"># imazethapyr). They then crossed the hybrid offspring and examined the</span>
|
||||
<span class="co"># F2 generation, where they found 772 resistant plants, 1611 moderately</span>
|
||||
<span class="co"># resistant plants, and 737 susceptible plants. If resistance is controlled</span>
|
||||
<span class="co"># by a single gene with two co-dominant alleles, you would expect a 1:2:1</span>
|
||||
<span class="co"># ratio.</span>
|
||||
|
||||
<div class='dont-index'><p><code><a href='https://rdrr.io/r/stats/chisq.test.html'>chisq.test()</a></code></p></div>
|
||||
<span class="va">x</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">772</span>, <span class="fl">1611</span>, <span class="fl">737</span><span class="op">)</span>
|
||||
<span class="va">G</span> <span class="op"><-</span> <span class="fu">g.test</span><span class="op">(</span><span class="va">x</span>, p <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">1</span><span class="op">)</span> <span class="op">/</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="co"># G$p.value = 0.12574.</span>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># = EXAMPLE 1 =</span>
|
||||
<span class='co'># Shivrain et al. (2006) crossed clearfield rice (which are resistant</span>
|
||||
<span class='co'># to the herbicide imazethapyr) with red rice (which are susceptible to</span>
|
||||
<span class='co'># imazethapyr). They then crossed the hybrid offspring and examined the</span>
|
||||
<span class='co'># F2 generation, where they found 772 resistant plants, 1611 moderately</span>
|
||||
<span class='co'># resistant plants, and 737 susceptible plants. If resistance is controlled</span>
|
||||
<span class='co'># by a single gene with two co-dominant alleles, you would expect a 1:2:1</span>
|
||||
<span class='co'># ratio.</span>
|
||||
|
||||
<span class='va'>x</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>772</span>, <span class='fl'>1611</span>, <span class='fl'>737</span><span class='op'>)</span>
|
||||
<span class='va'>G</span> <span class='op'><-</span> <span class='fu'>g.test</span><span class='op'>(</span><span class='va'>x</span>, p <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>1</span><span class='op'>)</span> <span class='op'>/</span> <span class='fl'>4</span><span class='op'>)</span>
|
||||
<span class='co'># G$p.value = 0.12574.</span>
|
||||
|
||||
<span class='co'># There is no significant difference from a 1:2:1 ratio.</span>
|
||||
<span class='co'># Meaning: resistance controlled by a single gene with two co-dominant</span>
|
||||
<span class='co'># alleles, is plausible.</span>
|
||||
<span class="co"># There is no significant difference from a 1:2:1 ratio.</span>
|
||||
<span class="co"># Meaning: resistance controlled by a single gene with two co-dominant</span>
|
||||
<span class="co"># alleles, is plausible.</span>
|
||||
|
||||
|
||||
<span class='co'># = EXAMPLE 2 =</span>
|
||||
<span class='co'># Red crossbills (Loxia curvirostra) have the tip of the upper bill either</span>
|
||||
<span class='co'># right or left of the lower bill, which helps them extract seeds from pine</span>
|
||||
<span class='co'># cones. Some have hypothesized that frequency-dependent selection would</span>
|
||||
<span class='co'># keep the number of right and left-billed birds at a 1:1 ratio. Groth (1992)</span>
|
||||
<span class='co'># observed 1752 right-billed and 1895 left-billed crossbills.</span>
|
||||
<span class="co"># = EXAMPLE 2 =</span>
|
||||
<span class="co"># Red crossbills (Loxia curvirostra) have the tip of the upper bill either</span>
|
||||
<span class="co"># right or left of the lower bill, which helps them extract seeds from pine</span>
|
||||
<span class="co"># cones. Some have hypothesized that frequency-dependent selection would</span>
|
||||
<span class="co"># keep the number of right and left-billed birds at a 1:1 ratio. Groth (1992)</span>
|
||||
<span class="co"># observed 1752 right-billed and 1895 left-billed crossbills.</span>
|
||||
|
||||
<span class='va'>x</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1752</span>, <span class='fl'>1895</span><span class='op'>)</span>
|
||||
<span class='fu'>g.test</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
|
||||
<span class='co'># p = 0.01787343</span>
|
||||
<span class="va">x</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">1752</span>, <span class="fl">1895</span><span class="op">)</span>
|
||||
<span class="fu">g.test</span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
<span class="co"># p = 0.01787343</span>
|
||||
|
||||
<span class='co'># There is a significant difference from a 1:1 ratio.</span>
|
||||
<span class='co'># Meaning: there are significantly more left-billed birds.</span>
|
||||
<span class="co"># There is a significant difference from a 1:1 ratio.</span>
|
||||
<span class="co"># Meaning: there are significantly more left-billed birds.</span>
|
||||
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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|
||||
<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
|
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<h1>Data Set with Bacterial Intrinsic Resistance</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
|
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<div class="hidden name"><code>intrinsic_resistant.Rd</code></div>
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|
||||
<p>Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='va'>intrinsic_resistant</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 93,892 observations and 2 variables:</p><ul>
|
||||
<li><p><code>microorganism</code><br /> Name of the microorganism</p></li>
|
||||
<li><p><code>antibiotic</code><br /> Name of the antibiotic drug</p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</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/intrinsic_resistant.txt'>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_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020).</p>
|
||||
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">intrinsic_resistant</span></code></pre></div></div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 93,892 observations and 2 variables:</p><ul><li><p><code>microorganism</code><br> Name of the microorganism</p></li>
|
||||
<li><p><code>antibiotic</code><br> Name of the antibiotic drug</p></li>
|
||||
</ul></div>
|
||||
<div id="details">
