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Merge branch 'development' of https://github.com/msberends/AMR into development

# Conflicts:
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#	docs/articles/AMR_files/figure-html/mic_plots-1.png
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dr. M.S. (Matthijs) Berends 2022-03-14 16:37:37 +01:00
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@ -205,14 +205,12 @@ Content not found. Please use links in the navbar.
<footer><div class="copyright"> <footer><div class="copyright">
<p></p> <p></p>
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p> <p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
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</footer> </footer>

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@ -416,13 +416,11 @@ END OF TERMS AND CONDITIONS
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
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</footer></div> </footer></div>

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@ -44,7 +44,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -185,7 +189,7 @@
</header><div class="row"> </header><script src="EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>How to apply EUCAST rules</h1> <h1 data-toc-skip>How to apply EUCAST rules</h1>
@ -431,8 +435,12 @@ Erwin E. A. Hassing.</p>
<div class="pkgdown"> <div class="pkgdown">
<p></p> <p></p>
<<<<<<< HEAD
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</footer> </footer>

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@ -44,7 +44,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -185,7 +189,7 @@
</header><div class="row"> </header><script src="MDR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>How to determine multi-drug resistance <h1 data-toc-skip>How to determine multi-drug resistance
@ -343,6 +347,7 @@ on this data set, we get:</p>
<span class="co"># Table 5 - Acinetobacter spp.... OK.</span> <span class="co"># Table 5 - Acinetobacter spp.... OK.</span>
<span class="co"># Warning: in `mdro()`: NA introduced for isolates where the available percentage of</span> <span class="co"># Warning: in `mdro()`: NA introduced for isolates where the available percentage of</span>
<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></code></pre></div> <span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
<<<<<<< HEAD
<p>Only results with ‘R’ are considered as resistance. Use <p>Only results with ‘R’ are considered as resistance. Use
<code>combine_SI = FALSE</code> to also consider ‘I’ as resistance.</p> <code>combine_SI = FALSE</code> to also consider ‘I’ as resistance.</p>
<p>Determining multidrug-resistant organisms (MDRO), according to: <p>Determining multidrug-resistant organisms (MDRO), according to:
@ -352,6 +357,10 @@ standard definitions for acquired resistance. Author(s): Magiorakos AP,
Srinivasan A, Carey RB, …, Vatopoulos A, Weber JT, Monnet DL Source: Srinivasan A, Carey RB, …, Vatopoulos A, Weber JT, Monnet DL Source:
Clinical Microbiology and Infection 18:3, 2012; doi: Clinical Microbiology and Infection 18:3, 2012; doi:
10.1111/j.1469-0691.2011.03570.x</p> 10.1111/j.1469-0691.2011.03570.x</p>
=======
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<p>(16 isolates had no test results)</p> <p>(16 isolates had no test results)</p>
<p><strong>Frequency table</strong></p> <p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br> <p>Class: factor &gt; ordered (numeric)<br>
@ -422,6 +431,7 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> <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> <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"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<<<<<<< HEAD
<span class="co"># 1 R S S I S I</span> <span class="co"># 1 R S S I S I</span>
<span class="co"># 2 R S S S R I</span> <span class="co"># 2 R S S S R I</span>
<span class="co"># 3 S S I I S S</span> <span class="co"># 3 S S I I S S</span>
@ -437,6 +447,22 @@ names or codes, this would have worked exactly the same way:</p>
<span class="co"># 6 I</span></code></pre></div> <span class="co"># 6 I</span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can <p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p> use:</p>
=======
<span class="co"># 1 I R I R I I</span>
<span class="co"># 2 I R I I I I</span>
<span class="co"># 3 S I I R S S</span>
<span class="co"># 4 R I R I R I</span>
<span class="co"># 5 S I S S R S</span>
<span class="co"># 6 S S I I I S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 I</span>
<span class="co"># 2 R</span>
<span class="co"># 3 I</span>
<span class="co"># 4 I</span>
<span class="co"># 5 R</span>
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> <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> <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>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p> <p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
@ -462,8 +488,12 @@ use:</p>
<p><strong>Frequency table</strong></p> <p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br> <p>Class: factor &gt; ordered (numeric)<br>
Length: 5,000<br> Length: 5,000<br>
<<<<<<< HEAD
Levels: 5: Negative &lt; Mono-resistant &lt; Poly-resistant &lt; Levels: 5: Negative &lt; Mono-resistant &lt; Poly-resistant &lt;
Multi-drug-resistant &lt;…<br> Multi-drug-resistant &lt;…<br>
=======
Levels: 5: Negative &lt; Mono-resistant &lt; Poly-resistant &lt; Multi-drug-resistant &lt;…<br>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
Available: 5,000 (100%, NA: 0 = 0%)<br> Available: 5,000 (100%, NA: 0 = 0%)<br>
Unique: 5</p> Unique: 5</p>
<table style="width:100%;" class="table"> <table style="width:100%;" class="table">
@ -487,40 +517,73 @@ Unique: 5</p>
<tr class="odd"> <tr class="odd">
<td align="left">1</td> <td align="left">1</td>
<td align="left">Mono-resistant</td> <td align="left">Mono-resistant</td>
<<<<<<< HEAD
<td align="right">3175</td> <td align="right">3175</td>
<td align="right">63.50%</td> <td align="right">63.50%</td>
<td align="right">3175</td> <td align="right">3175</td>
<td align="right">63.50%</td> <td align="right">63.50%</td>
=======
<td align="right">3243</td>
<td align="right">64.86%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">2</td> <td align="left">2</td>
<td align="left">Negative</td> <td align="left">Negative</td>
<<<<<<< HEAD
<td align="right">1057</td> <td align="right">1057</td>
<td align="right">21.14%</td> <td align="right">21.14%</td>
<td align="right">4232</td> <td align="right">4232</td>
<td align="right">84.64%</td> <td align="right">84.64%</td>
=======
<td align="right">969</td>
<td align="right">19.38%</td>
<td align="right">4212</td>
<td align="right">84.24%</td>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">3</td> <td align="left">3</td>
<td align="left">Multi-drug-resistant</td> <td align="left">Multi-drug-resistant</td>
<<<<<<< HEAD
<td align="right">431</td> <td align="right">431</td>
<td align="right">8.62%</td> <td align="right">8.62%</td>
<td align="right">4663</td> <td align="right">4663</td>
<td align="right">93.26%</td> <td align="right">93.26%</td>
=======
<td align="right">425</td>
<td align="right">8.50%</td>
<td align="right">4637</td>
<td align="right">92.74%</td>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">4</td> <td align="left">4</td>
<td align="left">Poly-resistant</td> <td align="left">Poly-resistant</td>
<<<<<<< HEAD
<td align="right">236</td> <td align="right">236</td>
<td align="right">4.72%</td> <td align="right">4.72%</td>
<td align="right">4899</td> <td align="right">4899</td>
<td align="right">97.98%</td> <td align="right">97.98%</td>
=======
<td align="right">263</td>
<td align="right">5.26%</td>
<td align="right">4900</td>
<td align="right">98.00%</td>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">5</td> <td align="left">5</td>
<td align="left">Extensively drug-resistant</td> <td align="left">Extensively drug-resistant</td>
<<<<<<< HEAD
<td align="right">101</td> <td align="right">101</td>
<td align="right">2.02%</td> <td align="right">2.02%</td>
=======
<td align="right">100</td>
<td align="right">2.00%</td>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<td align="right">5000</td> <td align="right">5000</td>
<td align="right">100.00%</td> <td align="right">100.00%</td>
</tr> </tr>
@ -545,8 +608,12 @@ Erwin E. A. Hassing.</p>
<div class="pkgdown"> <div class="pkgdown">
<p></p> <p></p>
<<<<<<< HEAD
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</footer> </footer>

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</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -185,7 +189,7 @@
</header><div class="row"> </header><script src="PCA_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>How to conduct principal component analysis <h1 data-toc-skip>How to conduct principal component analysis
@ -199,8 +203,12 @@
<<<<<<< HEAD
<p><strong>NOTE: This page will be updated soon, as the pca() function <p><strong>NOTE: This page will be updated soon, as the pca() function
is currently being developed.</strong></p> is currently being developed.</strong></p>
=======
<p><strong>NOTE: This page will be updated soon, as the pca() function is currently being developed.</strong></p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@ -208,12 +216,16 @@ is currently being developed.</strong></p>
<div class="section level2"> <div class="section level2">
<h2 id="transforming">Transforming<a class="anchor" aria-label="anchor" href="#transforming"></a> <h2 id="transforming">Transforming<a class="anchor" aria-label="anchor" href="#transforming"></a>
</h2> </h2>
<<<<<<< HEAD
<p>For PCA, we need to transform our AMR data first. This is what the <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> <code>example_isolates</code> data set in this package looks like:</p>