|
||||
<h2>Details</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/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_intrinsic_resistance/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020).</p>
|
||||
</div>
|
||||
<div id="reference-data-publicly-available">
|
||||
<h2>Reference Data Publicly Available</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 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</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 id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<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>
|
||||
</div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># \donttest{</span>
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='va'>intrinsic_resistant</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>antibiotic</span> <span class='op'>==</span> <span class='st'>"Vancomycin"</span>, <span class='va'>microorganism</span> <span class='op'>%like%</span> <span class='st'>"Enterococcus"</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/pull.html'>pull</a></span><span class='op'>(</span><span class='va'>microorganism</span><span class='op'>)</span>
|
||||
<span class='co'># [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"</span>
|
||||
<span class='op'>}</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
<div id="ref-examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># \donttest{</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 class="va">intrinsic_resistant</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="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="va">microorganism</span> <span class="op"><a href="like.html">%like%</a></span> <span class="st">"Enterococcus"</span><span class="op">)</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/pull.html" class="external-link">pull</a></span><span class="op">(</span><span class="va">microorganism</span><span class="op">)</span>
|
||||
<span class="co"># [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"</span>
|
||||
<span class="op">}</span>
|
||||
<span class="co"># }</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
|
||||
</nav></div>
|
||||
</div>
|
||||
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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|
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<div class="pkgdown">
|
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
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<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
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</html>
|
||||
|
||||
|
||||
</body></html>
|
||||
|
||||
|
||||
@@ -17,7 +17,7 @@
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||||
</button>
|
||||
<span class="navbar-brand">
|
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -219,7 +219,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
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|
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@@ -17,7 +17,7 @@
|
||||
</button>
|
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<span class="navbar-brand">
|
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -240,7 +240,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
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||||
|
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<footer><div class="copyright">
|
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<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
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</div>
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<div class="pkgdown">
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@@ -17,7 +17,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -306,7 +306,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -208,7 +208,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -19,7 +19,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -212,7 +212,7 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
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@@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -258,7 +258,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
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<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -348,7 +348,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
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|
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<footer><div class="copyright">
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<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
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@@ -1,80 +1,12 @@
|
||||
<!-- Generated by pkgdown: do not edit by hand -->
|
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<!DOCTYPE html>
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<title>Data Set with 5,604 Common Microorganism Codes — microorganisms.codes • AMR (for R)</title>
|
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<!-- favicons -->
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<meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions." />
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<div class="col-md-9 contents">
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<div class="page-header">
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<h1>Data Set with 5,604 Common Microorganism Codes</h1>
|
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
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||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
|
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<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
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</div>
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<div class="ref-description">
|
||||
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href='mo_source.html'>set_mo_source()</a></code>. They will all be searched when using <code><a href='as.mo.html'>as.mo()</a></code> and consequently all the <code><a href='mo_property.html'>mo_*</a></code> functions.</p>
|
||||
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href="mo_source.html">set_mo_source()</a></code>. They will all be searched when using <code><a href="as.mo.html">as.mo()</a></code> and consequently all the <code><a href="mo_property.html">mo_*</a></code> functions.</p>
|
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</div>
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<pre class="usage"><span class='va'>microorganisms.codes</span></pre>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>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>
|
||||
<li><p><code>mo</code><br /> ID of the microorganism in the <a href='microorganisms.html'>microorganisms</a> data set</p></li>
|
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</ul>
|
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<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
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<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms.codes</span></code></pre></div></div>
|
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<div id="format">
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<h2>Format</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>
|
||||
<li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
|
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</ul></div>
|
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<div id="reference-data-publicly-available">
|
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<h2>Reference Data Publicly Available</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 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</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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<div id="catalogue-of-life">
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<h2>Catalogue of Life</h2>
|
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||||
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<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <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'>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'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>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>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
|
||||
|
||||
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><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 id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code> <a href='microorganisms.html'>microorganisms</a></p></div>
|
||||
<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>
|
||||
</div>
|
||||
<div id="see-also">
|
||||
<h2>See also</h2>
|
||||
<div class="dont-index"><p><code><a href="as.mo.html">as.mo()</a></code> <a href="microorganisms.html">microorganisms</a></p></div>
|
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<meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 5 October 2021) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using as.mo()." />
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<h1>Data Set with 70,760 Microorganisms</h1>
|
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="hidden name"><code>microorganisms.Rd</code></div>
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</div>
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<div class="ref-description">
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<p>A data set containing the full microbial taxonomy (<strong>last updated: 5 October 2021</strong>) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using <code><a href='as.mo.html'>as.mo()</a></code>.</p>
|
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<p>A data set containing the full microbial taxonomy (<strong>last updated: 5 October 2021</strong>) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
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</div>
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<pre class="usage"><span class='va'>microorganisms</span></pre>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
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||||
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 70,760 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>
|
||||
<li><p><code>ref</code><br /> Author(s) and year of concerning scientific publication</p></li>
|
||||
<li><p><code>species_id</code><br /> ID of the species as used by the Catalogue of Life</p></li>
|
||||
<li><p><code>source</code><br /> Either "CoL", "LPSN" or "manually added" (see <em>Source</em>)</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>
|
||||
<li><p><code>snomed</code><br /> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, according to the US Edition of SNOMED CT from 1 September 2020 (see <em>Source</em>). Use <code><a href='mo_property.html'>mo_snomed()</a></code> to retrieve it quickly, see <code><a href='mo_property.html'>mo_property()</a></code>.</p></li>
|
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</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
<p>Catalogue of Life: 2019 Annual Checklist as currently implemented in this <code>AMR</code> package:</p><ul>
|
||||
<li><p>Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a></p></li>
|
||||
</ul>
|
||||
|
||||
<p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this <code>AMR</code> package:</p><ul>
|
||||
<li><p>Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi: <a href='https://doi.org/10.1099/ijsem.0.004332'>10.1099/ijsem.0.004332</a></p></li>
|
||||
<li><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; doi: <a href='https://doi.org/10.1099/ijsem.0.002786'>10.1099/ijsem.0.002786</a></p></li>
|
||||
<li><p>Parte, A.C. (2014). LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613–D616; doi: <a href='https://doi.org/10.1093/nar/gkt1111'>10.1093/nar/gkt1111</a></p></li>
|
||||
<li><p>Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; doi: <a href='https://doi.org/10.1099/00207713-47-2-590'>10.1099/00207713-47-2-590</a></p></li>
|
||||
</ul>
|
||||
|
||||
<p>US Edition of SNOMED CT from 1 September 2020 as currently implemented in this <code>AMR</code> package:</p><ul>
|
||||
<li><p>Retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href='https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009'>https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms</span></code></pre></div></div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 70,760 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>
|
||||
<li><p><code>ref</code><br> Author(s) and year of concerning scientific publication</p></li>
|
||||
<li><p><code>species_id</code><br> ID of the species as used by the Catalogue of Life</p></li>
|
||||