=======
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <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://msberends.github.io/AMR/">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="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="fu"><a href="https://dplyr.tidyverse.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"># Rows: 2,000</span>
<span class="co"># Columns: 49</span> <span class="co"># Columns: 49</span>
<span class="co"># $ date <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span> <span class="co"># $ date <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
@ -290,9 +302,13 @@ per taxonomic order and genus:</p>
<div class="section level2"> <div class="section level2">
<h2 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a> <h2 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a>
</h2> </h2>
<<<<<<< HEAD
<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows <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 that contain numeric values in all selected variables, so we now only
need to do:</p> need to do:</p>
=======
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">pca_result</span> <span class="op">&lt;-</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> <code class="sourceCode R"><span class="va">pca_result</span> <span class="op">&lt;-</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>
<span class="co"># ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span> <span class="co"># ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span>
@ -354,8 +370,12 @@ Erwin E. A. Hassing.</p>
<div class="pkgdown"> <div class="pkgdown">
<p></p> <p></p>
<<<<<<< HEAD
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
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@ -44,7 +44,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -185,14 +189,18 @@
</header><div class="row"> </header><script src="SPSS_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1> <h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 data-toc-skip class="author">Dr. Matthijs <h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4> Berends</h4>
<<<<<<< HEAD
<h4 data-toc-skip class="date">14 March 2022</h4> <h4 data-toc-skip class="date">14 March 2022</h4>
=======
<h4 data-toc-skip class="date">12 March 2022</h4>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<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> <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>
<div class="hidden name"><code>SPSS.Rmd</code></div> <div class="hidden name"><code>SPSS.Rmd</code></div>
@ -271,12 +279,16 @@ data using a custom made website. The webdesign knowledge needed
</li> </li>
<li> <li>
<p><strong>R has a huge community.</strong></p> <p><strong>R has a huge community.</strong></p>
<<<<<<< HEAD
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest <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">439,954 online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">439,954
R-related questions</a> have already been asked on this platform (that R-related questions</a> have already been asked on this platform (that
covers questions and answers for any programming language). In my own covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of experience, most questions are answered within a couple of
minutes.</p> 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">439,030 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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</li> </li>
<li> <li>
<p><strong>R understands any data type, including <p><strong>R understands any data type, including
@ -314,6 +326,7 @@ much PR as they want (like I do here), because nobody is officially
associated with or affiliated by R. It is really free.</p> associated with or affiliated by R. It is really free.</p>
</li> </li>
<li> <li>
<<<<<<< HEAD
<p><strong>R is (nowadays) the preferred analysis software in <p><strong>R is (nowadays) the preferred analysis software in
academic papers.</strong></p> academic papers.</strong></p>
<p>At present, R is among the world most powerful statistical languages, <p>At present, R is among the world most powerful statistical languages,
@ -333,6 +346,11 @@ restyled completely</a> by volunteers who are dedicated professionals in
the field of data science. SPSS was great when there was nothing else the field of data science. SPSS was great when there was nothing else
that could compete. But now in 2022, I don’t see any reason why SPSS that could compete. But now in 2022, I don’t see any reason why SPSS
would be of any better use than R.</p> would be of any better use than R.</p>
=======
<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/" 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 2022, I don’t see any reason why SPSS would be of any better use than R.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</li> </li>
</ul> </ul>
<p>To demonstrate the first point:</p> <p>To demonstrate the first point:</p>
@ -517,8 +535,12 @@ Erwin E. A. Hassing.</p>
<div class="pkgdown"> <div class="pkgdown">
<p></p> <p></p>
<<<<<<< HEAD
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
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@ -44,7 +44,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -185,7 +189,7 @@
</header><div class="row"> </header><script src="WHONET_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>How to work with WHONET data</h1> <h1 data-toc-skip>How to work with WHONET data</h1>
@ -442,8 +446,12 @@ Erwin E. A. Hassing.</p>
<div class="pkgdown"> <div class="pkgdown">
<p></p> <p></p>
<<<<<<< HEAD
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
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@ -44,7 +44,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -185,7 +189,7 @@
</header><div class="row"> </header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>Benchmarks</h1> <h1 data-toc-skip>Benchmarks</h1>
@ -238,8 +242,9 @@ microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span> 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="fu"><a href="https://rdrr.io/r/base/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"># Unit: milliseconds</span>
<<<<<<< HEAD
<span class="co"># expr min lq mean median uq max neval</span> <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 48 25</span> <span class="co"># as.mo("sau") 12.0 13 18.0 14.0 15.0 48 25</span>
<span class="co"># as.mo("stau") 54.0 59 80.0 91.0 96.0 99 25</span> <span class="co"># as.mo("stau") 54.0 59 80.0 91.0 96.0 99 25</span>
@ -263,6 +268,24 @@ determine.</p>
<p>To improve performance, we implemented two important algorithms to <p>To improve performance, we implemented two important algorithms to
save unnecessary calculations: <strong>repetitive results</strong> and save unnecessary calculations: <strong>repetitive results</strong> and
<strong>already precalculated results</strong>.</p> <strong>already precalculated results</strong>.</p>
=======
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 20.0 20.0 25.0 20.0 21 57 25</span>
<span class="co"># as.mo("stau") 94.0 94.0 110.0 95.0 130 130 25</span>
<span class="co"># as.mo("STAU") 94.0 95.0 110.0 130.0 130 130 25</span>
<span class="co"># as.mo("staaur") 20.0 20.0 28.0 20.0 21 58 25</span>
<span class="co"># as.mo("STAAUR") 20.0 20.0 25.0 20.0 21 57 25</span>
<span class="co"># as.mo("S. aureus") 56.0 56.0 72.0 57.0 92 97 25</span>
<span class="co"># as.mo("S aureus") 55.0 56.0 66.0 56.0 75 93 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 5.7 5.8 7.3 5.9 6 41 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 370.0 370.0 390.0 380.0 410 410 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 260.0 290.0 300.0 290.0 300 330 25</span>
<span class="co"># as.mo("MRSA") 20.0 20.0 23.0 20.0 20 56 25</span>
<span class="co"># as.mo("VISA") 34.0 35.0 48.0 35.0 35 220 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 65 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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<div class="section level3"> <div class="section level3">
<h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a> <h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
</h3> </h3>
@ -287,8 +310,13 @@ possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()<
<span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span> <span class="co"># what do these values look like? They are of class &lt;mo&gt;:</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="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 &lt;mo&gt;</span> <span class="co"># Class &lt;mo&gt;</span>
<<<<<<< HEAD
<span class="co"># [1] B_ESCHR_COLI B_STRPT_MITS B_STRPT_ANGN B_STPHY_CONS B_ESCHR_COLI</span> <span class="co"># [1] B_ESCHR_COLI B_STRPT_MITS B_STRPT_ANGN B_STPHY_CONS B_ESCHR_COLI</span>
<span class="co"># [6] B_ESCHR_COLI</span> <span class="co"># [6] B_ESCHR_COLI</span>
=======
<span class="co"># [1] B_PROTS_MRBL B_STPHY_CONS B_ESCHR_COLI B_PSDMN_AERG B_ENTRC_FCLS</span>
<span class="co"># [6] B_STPHY_AURS</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</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> <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>
@ -301,14 +329,19 @@ possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()<
<span class="co"># now let's see:</span> <span class="co"># now let's see:</span>
<span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</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">x</span><span class="op">)</span>, <span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</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">x</span><span class="op">)</span>,