<li><p><code>source</code><br> Either "CoL", "LPSN" or "manually added" (see <em>Source</em>)</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>
|
||||
<li><p><code>snomed</code><br> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, according to the US Edition of SNOMED CT from 1 September 2020 (see <em>Source</em>). Use <code><a href="mo_property.html">mo_snomed()</a></code> to retrieve it quickly, see <code><a href="mo_property.html">mo_property()</a></code>.</p></li>
|
||||
</ul></div>
|
||||
<div id="source">
|
||||
<h2>Source</h2>
|
||||
<p>Catalogue of Life: 2019 Annual Checklist as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Annual Checklist (public online taxonomic database), <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a></p></li>
|
||||
</ul><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi: <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">10.1099/ijsem.0.004332</a></p></li>
|
||||
<li><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; doi: <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">10.1099/ijsem.0.002786</a></p></li>
|
||||
<li><p>Parte, A.C. (2014). LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613–D616; doi: <a href="https://doi.org/10.1093/nar/gkt1111" class="external-link">10.1093/nar/gkt1111</a></p></li>
|
||||
<li><p>Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; doi: <a href="https://doi.org/10.1099/00207713-47-2-590" class="external-link">10.1099/00207713-47-2-590</a></p></li>
|
||||
</ul><p>US Edition of SNOMED CT from 1 September 2020 as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
|
||||
</ul></div>
|
||||
<div id="details">
|
||||
<h2>Details</h2>
|
||||
<p>Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.</p>
|
||||
<p>For example, <em>Staphylococcus pettenkoferi</em> was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (doi: <a href='https://doi.org/10.1016/s0732-8893(02)00399-1'>10.1016/s0732-8893(02)00399-1</a>
|
||||
), but it was not before 2007 that a publication in IJSEM followed (doi: <a href='https://doi.org/10.1099/ijs.0.64381-0'>10.1099/ijs.0.64381-0</a>
|
||||
). Consequently, the <code>AMR</code> package returns 2007 for <code><a href='mo_property.html'>mo_year("S. pettenkoferi")</a></code>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Manual additions</h3>
|
||||
<p>For example, <em>Staphylococcus pettenkoferi</em> was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (doi: <a href="https://doi.org/10.1016/s0732-8893(02)00399-1" class="external-link">10.1016/s0732-8893(02)00399-1</a>
|
||||
), but it was not before 2007 that a publication in IJSEM followed (doi: <a href="https://doi.org/10.1099/ijs.0.64381-0" class="external-link">10.1099/ijs.0.64381-0</a>
|
||||
). Consequently, the <code>AMR</code> package returns 2007 for <code>mo_year("S. pettenkoferi")</code>.</p><div class="section">
|
||||
<h3 id="manual-additions">Manual additions<a class="anchor" aria-label="anchor" href="#manual-additions"></a></h3>
|
||||
|
||||
|
||||
<p>For convenience, some entries were added manually:</p><ul>
|
||||
<li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li>
|
||||
<p>For convenience, some entries were added manually:</p><ul><li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li>
|
||||
<li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative (CoNS) and coagulase-positive (CoPS))</p></li>
|
||||
<li><p>3 entries of <em>Trichomonas</em> (<em>T. vaginalis</em>, and its family and genus)</p></li>
|
||||
<li><p>1 entry of <em>Candida</em> (<em>C. krusei</em>), that is not (yet) in the Catalogue of Life</p></li>
|
||||
@@ -289,73 +201,70 @@
|
||||
<li><p>1 entry of <em>Moraxella</em> (<em>M. catarrhalis</em>), which was formally named <em>Branhamella catarrhalis</em> (Catlin, 1970) though this change was never accepted within the field of clinical microbiology</p></li>
|
||||
<li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
|
||||
<li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not (yet) in the Catalogue of Life</p></li>
|
||||
</ul>
|
||||
</ul></div>
|
||||
|
||||
<div class="section">
|
||||
<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
|
||||
|
||||
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</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:</p><ul>
|
||||
<li><p><a href='https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt'>https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt</a></p></li>
|
||||
</ul>
|
||||
|
||||
<p>The file 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/microorganisms.rda'>https://github.com/msberends/AMR/raw/main/data/microorganisms.rda</a></p></li>
|
||||
</ul>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="about-the-records-from-lpsn-see-source-"><a class="anchor" href="#about-the-records-from-lpsn-see-source-"></a>About the Records from LPSN (see <em>Source</em>)</h2>
|
||||
<p>This data set is available as 'flat file' for use even without <span style="R">R</span> - you can find the file here:</p><ul><li><p><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></li>
|
||||
</ul><p>The file 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/microorganisms.rda" class="external-link">https://github.com/msberends/AMR/raw/main/data/microorganisms.rda</a></p></li>
|
||||
</ul></div>
|
||||
|
||||
</div>
|
||||
<div id="about-the-records-from-lpsn-see-source-">
|
||||
<h2>About the Records from LPSN (see <em>Source</em>)</h2>
|
||||
|
||||
|
||||
<p>The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes. LPSN is a free to use service founded by Jean P. Euzeby in 1997 and later on maintained by Aidan C. Parte.</p>
|
||||
<p>As of February 2020, the regularly augmented LPSN database at DSMZ is the basis of the new LPSN service. The new database was implemented for the Type-Strain Genome Server and augmented in 2018 to store all kinds of nomenclatural information. Data from the previous version of LPSN and from the Prokaryotic Nomenclature Up-to-date (PNU) service were imported into the new system. PNU had been established in 1993 as a service of the Leibniz Institute DSMZ, and was curated by Norbert Weiss, Manfred Kracht and Dorothea Gleim.</p>
|
||||
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
|
||||
|
||||
</div>
|
||||
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|
||||
<h2>Catalogue of Life</h2>
|
||||
|
||||
|
||||