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span> times <span class="op">=</span> <span class="fl">10</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">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="fu"><a href="https://rdrr.io/r/base/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"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span> <span class="co"># expr min lq mean median uq max neval</span>
<<<<<<< HEAD
<span class="co"># mo_name(x) 207 225 288 233 370 414 10</span></code></pre></div> <span class="co"># mo_name(x) 207 225 288 233 370 414 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items <p>So getting official taxonomic names of 2,000,000 (!!) items
consisting of 90 unique values only takes 0.233 seconds. That is 117 consisting of 90 unique values only takes 0.233 seconds. That is 117
nanoseconds on average. You only lose time on your unique input nanoseconds on average. You only lose time on your unique input
values.</p> values.</p>
=======
<span class="co"># mo_name(x) 265 269 357 298 471 516 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.298 seconds. That is 149 nanoseconds on average. You only lose time on your unique input values.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a> <h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
@ -323,8 +356,9 @@ will return the results immediately (see ‘C’ below):</p>
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>, B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>, C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span> times <span class="op">=</span> <span class="fl">10</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">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="fu"><a href="https://rdrr.io/r/base/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"># Unit: milliseconds</span>
<<<<<<< HEAD
<span class="co"># expr min lq mean median uq max neval</span> <span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 10.3 10.90 11.20 11.10 11.20 12.40 10</span> <span class="co"># A 10.3 10.90 11.20 11.10 11.20 12.40 10</span>
<span class="co"># B 31.3 32.70 38.20 33.90 35.20 79.80 10</span> <span class="co"># B 31.3 32.70 38.20 33.90 35.20 79.80 10</span>
@ -333,6 +367,13 @@ will return the results immediately (see ‘C’ below):</p>
<code>"Staphylococcus aureus"</code> takes 0.0028 seconds - it doesn’t <code>"Staphylococcus aureus"</code> takes 0.0028 seconds - it doesn’t
even start calculating <em>if the result would be the same as the even start calculating <em>if the result would be the same as the
expected resulting value</em>. That goes for all helper functions:</p> expected resulting value</em>. That goes for all helper functions:</p>
=======
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 12.30 12.30 12.60 12.50 12.60 14.2 10</span>
<span class="co"># B 61.70 61.90 62.70 62.40 62.50 66.2 10</span>
<span class="co"># C 3.04 3.05 6.92 3.12 3.21 40.9 10</span></code></pre></div>
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0031 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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</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>, <code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</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>, 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>,
@ -343,9 +384,10 @@ expected resulting value</em>. That goes for all helper functions:</p>
G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>, G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>, H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span> times <span class="op">=</span> <span class="fl">10</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">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="fu"><a href="https://rdrr.io/r/base/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"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span> <span class="co"># expr min lq mean median uq max neval</span>
<<<<<<< HEAD
<span class="co"># A 2.30 2.55 2.68 2.66 2.85 2.94 10</span> <span class="co"># A 2.30 2.55 2.68 2.66 2.85 2.94 10</span>
<span class="co"># B 2.27 2.38 2.59 2.56 2.83 2.88 10</span> <span class="co"># B 2.27 2.38 2.59 2.56 2.83 2.88 10</span>
<span class="co"># C 2.22 2.25 2.51 2.47 2.74 2.87 10</span> <span class="co"># C 2.22 2.25 2.51 2.47 2.74 2.87 10</span>
@ -360,6 +402,17 @@ function has zero knowledge about the actual microorganism, namely
<code>"Firmicutes"</code> anyway, there is no point in calculating the <code>"Firmicutes"</code> anyway, there is no point in calculating the
result. And because this package contains all phyla of all known result. And because this package contains all phyla of all known
bacteria, it can just return the initial value immediately.</p> bacteria, it can just return the initial value immediately.</p>
=======
<span class="co"># A 3.02 3.09 3.22 3.10 3.46 3.55 10</span>
<span class="co"># B 3.03 3.04 3.21 3.12 3.42 3.48 10</span>
<span class="co"># C 3.03 3.05 3.08 3.06 3.12 3.16 10</span>
<span class="co"># D 2.98 3.01 3.17 3.09 3.40 3.47 10</span>
<span class="co"># E 3.01 3.06 3.19 3.12 3.43 3.43 10</span>
<span class="co"># F 2.95 2.99 3.11 3.05 3.16 3.46 10</span>
<span class="co"># G 2.94 3.06 3.19 3.13 3.41 3.54 10</span>
<span class="co"># H 2.93 3.01 3.12 3.08 3.19 3.42 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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
<div class="section level3"> <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 id="results-in-other-languages">Results in other languages<a class="anchor" aria-label="anchor" href="#results-in-other-languages"></a>
@ -394,8 +447,9 @@ with the other languages):</p>
ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>, ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>, sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>,
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span> times <span class="op">=</span> <span class="fl">100</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">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="fu"><a href="https://rdrr.io/r/base/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"># Unit: milliseconds</span>
<<<<<<< HEAD
<span class="co"># expr min lq mean median uq max neval</span> <span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># da 2.1730 2.476 3.956 2.609 2.873 45.180 100</span> <span class="co"># da 2.1730 2.476 3.956 2.609 2.873 45.180 100</span>
<span class="co"># de 2.2170 2.497 3.161 2.646 2.855 48.260 100</span> <span class="co"># de 2.2170 2.497 3.161 2.646 2.855 48.260 100</span>
@ -409,6 +463,20 @@ with the other languages):</p>
<span class="co"># sv 2.2030 2.443 3.077 2.545 2.703 43.350 100</span></code></pre></div> <span class="co"># sv 2.2030 2.443 3.077 2.545 2.703 43.350 100</span></code></pre></div>
<p>Currently supported languages are Danish, Dutch, English, French, <p>Currently supported languages are Danish, Dutch, English, French,
German, Italian, Portuguese, Russian, Spanish and Swedish.</p> German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
=======
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># da 3.579 3.689 3.811 3.737 3.894 4.626 100</span>
<span class="co"># de 3.600 3.694 4.205 3.750 3.869 43.820 100</span>
<span class="co"># en 1.686 1.720 1.828 1.766 1.822 2.244 100</span>
<span class="co"># es 3.618 3.688 4.633 3.772 4.083 43.890 100</span>
<span class="co"># fr 3.493 3.602 4.104 3.658 3.785 41.860 100</span>
<span class="co"># it 3.543 3.628 4.152 3.702 3.810 44.040 100</span>
<span class="co"># nl 3.625 3.716 5.024 3.763 3.924 44.220 100</span>
<span class="co"># pt 3.510 3.610 3.742 3.684 3.861 4.096 100</span>
<span class="co"># ru 3.568 3.680 4.534 3.742 3.871 41.170 100</span>
<span class="co"># sv 3.585 3.664 3.833 3.748 4.046 4.987 100</span></code></pre></div>
<p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</div> </div>
@ -428,8 +496,12 @@ Erwin E. A. Hassing.</p>
<div class="pkgdown"> <div class="pkgdown">
<p></p> <p></p>
<<<<<<< HEAD
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</footer> </footer>

338
docs/articles/datasets.html
View File

@ -185,12 +185,16 @@
</header><div class="row"> </header><script src="datasets_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1> <h1 data-toc-skip>Data sets for download / own use</h1>
<<<<<<< HEAD
<h4 data-toc-skip class="date">14 March 2022</h4> <h4 data-toc-skip class="date">14 March 2022</h4>
=======
<h4 data-toc-skip class="date">12 March 2022</h4>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<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> <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> <div class="hidden name"><code>datasets.Rmd</code></div>
@ -199,71 +203,42 @@
<p>All reference data (about microorganisms, antibiotics, R/SI <p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply tab separated files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are <p>On this page, we explain how to download them and how the structure of the data sets look like.</p>
reliable, up-to-date and freely available. We continually export our
data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also
supply tab separated files that are machine-readable and suitable for
input in any software program, such as laboratory information
systems.</p>
<p>On this page, we explain how to download them and how the structure
of the data sets look like.</p>
<p class="dataset-within-r"> <p class="dataset-within-r">
If you are reading this page from within R, please If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.
<a href="https://msberends.github.io/AMR/articles/datasets.html">visit
our website</a>, which is automatically updated with every code change.
</p> </p>
<div class="section level2"> <div class="section level2">
<h2 id="microorganisms-currently-accepted-names">Microorganisms (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-currently-accepted-names"></a> <h2 id="microorganisms-currently-accepted-names">Microorganisms (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-currently-accepted-names"></a>
</h2> </h2>
<p>A data set with 70,760 rows and 16 columns, containing the following <p>A data set with 70,760 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <p>It was last updated on 1 February 2022 22:08:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>,
<em>species_id</em>, <em>source</em>, <em>prevalence</em> and
<em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (1.3 MB)<br>
file</a> (1.3 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel file</a> (6.4 MB)<br>
file</a> (6.4 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain text file</a> (13.1 MB)<br>
text file</a> (13.1 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS file</a> (30.7 MB)<br>
file</a> (30.7 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS file</a> (16.3 MB)<br>
file</a> (16.3 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata file</a> (27.5 MB)</li>
file</a> (27.5 MB)</li>
</ul> </ul>
<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not <p><strong>NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
contain SNOMED codes, as their file size would exceed 100 MB; the file
size limit of GitHub.</strong> Advice? Use R instead.</p>
<div class="section level3"> <div class="section level3">
<h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a> <h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
</h3> </h3>
<p>Our full taxonomy of microorganisms is based on the authoritative and <p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
comprehensive:</p>
<ul> <ul>
<li> <li>
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
(included version: 2019)</li>
<li> <li>
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li> <li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public
Health Information Network Vocabulary Access and Distribution System
(PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
</ul> </ul>
</div> </div>
<div class="section level3"> <div class="section level3">
@ -456,64 +431,40 @@ Health Information Network Vocabulary Access and Distribution System
<div class="section level2"> <div class="section level2">
<h2 id="microorganisms-previously-accepted-names">Microorganisms (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-previously-accepted-names"></a> <h2 id="microorganisms-previously-accepted-names">Microorganisms (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-previously-accepted-names"></a>
</h2> </h2>
<p>A data set with 14,338 rows and 4 columns, containing the following <p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<em>prevalence</em>.</p> <p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the <p>It was last updated on 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
scientific reference to the old taxonomic entries, i.e. of column
<em>‘fullname’</em>. For the scientific reference of the new names,
i.e. of column <em>‘fullname_new’</em>, see the
<code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
file</a> (0.2 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel file</a> (0.5 MB)<br>
file</a> (0.5 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain text file</a> (1 MB)<br>
text file</a> (1 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS file</a> (2.1 MB)<br>
file</a> (2.1 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS file</a> (1.3 MB)<br>
file</a> (1.3 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata file</a> (2 MB)</li>
file</a> (2 MB)</li>
</ul> </ul>
<div class="section level3"> <div class="section level3">
<h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a> <h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
</h3> </h3>
<p>This data set contains old, previously accepted taxonomic names. The <p>This data set contains old, previously accepted taxonomic names. The data sources are the same as the <code>microorganisms</code> data set:</p>
data sources are the same as the <code>microorganisms</code> data
set:</p>
<ul> <ul>
<li> <li>
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
(included version: 2019)</li>
<li> <li>
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
</ul> </ul>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a> <h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
</h3> </h3>
<p>Example rows when filtering on <em>Escherichia</em>:</p> <p>Example rows when filtering on <em>Escherichia</em>:</p>
<table style="width:100%;" class="table"> <table class="table">
<colgroup>
<col width="31%">
<col width="30%">
<col width="24%">
<col width="13%">
</colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="center">fullname</th> <th align="center">fullname</th>
<th align="center">fullname_new</th> <th align="center">fullname_new</th>
@ -546,50 +497,31 @@ Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
<div class="section level2"> <div class="section level2">
<h2 id="antibiotic-agents">Antibiotic agents<a class="anchor" aria-label="anchor" href="#antibiotic-agents"></a> <h2 id="antibiotic-agents">Antibiotic agents<a class="anchor" aria-label="anchor" href="#antibiotic-agents"></a>
</h2> </h2>
<p>A data set with 464 rows and 14 columns, containing the following <p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <p>It was last updated on 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
<em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (33 kB)<br>
file</a> (33 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel file</a> (65 kB)<br>
file</a> (65 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain text file</a> (0.1 MB)<br>
text file</a> (0.1 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS file</a> (1.8 MB)<br>
file</a> (1.8 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS file</a> (0.3 MB)<br>
file</a> (0.3 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata file</a> (0.3 MB)</li>
file</a> (0.3 MB)</li>
</ul> </ul>
<div class="section level3"> <div class="section level3">
<h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a> <h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
</h3> </h3>
<p>This data set contains all EARS-Net and ATC codes gathered from WHO <p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
and WHONET, and all compound IDs from PubChem. It also contains all
brand names (synonyms) as found on PubChem and Defined Daily Doses
(DDDs) for oral and parenteral administration.</p>
<ul> <ul>
<li> <li>
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO <a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
Collaborating Centre for Drug Statistics Methodology</a> (note: this may <li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
not be used for commercial purposes, but is freely available from the
WHO CC website for personal use)</li>
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
National Library of Medicine</a></li>
<li><a href="https://whonet.org" class="external-link">WHONET software 2019</a></li> <li><a href="https://whonet.org" class="external-link">WHONET software 2019</a></li>
</ul> </ul>
</div> </div>
@ -669,8 +601,7 @@ National Library of Medicine</a></li>
<td align="center">Beta-lactams/penicillins</td> <td align="center">Beta-lactams/penicillins</td>
<td align="center">J01CR02</td> <td align="center">J01CR02</td>
<td align="center">Beta-lactam antibacterials, penicillins</td> <td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Combinations of penicillins, incl. beta-lactamase <td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td>
inhibitors</td>
<td align="center">a/c, amcl, aml, …</td> <td align="center">a/c, amcl, aml, …</td>
<td align="center">amocla, amoclan, amoclav, …</td> <td align="center">amocla, amoclan, amoclav, …</td>
<td align="center">1.5</td> <td align="center">1.5</td>
@ -734,49 +665,31 @@ inhibitors</td>
<div class="section level2"> <div class="section level2">
<h2 id="antiviral-agents">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents"></a> <h2 id="antiviral-agents">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents"></a>
</h2> </h2>
<p>A data set with 102 rows and 9 columns, containing the following <p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <p>It was last updated on 23 July 2021 20:35:47 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
file</a> (5 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel file</a> (14 kB)<br>
file</a> (14 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain text file</a> (16 kB)<br>
text file</a> (16 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS file</a> (80 kB)<br>
file</a> (80 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS file</a> (68 kB)<br>
file</a> (68 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata file</a> (67 kB)</li>
file</a> (67 kB)</li>
</ul> </ul>
<div class="section level3"> <div class="section level3">
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a> <h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
</h3> </h3>
<p>This data set contains all ATC codes gathered from WHO and all <p>This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
compound IDs from PubChem. It also contains all brand names (synonyms)
as found on PubChem and Defined Daily Doses (DDDs) for oral and
parenteral administration.</p>
<ul> <ul>
<li> <li>
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO <a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
Collaborating Centre for Drug Statistics Methodology</a> (note: this may <li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
not be used for commercial purposes, but is freely available from the
WHO CC website for personal use)</li>
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
National Library of Medicine</a></li>
</ul> </ul>
</div> </div>
<div class="section level3"> <div class="section level3">
@ -810,8 +723,7 @@ National Library of Medicine</a></li>
<td align="center">J05AF06</td> <td align="center">J05AF06</td>
<td align="center">441300</td> <td align="center">441300</td>
<td align="center">Abacavir</td> <td align="center">Abacavir</td>
<td align="center">Nucleoside and nucleotide reverse transcriptase <td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
inhibitors</td>
<td align="center">Abacavir, Abacavir sulfate, Ziagen</td> <td align="center">Abacavir, Abacavir sulfate, Ziagen</td>
<td align="center">0.6</td> <td align="center">0.6</td>
<td align="center">g</td> <td align="center">g</td>
@ -822,8 +734,7 @@ inhibitors</td>
<td align="center">J05AB01</td> <td align="center">J05AB01</td>
<td align="center">135398513</td> <td align="center">135398513</td>
<td align="center">Aciclovir</td> <td align="center">Aciclovir</td>
<td align="center">Nucleosides and nucleotides excl. reverse <td align="center">Nucleosides and nucleotides excl. reverse transcriptase inhibitors</td>
transcriptase inhibitors</td>
<td align="center">Acicloftal, Aciclovier, Aciclovir, …</td> <td align="center">Acicloftal, Aciclovier, Aciclovir, …</td>
<td align="center">4.0</td> <td align="center">4.0</td>
<td align="center">g</td> <td align="center">g</td>
@ -834,10 +745,8 @@ transcriptase inhibitors</td>
<td align="center">J05AF08</td> <td align="center">J05AF08</td>
<td align="center">60871</td> <td align="center">60871</td>
<td align="center">Adefovir dipivoxil</td> <td align="center">Adefovir dipivoxil</td>
<td align="center">Nucleoside and nucleotide reverse transcriptase <td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
inhibitors</td> <td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, …</td>
<td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir
Dipivoxil, …</td>
<td align="center">10.0</td> <td align="center">10.0</td>
<td align="center">mg</td> <td align="center">mg</td>
<td align="center"></td> <td align="center"></td>
@ -883,39 +792,27 @@ Dipivoxil, …</td>
<div class="section level2"> <div class="section level2">
<h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a> <h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a>
</h2> </h2>
<p>A data set with 134,956 rows and 2 columns, containing the following <p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
column names:<br><em>mo</em> and <em>ab</em>.</p> <p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, <p>It was last updated on 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (78 kB)<br>
file</a> (78 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (0.9 MB)<br>
file</a> (0.9 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (5.1 MB)<br>
text file</a> (5.1 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (10.4 MB)<br>
file</a> (10.4 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (7.4 MB)<br>
file</a> (7.4 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (10.2 MB)</li>
file</a> (10.2 MB)</li>
</ul> </ul>
<div class="section level3"> <div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a> <h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
</h3> </h3>
<p>This data set contains all defined intrinsic resistance by EUCAST of <p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and 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’ v3.3</a> (2021).</p>
all bug-drug combinations, and 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’