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <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'>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'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>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>
|
||||
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
||||
|
||||
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><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 id="reference-data-publicly-available">
|
||||
<h2>Reference Data Publicly Available</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 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</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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</div>
|
||||
<div id="read-more-on-our-website-">
|
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<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code>, <code><a href='mo_property.html'>mo_property()</a></code>, <a href='microorganisms.codes.html'>microorganisms.codes</a>, <a href='intrinsic_resistant.html'>intrinsic_resistant</a></p></div>
|
||||
<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>
|
||||
</div>
|
||||
<div id="see-also">
|
||||
<h2>See also</h2>
|
||||
<div class="dont-index"><p><code><a href="as.mo.html">as.mo()</a></code>, <code><a href="mo_property.html">mo_property()</a></code>, <a href="microorganisms.codes.html">microorganisms.codes</a>, <a href="intrinsic_resistant.html">intrinsic_resistant</a></p></div>
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||||
<h1>Data Set with Previously Accepted Taxonomic Names</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
|
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="hidden name"><code>microorganisms.old.Rd</code></div>
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||||
<div class="ref-description">
|
||||
<p>A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by <code><a href='as.mo.html'>as.mo()</a></code>.</p>
|
||||
<p>A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by <code><a href="as.mo.html">as.mo()</a></code>.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='va'>microorganisms.old</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>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>
|
||||
<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>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>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; doi: <a href='https://doi.org/10.1099/ijsem.0.002786'>10.1099/ijsem.0.002786</a></p>
|
||||
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms.old</span></code></pre></div></div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</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>
|
||||
<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>
|
||||
</ul></div>
|
||||
<div id="source">
|
||||
<h2>Source</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; doi: <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">10.1099/ijsem.0.002786</a></p>
|
||||
</div>
|
||||
<div id="catalogue-of-life">
|
||||
<h2>Catalogue of Life</h2>
|
||||
|
||||
|
||||
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <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'>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'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>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>
|
||||
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
||||
|
||||
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><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 id="reference-data-publicly-available">
|
||||
<h2>Reference Data Publicly Available</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 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</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 id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo()</a></code> <code><a href='mo_property.html'>mo_property()</a></code> <a href='microorganisms.html'>microorganisms</a></p></div>
|
||||
<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>
|
||||
</div>
|
||||
<div id="see-also">
|
||||
<h2>See also</h2>
|
||||
<div class="dont-index"><p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="mo_property.html">mo_property()</a></code> <a href="microorganisms.html">microorganisms</a></p></div>
|
||||
</div>
|
||||
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
</nav>
|
||||
</div>
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
|
||||
</nav></div>
|
||||
</div>
|
||||
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
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<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
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||||
</html>
|
||||
|
||||
|
||||
</body></html>
|
||||
|
||||
|
||||
@@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -228,7 +228,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -427,7 +427,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -18,7 +18,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -265,7 +265,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
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<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
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|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
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|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -264,7 +264,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
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|
||||
</button>
|
||||
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|
||||
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|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -330,7 +330,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -18,7 +18,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</button>
|
||||
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|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -379,7 +379,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
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||||
|
||||
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|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
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|
||||
|
||||
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|
||||
|
||||
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|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -230,7 +230,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