v3.3</a> (2021).</p>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a> <h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
@ -1162,40 +1059,27 @@ v3.3</a> (2021).</p>
<div class="section level2"> <div class="section level2">
<h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a> <h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
</h2> </h2>
<p>A data set with 20,318 rows and 11 columns, containing the following <p>A data set with 20,318 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <p>It was last updated on 1 February 2022 22:08:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (39 kB)<br>
file</a> (39 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel file</a> (0.7 MB)<br>
file</a> (0.7 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.7 MB)<br>
text file</a> (1.7 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (3.6 MB)<br>
file</a> (3.6 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.2 MB)<br>
file</a> (2.2 MB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.4 MB)</li>
file</a> (3.4 MB)</li>
</ul> </ul>
<div class="section level3"> <div class="section level3">
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a> <h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
</h3> </h3>
<p>This data set contains interpretation rules for MIC values and disk <p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST (2011-2021).</p>
diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
(2011-2021).</p>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a> <h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
@ -1313,57 +1197,33 @@ diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
<div class="section level2"> <div class="section level2">
<h2 id="dosage-guidelines-from-eucast">Dosage guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-guidelines-from-eucast"></a> <h2 id="dosage-guidelines-from-eucast">Dosage guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-guidelines-from-eucast"></a>
</h2> </h2>
<p>A data set with 169 rows and 9 columns, containing the following <p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<em>dose_times</em>, <em>administration</em>, <em>notes</em>, <p>It was last updated on 23 July 2021 20:35:47 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>
file</a> (3 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel file</a> (14 kB)<br>
file</a> (14 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain text file</a> (15 kB)<br>
text file</a> (15 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS file</a> (52 kB)<br>
file</a> (52 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS file</a> (45 kB)<br>
file</a> (45 kB)<br>
</li> </li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata file</a> (44 kB)</li>
file</a> (44 kB)</li>
</ul> </ul>
<div class="section level3"> <div class="section level3">
<h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a> <h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
</h3> </h3>
<p>EUCAST breakpoints used in this package are based on the dosages in <p>EUCAST breakpoints used in this package are based on the dosages in this data set.</p>
this data set.</p> <p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v11.0</a> (2021).</p>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="example-content-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a> <h3 id="example-content-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a>
</h3> </h3>
<table class="table"> <table class="table">
<colgroup>
<col width="4%">
<col width="10%">
<col width="15%">
<col width="10%">
<col width="9%">
<col width="13%">
<col width="5%">
<col width="16%">
<col width="13%">
</colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="center">ab</th> <th align="center">ab</th>
<th align="center">name</th> <th align="center">name</th>
@ -1460,14 +1320,12 @@ Breakpoint Tables’ v11.0</a> (2021).</p>
<footer><div class="copyright"> <footer><div class="copyright">
<p></p> <p></p>
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p> <p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer> </footer>

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@ -185,13 +185,11 @@
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

31
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@ -44,7 +44,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -185,7 +189,7 @@
</header><div class="row"> </header><script src="resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>How to predict antimicrobial resistance</h1> <h1 data-toc-skip>How to predict antimicrobial resistance</h1>
@ -225,6 +229,7 @@ AMR data analysis</a>. Based on a date column, it calculates cases per
year and uses a regression model to predict antimicrobial year and uses a regression model to predict antimicrobial
resistance.</p> resistance.</p>
<p>It is basically as easy as:</p> <p>It is basically as easy as:</p>
<<<<<<< HEAD
<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> <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>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">resistance_predict</span>(<span class="at">tbl =</span> example_isolates, <span class="at">col_date =</span> <span class="st">"date"</span>, <span class="at">col_ab =</span> <span class="st">"TZP"</span>, <span class="at">model =</span> <span class="st">"binomial"</span>)</span> <span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">resistance_predict</span>(<span class="at">tbl =</span> example_isolates, <span class="at">col_date =</span> <span class="st">"date"</span>, <span class="at">col_ab =</span> <span class="st">"TZP"</span>, <span class="at">model =</span> <span class="st">"binomial"</span>)</span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span> <span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
@ -242,6 +247,22 @@ resistance.</p>
<p>When running any of these commands, a summary of the regression model <p>When running any of these commands, a summary of the regression model
will be printed unless using will be printed unless using
<code>resistance_predict(..., info = FALSE)</code>.</p> <code>resistance_predict(..., info = FALSE)</code>.</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"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true"></a><span class="kw">resistance_predict</span>(<span class="dt">tbl =</span> example_isolates, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>, <span class="dt">model =</span> <span class="st">"binomial"</span>)</span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true"></a></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true"></a><span class="co"># or:</span></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true"></a>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true"></a><span class="st"> </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true"></a> model <span class="st">"binomial"</span>)</span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true"></a></span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true"></a>predict_TZP &lt;-<span class="st"> </span>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true"></a><span class="st"> </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true"></a> <span class="dt">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>resistance_predict(..., info = FALSE)</code>.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<pre><code><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre> <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 <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 the function is a <code>data.frame</code> containing for each year: the
@ -281,9 +302,13 @@ resistance and the standard error below and above the estimation:</p>
<span class="co"># 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359</span> <span class="co"># 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359</span>
<span class="co"># 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592</span> <span class="co"># 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592</span>
<span class="co"># 31 2032 0.53574417 0.4169574 0.6545309 NA NA 0.53574417</span></code></pre></div> <span class="co"># 31 2032 0.53574417 0.4169574 0.6545309 NA NA 0.53574417</span></code></pre></div>
<<<<<<< HEAD
<p>The function <code>plot</code> is available in base R, and can be <p>The function <code>plot</code> is available in base R, and can be
extended by other packages to depend the output based on the type of extended by other packages to depend the output based on the type of
input. We extended its function to cope with resistance predictions:</p> input. We extended its function to cope with resistance predictions:</p>
=======
<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div> <code class="sourceCode R"><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p> <p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
@ -405,8 +430,12 @@ Erwin E. A. Hassing.</p>
<div class="pkgdown"> <div class="pkgdown">
<p></p> <p></p>
<<<<<<< HEAD
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</footer> </footer>

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@ -44,7 +44,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -185,7 +189,7 @@
</header><div class="row"> </header><script src="welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>Welcome to the <code>AMR</code> package</h1> <h1 data-toc-skip>Welcome to the <code>AMR</code> package</h1>
@ -293,8 +297,12 @@ Erwin E. A. Hassing.</p>
<div class="pkgdown"> <div class="pkgdown">
<p></p> <p></p>
<<<<<<< HEAD
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</footer> </footer>

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@ -269,13 +269,11 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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@ -195,75 +195,22 @@
<code>AMR</code> (for R) <img src="./logo.svg" align="right"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a> <code>AMR</code> (for R) <img src="./logo.svg" align="right"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a>
</h1></div> </h1></div>
<blockquote> <blockquote>
<p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST <p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST guideline for intrinsic resistance</a> (v3.3, October 2021) is now supported, the CLSI 2021 interpretation guideline is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021).</p>
guideline for intrinsic resistance</a> (v3.3, October 2021) is now
supported, the CLSI 2021 interpretation guideline is now supported, and
our taxonomy tables have been updated as well (LPSN, 5 October
2021).</p>
</blockquote> </blockquote>
<div class="section level3"> <div class="section level3">
<h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a> <h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a>
</h3> </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 <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>
of Antimicrobial Resistance (AMR) and to work with microbial and <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>~570 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, WHONET/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.</p>
antimicrobial data and properties, by using evidence-based methods. <p>The <code>AMR</code> package is available in <img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;"> Dutch, <img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;"> English, <img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;"> German, <img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;"> Italian, <img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;"> Portuguese, <img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;"> Spanish and <img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;"> Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
<strong>Our aim is to provide a standard</strong> for clean and <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.192486375</a>) but is <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
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>~570 antibiotic, antimycotic
and antiviral drugs</strong></a> by name and code (including ATC,
WHONET/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.</p>
<p>The <code>AMR</code> package is available in
<img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;">
Danish,
<img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;">
Dutch,
<img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;">
English,
<img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;">
French,
<img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;">
German,
<img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;">
Italian,
<img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;">
Portuguese,
<img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;">
Russian,
<img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;">
Spanish and
<img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;">
Swedish. Antimicrobial drug (group) names and colloquial microorganism
names are provided in these languages.</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.192486375</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;"> <div class="main-content" style="display: inline-block;">
<p> <p>
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <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.
<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.
</p> </p>
</div> </div>
<div class="section level5"> <div class="section level5">
<h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable <h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
</h5> </h5>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span> <code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
@ -277,12 +224,7 @@ microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-am
<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">bacteria</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">bacteria</span>,
<span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,
<span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div> <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>With only having defined a row filter on Gram-negative bacteria with <p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code>
and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on
two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and
<code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the
<code>AMR</code> package make sure you get what you meant:</p>
<table class="table"> <table class="table">
<thead><tr class="header"> <thead><tr class="header">
<th align="left">bacteria</th> <th align="left">bacteria</th>
@ -396,14 +338,9 @@ two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html"
<div class="section level4"> <div class="section level4">
<h4 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a> <h4 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>
</h4> </h4>
<p>The development of this package is part of, related to, or made <p>The development of this package is part of, related to, or made possible by:</p>
possible by:</p>
<div align="center"> <div align="center">
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
<a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a>
<a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a>
<a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a>
<a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
</div> </div>
</div> </div>
</div> </div>
@ -412,33 +349,21 @@ possible by:</p>
</h3> </h3>
<p>This package can be used for:</p> <p>This package can be used for:</p>
<ul> <ul>
<li>Reference for the taxonomy of microorganisms, since the package <li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in <li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li> <li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
<li>Interpreting raw MIC and disk diffusion values, based on the latest
CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
<li>Retrieving antimicrobial drug names, doses and forms of
administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
<li>Determining first isolates to be used for AMR data analysis (<a href="./reference/first_isolate.html">manual</a>)</li> <li>Determining first isolates to be used for AMR data analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
<li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li> <li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
<li>Determining multi-drug resistance (MDR) / multi-drug resistant <li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li> <li>Calculating (empirical) susceptibility of both mono therapy and combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
<li>Calculating (empirical) susceptibility of both mono therapy and <li>Predicting future antimicrobial resistance using regression models (<a href="./articles/resistance_predict.html">tutorial</a>)</li>
combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li> <li>Getting properties for any microorganism (like Gram stain, species, genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Predicting future antimicrobial resistance using regression models <li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
(<a href="./articles/resistance_predict.html">tutorial</a>)</li>
<li>Getting properties for any microorganism (like Gram stain, species,
genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Getting properties for any antibiotic (like name, code of
EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
<li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li> <li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li> <li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
<li>Getting SNOMED codes of a microorganism, or getting properties of a <li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li> <li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
<li>Getting LOINC codes of an antibiotic, or getting properties of an <li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to
translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
<li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li> <li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
</ul> </ul>
</div> </div>
@ -449,24 +374,17 @@ translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/d
<h4 id="latest-released-version">Latest released version<a class="anchor" aria-label="anchor" href="#latest-released-version"></a> <h4 id="latest-released-version">Latest released version<a class="anchor" aria-label="anchor" href="#latest-released-version"></a>
</h4> </h4>
<p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p> <p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R <p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
network (CRAN)</a>. Install this package in R from CRAN by using the
command:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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">"AMR"</span><span class="op">)</span></code></pre></div> <code class="sourceCode R"><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">"AMR"</span><span class="op">)</span></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click <p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type <p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
in “AMR” and press <kbd>Install</kbd>.</p>
<p><strong>Note:</strong> Not all functions on this website may be
available in this latest release. To use all functions and data sets
mentioned on this website, install the latest development version.</p>
</div> </div>
<div class="section level4"> <div class="section level4">
<h4 id="latest-development-version">Latest development version<a class="anchor" aria-label="anchor" href="#latest-development-version"></a> <h4 id="latest-development-version">Latest development version<a class="anchor" aria-label="anchor" href="#latest-development-version"></a>
</h4> </h4>
<p><a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p> <p><a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p>
<p>The latest and unpublished development version can be installed from <p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
GitHub in two ways:</p>
<ol style="list-style-type: decimal"> <ol style="list-style-type: decimal">
<li> <li>
<p>Manually, using:</p> <p>Manually, using:</p>
@ -475,16 +393,11 @@ GitHub in two ways:</p>
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div> <span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
</li> </li>
<li> <li>
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe <p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our
R-universe address</a> to your list of repositories (‘repos’):</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>, <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div> msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>After this, you can install and update this <code>AMR</code> package <p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em> &gt; <em>Check for Package Updates…</em>).</p>
like any official release (e.g., using
<code>install.packages("AMR")</code> or in RStudio via <em>Tools</em>
&gt; <em>Check for Package Updates…</em>).</p>
</li> </li>
</ol> </ol>
<p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz" class="external-link uri">https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz</a></p> <p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz" class="external-link uri">https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz</a></p>
@ -493,8 +406,7 @@ like any official release (e.g., using
<div class="section level3"> <div class="section level3">
<h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a> <h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a>
</h3> </h3>
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or <p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="short-introduction">Short introduction<a class="anchor" aria-label="anchor" href="#short-introduction"></a> <h3 id="short-introduction">Short introduction<a class="anchor" aria-label="anchor" href="#short-introduction"></a>
@ -502,181 +414,66 @@ click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How t
<div class="section level4"> <div class="section level4">
<h4 id="microbial-taxonomic-reference-data">Microbial (taxonomic) reference data<a class="anchor" aria-label="anchor" href="#microbial-taxonomic-reference-data"></a> <h4 id="microbial-taxonomic-reference-data">Microbial (taxonomic) reference data<a class="anchor" aria-label="anchor" href="#microbial-taxonomic-reference-data"></a>
</h4> </h4>
<p>This package contains the complete taxonomic tree of almost all <p>This package contains the complete taxonomic tree of almost all ~70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>), supplemented by 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/Sp2000/colplus" class="external-link">CoL+ project</a> is finished, which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
~70,000 microorganisms from the authoritative and comprehensive
Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>),
supplemented by 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/Sp2000/colplus" class="external-link">CoL+ project</a> is finished,
which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be
checked which version of the CoL is included in this package.</p>
<p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p> <p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
</div> </div>
<div class="section level4"> <div class="section level4">
<h4 id="antimicrobial-reference-data">Antimicrobial reference data<a class="anchor" aria-label="anchor" href="#antimicrobial-reference-data"></a> <h4 id="antimicrobial-reference-data">Antimicrobial reference data<a class="anchor" aria-label="anchor" href="#antimicrobial-reference-data"></a>
</h4> </h4>
<p>This package contains <strong>all ~550 antibiotic, antimycotic and <p>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, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals Community Register of the European Commission</a>.</p>
antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) <p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the
World Health Organization Collaborating Centre for Drug Statistics
Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals
Community Register of the European Commission</a>.</p>
<p><strong>NOTE: The WHOCC copyright does not allow use for commercial
purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
<p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p> <p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
</div> </div>
<div class="section level4"> <div class="section level4">
<h4 id="whonet--ears-net">WHONET / EARS-Net<a class="anchor" aria-label="anchor" href="#whonet--ears-net"></a> <h4 id="whonet--ears-net">WHONET / EARS-Net<a class="anchor" aria-label="anchor" href="#whonet--ears-net"></a>
</h4> </h4>
<p>We support WHONET and EARS-Net data. Exported files from WHONET can <p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
be imported into R and can be analysed easily using this package. For <p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a>
with the exact same structure as a WHONET export file. Furthermore, this
package also contains a <a href="./reference/antibiotics.html">data set
antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows
almost all WHONET abbreviations for microorganisms. When using WHONET
data as input for analysis, all input parameters will be set
automatically.</p>
<p>Read our tutorial about <a href="./articles/WHONET.html">how to work
with WHONET data here</a>.</p>
</div> </div>
<div class="section level4"> <div class="section level4">
<h4 id="overview-of-functions">Overview of functions<a class="anchor" aria-label="anchor" href="#overview-of-functions"></a> <h4 id="overview-of-functions">Overview of functions<a class="anchor" aria-label="anchor" href="#overview-of-functions"></a>
</h4> </h4>
<p>The <code>AMR</code> package basically does four important <p>The <code>AMR</code> package basically does four important things:</p>
things:</p>
<ol style="list-style-type: decimal"> <ol style="list-style-type: decimal">
<li> <li>
<p>It <strong>cleanses existing data</strong> by providing new <p>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use intelligent rules to guess results that you would expect:</p>
<em>classes</em> for microoganisms, antibiotics and antimicrobial
results (both S/I/R and MIC). By installing this package, you teach R
everything about microbiology that is needed for analysis. These
functions all use intelligent rules to guess results that you would
expect:</p>
<ul> <ul>
<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human <li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AURS”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> <li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial IDs, these IDs are also human readable based on those used by EARS-Net. For example, the ID of amoxicillin is <code>AMX</code> and the ID of gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also uses intelligent rules to find results like accepting misspelling, trade names and abbrevations used in many laboratory systems. For instance, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine. To accomplish this, the package contains a database with most LIS codes, official names, trade names, ATC codes, defined daily doses (DDD) and drug categories of antibiotics.</li>
is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S. <li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on raw MIC values (in mg/L) or disk diffusion values (in mm), or transform existing values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
aureus</em> is “B_STPHY_AURS”. The function takes almost any text as <li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result in “&lt;=0.002”.</li>
input that looks like the name or code of a microorganism like “E.
coli”, “esco” or “esccol” and tries to find expected results using
intelligent rules combined with the included Catalogue of Life data set.
It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group
<em>Staphylococci</em> into coagulase negative and positive (CoNS and
CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can
categorise <em>Streptococci</em> into Lancefield groups (like
beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial
IDs, these IDs are also human readable based on those used by EARS-Net.
For example, the ID of amoxicillin is <code>AMX</code> and the ID of
gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also
uses intelligent rules to find results like accepting misspelling, trade
names and abbrevations used in many laboratory systems. For instance,
the values “Furabid”, “Furadantin”, “nitro” all return the ID of
Nitrofurantoine. To accomplish this, the package contains a database
with most LIS codes, official names, trade names, ATC codes, defined
daily doses (DDD) and drug categories of antibiotics.</li>
<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on
raw MIC values (in mg/L) or disk diffusion values (in mm), or transform
existing values to valid antimicrobial results. It produces just S, I or
R based on your input and warns about invalid values. Even values like
“&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a
so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values
as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result
in “&lt;=0.002”.</li>
</ul> </ul>
</li> </li>
<li> <li>
<p>It <strong>enhances existing data</strong> and <strong>adds new <p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
data</strong> from data sets included in this package.</p>
<ul> <ul>
<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST <li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST expert rules to isolates</a> (not the translation from MIC to R/SI values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
expert rules to isolates</a> (not the translation from MIC to R/SI <li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of
every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using
guidelines from the CLSI</a> (Clinical and Laboratory Standards
Institute).