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|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
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|
||||
|
||||
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|
||||
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|
||||
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|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
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|
||||
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|
||||
|
||||
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|
||||
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||||
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<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
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|
||||
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||||
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|
||||
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||||
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|
||||
<!-- Generated by pkgdown: do not edit by hand -->
|
||||
<!DOCTYPE html>
|
||||
<html lang="en">
|
||||
<head>
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<meta charset="utf-8">
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Data Set for R/SI Interpretation — rsi_translation • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
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<!-- jquery -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- bootstrap-toc -->
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<link rel="stylesheet" href="../bootstrap-toc.css">
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||||
<h1>Data Set for R/SI Interpretation</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
|
||||
<div class="hidden name"><code>rsi_translation.Rd</code></div>
|
||||
</div>
|
||||
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||||
<div class="ref-description">
|
||||
<p>Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
|
||||
<p>Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020). Use <code><a href="as.rsi.html">as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='va'>rsi_translation</span></pre>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 22,000 observations and 10 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>
|
||||
<li><p><code>ab</code><br /> Antibiotic ID, see <code><a href='as.ab.html'>as.ab()</a></code></p></li>
|
||||
<li><p><code>ref_tbl</code><br /> Info about where the guideline rule can be found</p></li>
|
||||
<li><p><code>disk_dose</code><br /> Dose of the used disk diffusion method</p></li>
|
||||
<li><p><code>breakpoint_S</code><br /> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
|
||||
<li><p><code>breakpoint_R</code><br /> Highest MIC value or lowest number of millimetres that leads to "R"</p></li>
|
||||
<li><p><code>uti</code><br /> A <a href='https://rdrr.io/r/base/logical.html'>logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the rule applies to a urinary tract infection (UTI)</p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</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'>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.</p>
|
||||
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
||||
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">rsi_translation</span></code></pre></div></div>
|
||||
|
||||
<div id="format">
|
||||
<h2>Format</h2>
|
||||
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 22,000 observations and 10 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>
|
||||
<li><p><code>ab</code><br> Antibiotic ID, see <code><a href="as.ab.html">as.ab()</a></code></p></li>
|
||||
<li><p><code>ref_tbl</code><br> Info about where the guideline rule can be found</p></li>
|
||||
<li><p><code>disk_dose</code><br> Dose of the used disk diffusion method</p></li>
|
||||
<li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
|
||||
<li><p><code>breakpoint_R</code><br> Highest MIC value or lowest number of millimetres that leads to "R"</p></li>
|
||||
<li><p><code>uti</code><br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the rule applies to a urinary tract infection (UTI)</p></li>
|
||||
</ul></div>
|
||||
<div id="details">
|
||||
<h2>Details</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.</p>
|
||||
</div>
|
||||
<div id="reference-data-publicly-available">
|
||||
<h2>Reference Data Publicly Available</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 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</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 id="read-more-on-our-website-">
|
||||
<h2>Read more on Our Website!</h2>
|
||||
|
||||
|
||||
<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>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><a href='intrinsic_resistant.html'>intrinsic_resistant</a></p></div>
|
||||
<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>
|
||||
</div>
|
||||
<div id="see-also">
|
||||
<h2>See also</h2>
|
||||
<div class="dont-index"><p><a href="intrinsic_resistant.html">intrinsic_resistant</a></p></div>
|
||||
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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@@ -18,7 +18,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
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@@ -208,7 +208,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -235,7 +235,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
@@ -17,7 +17,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9058</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9062</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -168,7 +168,7 @@
|
||||
|
||||
|
||||
<footer><div class="copyright">
|
||||
<p></p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
||||
2
index.md
2
index.md
@@ -8,7 +8,7 @@
|
||||
|
||||
After installing this package, R knows [**~71,000 distinct microbial species**](./reference/microorganisms.html) and all [**~560 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
|
||||
|
||||
This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.192486375)) but is [actively and durably maintained](./news) by two public healthcare organisations in the Netherlands.
|
||||
This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.192486375)) but is [actively and durably maintained](./news) by two public healthcare organisations in the Netherlands.