<ul> <ul>
<li>You can also identify first <em>weighted</em> isolates of every <li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
patient, an adjusted version of the CLSI guideline. This takes into
account key antibiotics of every strain and compares them.</li>
</ul> </ul>
</li> </li>
<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are <li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos <em>et al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID 21793988</a>), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.</li>
multi-drug resistant organisms (MDRO). It supports a variety of <li>The <a href="./reference/microorganisms.html">data set microorganisms</a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any SNOMED CT code associated with a microorganism. As all these function use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code>mo_genus("MRSA")</code> and <code>mo_genus("S. aureus")</code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Danish, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
international guidelines, such as the MDR-paper by Magiorakos <em>et <li>The <a href="./reference/antibiotics.html">data set antibiotics</a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, LOINC code, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>, <code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code>ab_name("Fluclox")</code>, <code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID
21793988</a>), the exceptional phenotype definitions of EUCAST and the
WHO guideline on multi-drug resistant TB. It also supports the national
guidelines of the Netherlands and Germany.</li>
<li>The <a href="./reference/microorganisms.html">data set
microorganisms</a> contains the complete taxonomic tree of ~70,000
microorganisms. Furthermore, some colloquial names and all Gram stains
are available, which enables resistance analysis of e.g. different
antibiotics per Gram stain. The package also contains functions to look
up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>,
<code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even
<code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any
SNOMED CT code associated with a microorganism. As all these function
use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent
rules for determination. For example, <code>mo_genus("MRSA")</code> and
<code>mo_genus("S. aureus")</code> will both return
<code>"Staphylococcus"</code>. They also come with support for German,
Danish, Dutch, Spanish, Italian, French and Portuguese. These functions
can be used to add new variables to your data.</li>
<li>The <a href="./reference/antibiotics.html">data set antibiotics</a>
contains ~450 antimicrobial drugs with their EARS-Net code, ATC code,
PubChem compound ID, LOINC code, official name, common LIS codes and
DDDs of both oral and parenteral administration. It also contains all
(thousands of) trade names found in PubChem. Use functions like
<code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>,
<code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up
values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code>
internally so they support the same intelligent rules to guess the most
probable result. For example, <code>ab_name("Fluclox")</code>,
<code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code>
will all return <code>"Flucloxacillin"</code>. These functions can again
be used to add new variables to your data.</li>
</ul> </ul>
</li> </li>
<li> <li>
<p>It <strong>analyses the data</strong> with convenient functions <p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
that use well-known methods.</p>
<ul> <ul>
<li>Calculate the microbial susceptibility or resistance (and even <li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
<code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
<code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>,
<code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and
<code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of
isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>,
<code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions.
All these functions can be used with the <code>dplyr</code> package
(e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for
the <code>ggplot2</code> package</li>
<li>Predict antimicrobial resistance for the nextcoming years using
logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code>
function</li>
</ul> </ul>
</li> </li>
<li> <li>
<p>It <strong>teaches the user</strong> how to use all the above <p>It <strong>teaches the user</strong> how to use all the above actions.</p>
actions.</p>
<ul> <ul>
<li>Aside from this website with many tutorials, the package itself <li>Aside from this website with many tutorials, the package itself contains extensive help pages with many examples for all functions.</li>
contains extensive help pages with many examples for all functions.</li>
<li>The package also contains example data sets: <li>The package also contains example data sets:
<ul> <ul>
<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code> <li>The <a href="./reference/example_isolates.html"><code>example_isolates</code> data set</a>. This data set contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis.</li>
data set</a>. This data set contains 2,000 microbial isolates with their <li>The <a href="./reference/WHONET.html"><code>WHONET</code> data set</a>. This data set only contains fake data, but with the exact same structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
full antibiograms. It reflects reality and can be used to practice AMR
data analysis.</li>
<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data
set</a>. This data set only contains fake data, but with the exact same
structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
</ul> </ul>
</li> </li>
</ul> </ul>
@ -687,9 +484,7 @@ structure as files exported by WHONET. Read more about WHONET <a href="./article
<div class="section level3"> <div class="section level3">
<h3 id="copyright">Copyright<a class="anchor" aria-label="anchor" href="#copyright"></a> <h3 id="copyright">Copyright<a class="anchor" aria-label="anchor" href="#copyright"></a>
</h3> </h3>
<p>This R package is free, open-source software and licensed under the <p>This R package is free, open-source software and licensed under the <a href="./LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. In a nutshell, this means that this package:</p>
<a href="./LICENSE-text.html">GNU General Public License v2.0
(GPL-2)</a>. In a nutshell, this means that this package:</p>
<ul> <ul>
<li><p>May be used for commercial purposes</p></li> <li><p>May be used for commercial purposes</p></li>
<li><p>May be used for private purposes</p></li> <li><p>May be used for private purposes</p></li>
@ -697,18 +492,15 @@ structure as files exported by WHONET. Read more about WHONET <a href="./article
<li> <li>
<p>May be modified, although:</p> <p>May be modified, although:</p>
<ul> <ul>
<li>Modifications <strong>must</strong> be released under the same <li>Modifications <strong>must</strong> be released under the same license when distributing the package</li>
license when distributing the package</li>
<li>Changes made to the code <strong>must</strong> be documented</li> <li>Changes made to the code <strong>must</strong> be documented</li>
</ul> </ul>
</li> </li>
<li> <li>
<p>May be distributed, although:</p> <p>May be distributed, although:</p>
<ul> <ul>
<li>Source code <strong>must</strong> be made available when the package <li>Source code <strong>must</strong> be made available when the package is distributed</li>
is distributed</li> <li>A copy of the license and copyright notice <strong>must</strong> be included with the package.</li>
<li>A copy of the license and copyright notice <strong>must</strong> be
included with the package.</li>
</ul> </ul>
</li> </li>
<li><p>Comes with a LIMITATION of liability</p></li> <li><p>Comes with a LIMITATION of liability</p></li>
@ -764,14 +556,12 @@ included with the package.</li>
<footer><div class="copyright"> <footer><div class="copyright">
<p></p> <p></p>
<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p> <p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer> </footer>

114
docs/news/index.html
View File

@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -157,6 +161,7 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<<<<<<< HEAD
<h2 class="page-header" data-toc-text="1.8.1" id="amr-181"> <h2 class="page-header" data-toc-text="1.8.1" id="amr-181">
<code>AMR</code> 1.8.1<a class="anchor" aria-label="anchor" href="#amr-181"></a></h2> <code>AMR</code> 1.8.1<a class="anchor" aria-label="anchor" href="#amr-181"></a></h2>
<p>All functions in this package are considered to be stable. Updates to <p>All functions in this package are considered to be stable. Updates to
@ -174,6 +179,19 @@ for I (‘susceptible dose-dependent’)</p></li>
<li> <li>
<p>Improved algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code>, especially for <p>Improved algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code>, especially for
ignoring non-taxonomic text, such as:</p> ignoring non-taxonomic text, such as:</p>
=======
<h2 class="page-header" data-toc-text="1.8.0.9005" id="amr-1809005">
<code>AMR</code> 1.8.0.9005<a class="anchor" aria-label="anchor" href="#amr-1809005"></a></h2>
<div class="section level3">
<h3 id="last-updated-march-1-8-0-9005"><small>Last updated: 10 March 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-march-1-8-0-9005"></a></h3>
<p>All functions in this package are 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.</p>
<div class="section level4">
<h4 id="changed-1-8-0-9005">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9005"></a></h4>
<ul><li><p>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on values containing capped values (such as <code>&gt;=</code>), sometimes leading to <code>NA</code></p></li>
<li><p>Support for antibiotic interpretations of the MIPS laboratory system: <code>"U"</code> for S (‘susceptible urine’), <code>"D"</code> for I (‘susceptible dose-dependent’)</p></li>
<li>
<p>Improved algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code>, especially for ignoring non-taxonomic text, such as:</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="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">"methicillin-resistant S. aureus (MRSA)"</span><span class="op">)</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"methicillin-resistant S. aureus (MRSA)"</span><span class="op">)</span>
@ -184,7 +202,11 @@ ignoring non-taxonomic text, such as:</p>
<li><p>Updated MIC printing in tibbles</p></li> <li><p>Updated MIC printing in tibbles</p></li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<<<<<<< HEAD
<h4 id="other-1-8-1">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1"></a></h4> <h4 id="other-1-8-1">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1"></a></h4>
=======
<h4 id="other-1-8-0-9005">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9005"></a></h4>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<ul><li>Fix for unit testing on R 3.3</li> <ul><li>Fix for unit testing on R 3.3</li>
<li>Fix for size of some image elements, as requested by CRAN</li> <li>Fix for size of some image elements, as requested by CRAN</li>
</ul></div> </ul></div>
@ -366,6 +388,7 @@ guideline</li>
<code><a href="../reference/random.html">random_mic()</a></code> <code><a href="../reference/random.html">random_mic()</a></code>
</li> </li>
<li>Improved plot legends for MICs and disk diffusion values</li> <li>Improved plot legends for MICs and disk diffusion values</li>
<<<<<<< HEAD
<li>Improved speed of <code><a href="../reference/as.ab.html">as.ab()</a></code> and all <code>ab_*()</code> <li>Improved speed of <code><a href="../reference/as.ab.html">as.ab()</a></code> and all <code>ab_*()</code>
functions</li> functions</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>Added <code><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify()</a></code> extensions for plotting methods</li>