|
||||
|
||||
<div class="main-content" style="display: inline-block;">
|
||||
<p>
|
||||
|
||||
@@ -38,6 +38,9 @@
|
||||
#r4ds .img {
|
||||
width: 33%;
|
||||
}
|
||||
#r4ds .img img {
|
||||
height: 120px;
|
||||
}
|
||||
|
||||
/* class for footer */
|
||||
.footer_logo {
|
||||
@@ -52,7 +55,7 @@
|
||||
.countries_map {
|
||||
float: left;
|
||||
padding: 0 10px 10px 0;
|
||||
max-width: 35%;
|
||||
max-width: 35% !important;
|
||||
}
|
||||
@media only screen and (max-width: 992px) {
|
||||
.footer_logo {
|
||||
@@ -63,6 +66,9 @@
|
||||
footer p {
|
||||
display: inline-block;
|
||||
}
|
||||
footer {
|
||||
padding: 15px 0 20px !important;
|
||||
}
|
||||
|
||||
/* Supports icons for brand using font-awesome */
|
||||
.fab {
|
||||
@@ -116,13 +122,11 @@ pre {
|
||||
kbd {
|
||||
display: inline-block;
|
||||
padding: 0 4px;
|
||||
box-shadow: 1px 1px 1px #2c3e50;
|
||||
margin: 2px;
|
||||
box-shadow: 1px 1px 1px slategrey;
|
||||
margin: 1px;
|
||||
font-size: small;
|
||||
vertical-align: text-bottom;
|
||||
color: #2c3e50;
|
||||
background: #eeeeee;
|
||||
font-weight: bold;
|
||||
}
|
||||
|
||||
li, p {
|
||||
@@ -134,6 +138,9 @@ li p {
|
||||
.template-news li p {
|
||||
margin: 0;
|
||||
}
|
||||
.template-news h3 {
|
||||
padding-top: 10px;
|
||||
}
|
||||
|
||||
/* slightly smaller blockquote */
|
||||
blockquote {
|
||||
@@ -258,16 +265,9 @@ table a:not(.btn):hover {
|
||||
font-size: 16px;
|
||||
}
|
||||
|
||||
/* logos on index page */
|
||||
.logo_img {
|
||||
display: inline-block;
|
||||
}
|
||||
.logo_txt {
|
||||
display: inline;
|
||||
font-size: 125%;
|
||||
vertical-align: middle;
|
||||
color: black;
|
||||
font-weight: bold;
|
||||
/* AMR logo on index page */
|
||||
.template-home h1 img {
|
||||
height: 120px;
|
||||
}
|
||||
|
||||
.btn.btn-info.btn-amr {
|
||||
|
||||
@@ -85,11 +85,9 @@ $(document).ready(function() {
|
||||
// edit footer
|
||||
$('footer').html(
|
||||
'<div>' +
|
||||
'<p><code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>.</p>' +
|
||||
'<a href="https://www.rug.nl"><img src="https://github.com/msberends/AMR/raw/main/docs/logo_rug.png" class="footer_logo"></a>' +
|
||||
'<p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl">University Medical Center Groningen</a>.</p>' +
|
||||
'<a target="_blank" href="https://www.rug.nl"><img src="https://github.com/msberends/AMR/raw/main/docs/logo_rug.png" class="footer_logo"></a>' +
|
||||
'</div>');
|
||||
// all links should open in new tab/window
|
||||
$('footer').html($('footer').html().replace(/href/g, 'target="_blank" href'));
|
||||
|
||||
// doctoral titles of authors
|
||||
function doct_tit(x) {
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
---
|
||||
title: "How to conduct AMR data analysis"
|
||||
author: "Matthijs S. Berends"
|
||||
author: "Dr. Matthijs Berends"
|
||||
date: '`r format(Sys.Date(), "%d %B %Y")`'
|
||||
output:
|
||||
rmarkdown::html_vignette:
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
---
|
||||
title: "How to import data from SPSS / SAS / Stata"
|
||||
author: "Matthijs S. Berends"
|
||||
author: "Dr. Matthijs Berends"
|
||||
date: '`r format(Sys.Date(), "%d %B %Y")`'
|
||||
output:
|
||||
rmarkdown::html_vignette:
|
||||
|
||||
@@ -30,7 +30,7 @@ Note: to keep the package size as small as possible, we only included this vigne
|
||||
|
||||
After installing this package, R knows `r AMR:::format_included_data_number(AMR::microorganisms)` distinct microbial species and all `r AMR:::format_included_data_number(rbind(AMR::antibiotics[, "atc", drop = FALSE], AMR::antivirals[, "atc", drop = FALSE]))` antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
|
||||
|
||||
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. Since its first public release in early 2018, this package has been downloaded from more than 160 countries.
|
||||
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.
|
||||
|
||||
This package can be used for:
|
||||
|
||||
|
||||
Reference in New Issue
Block a user