@ -392,6 +415,19 @@ change.</li>
<li> <li>
<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 <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> cope with <code>NA</code>s</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><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>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code> and <code>&lt;rsi&gt;</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>
<li>The <code><a href="../reference/mdro.html">mdro()</a></code> function now returns <code>NA</code> for all rows that have no test results</li>
<li>The <code>species_id</code> column in the <code>microorganisms</code> data set now only contains LPSN record numbers. For this reason, this column is now numeric instead of a character, and <code><a href="../reference/mo_property.html">mo_url()</a></code> has been updated to reflect this change.</li>
<li>Fixed a small bug in the 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>
</li>
<li>
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="other-1-8-0">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0"></a></h4> <h4 id="other-1-8-0">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0"></a></h4>
@ -480,12 +516,17 @@ deprecated.</li>
<code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> functions has been completely <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> functions has been completely
rewritten.</li> rewritten.</li>
</ul></li> </ul></li>
<<<<<<< HEAD
<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column <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 selector and function <code>filter_betalactams()</code> as additional
antbiotic column filter. The group of betalactams consists of all antbiotic column filter. The group of betalactams consists of all
carbapenems, cephalosporins and penicillins.</li> carbapenems, cephalosporins and penicillins.</li>
<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> method for <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> <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
=======
<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><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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</li> </li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
@ -538,6 +579,7 @@ throw an error</li>
when the <code>vctrs</code> package is loaded (i.e., when using when the <code>vctrs</code> package is loaded (i.e., when using
tidyverse)</li> tidyverse)</li>
<li>Colour fix for using <code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code> on an RSI class</li> <li>Colour fix for using <code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code> on an RSI class</li>
<<<<<<< HEAD
<li>Added 25 common system codes for bacteria to the <li>Added 25 common system codes for bacteria to the
<code>microorganisms.codes</code> data set</li> <code>microorganisms.codes</code> data set</li>
<li>Added 16 common system codes for antimicrobial agents to the <li>Added 16 common system codes for antimicrobial agents to the
@ -547,6 +589,12 @@ tidyverse)</li>
<code>dplyr</code> v1.0.6</li> <code>dplyr</code> v1.0.6</li>
<li>Updated <code><a href="https://docs.ropensci.org/skimr/reference/skim.html" class="external-link">skimr::skim()</a></code> usage for MIC values to also <li>Updated <code><a href="https://docs.ropensci.org/skimr/reference/skim.html" class="external-link">skimr::skim()</a></code> usage for MIC values to also
include 25th and 75th percentiles</li> include 25th and 75th percentiles</li>
=======
<li>Added 25 common system codes for bacteria to the <code>microorganisms.codes</code> data set</li>
<li>Added 16 common system codes for antimicrobial agents to the <code>antibiotics</code> data set</li>
<li>Fix for using <code>skimr::skim()</code> on classes <code>mo</code>, <code>mic</code> and <code>disk</code> when using the just released <code>dplyr</code> v1.0.6</li>
<li>Updated <code>skimr::skim()</code> usage for MIC values to also include 25th and 75th percentiles</li>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<li>Fix for plotting missing MIC/disk diffusion values</li> <li>Fix for plotting missing MIC/disk diffusion values</li>
<li>Updated join functions to always use <code>dplyr</code> join <li>Updated join functions to always use <code>dplyr</code> join
functions if the <code>dplyr</code> package is installed - now also functions if the <code>dplyr</code> package is installed - now also
@ -625,11 +673,16 @@ function) to select/filter on e.g. linezolid and tedizolid</p>
<span class="va">x</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">filter_oxazolidinones</span><span class="op">(</span><span class="op">)</span> <span class="va">x</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu">filter_oxazolidinones</span><span class="op">(</span><span class="op">)</span>
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div> <span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li> </li>
<<<<<<< HEAD
<li><p>Support for custom MDRO guidelines, using the new <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">custom_mdro_guideline()</a></code> function, please see
<code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li> <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> generics for classes <li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> generics for classes
<code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li> <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></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><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<li> <li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a <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 microorganism is a member of the taxonomic class Saccharomycetes or the
@ -686,6 +739,7 @@ synomyms</li>
to <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> to <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a>
</li> </li>
</ul></li> </ul></li>
<<<<<<< HEAD
<li>Big update for plotting classes <code>rsi</code>, <li>Big update for plotting classes <code>rsi</code>,
<code>&lt;mic&gt;</code>, and <code>&lt;disk&gt;</code>: <code>&lt;mic&gt;</code>, and <code>&lt;disk&gt;</code>:
<ul><li>Plotting of MIC and disk diffusion values now support interpretation <ul><li>Plotting of MIC and disk diffusion values now support interpretation
@ -699,6 +753,13 @@ translated if the system language is German, Dutch or Spanish (see
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and <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 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> diffusion values</li>
=======
<li>Big update for plotting classes <code>rsi</code>, <code>&lt;mic&gt;</code>, and <code>&lt;disk&gt;</code>:
<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><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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</ul></li> </ul></li>
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September <li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September
2020 and added the source to the help page of the 2020 and added the source to the help page of the
@ -1266,6 +1327,7 @@ 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 settings where the resources are very limited. Fewer dependencies on
newer software is helpful for such settings.</p> newer software is helpful for such settings.</p>
<p>Negative effects of this change are:</p> <p>Negative effects of this change are:</p>
<<<<<<< HEAD
<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 <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>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> <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>
@ -1282,6 +1344,12 @@ slower when running on hundreds of thousands of rows.</del></li>
also inherit class <code>character</code>, to support any data also inherit class <code>character</code>, to support any data
transformation. This change invalidates code that checks for class transformation. This change invalidates code that checks for class
length == 1.</li> length == 1.</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>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</ul></li> </ul></li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
@ -1694,6 +1762,7 @@ data integrity, this means that invalid assignments will now result in
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="st">"testvalue"</span> <span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="st">"testvalue"</span>
<span class="co">#&gt; Warning message:</span> <span class="co">#&gt; Warning message:</span>
<span class="co">#&gt; invalid microorganism code, NA generated</span></code></pre></div> <span class="co">#&gt; invalid microorganism code, NA generated</span></code></pre></div>
<<<<<<< HEAD
<p>This is important, because a value like <code>"testvalue"</code> <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 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> class would suggest a valid microbial code.</p>
@ -1705,6 +1774,12 @@ re-exported from the <code>clean</code> package (which will be installed
automatically upon updating this <code>AMR</code> package).</p></li> automatically upon updating this <code>AMR</code> package).</p></li>
<li><p>Renamed data set <code>septic_patients</code> to <li><p>Renamed data set <code>septic_patients</code> to
<code>example_isolates</code></p></li> <code>example_isolates</code></p></li>
=======
<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><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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="new-0-8-0">New<a class="anchor" aria-label="anchor" href="#new-0-8-0"></a></h4> <h4 id="new-0-8-0">New<a class="anchor" aria-label="anchor" href="#new-0-8-0"></a></h4>
@ -2053,6 +2128,7 @@ be viewed here</a>
<code>caption</code>, <code>x.title</code> and <code>y.title</code> to <code>caption</code>, <code>x.title</code> and <code>y.title</code> to
set titles and axis descriptions</li> set titles and axis descriptions</li>
</ul></li> </ul></li>
<<<<<<< HEAD
<li>Improved intelligence of looking up antibiotic columns in a data set <li>Improved intelligence of looking up antibiotic columns in a data set
using <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> using <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
</li> </li>
@ -2071,6 +2147,14 @@ since it uses <code><a href="../reference/count.html">count_df()</a></code> inte
<li>Removed deprecated functions <code>guess_mo()</code>, <li>Removed deprecated functions <code>guess_mo()</code>,
<code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>,
<code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code> <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
=======
<li>Improved intelligence of looking up antibiotic columns in a data set using <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
</li>
<li>Added ~5,000 more old taxonomic names to the <code>microorganisms.old</code> data set, which leads to better results finding when using the <code><a href="../reference/as.mo.html">as.mo()</a></code> function</li>
<li>This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as ‘increased exposure’ and not ‘intermediate’ anymore. For functions like <code>portion_df()</code> and <code><a href="../reference/count.html">count_df()</a></code> this means that their new argument <code>combine_SI</code> is TRUE at default. Our plotting function <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> also reflects this change since it uses <code><a href="../reference/count.html">count_df()</a></code> internally.</li>
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</li> </li>
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></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> <ul><li><p>speed improvement for microbial IDs</p></li>
@ -2097,10 +2181,15 @@ be viewed here</a>
</li> </li>
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em> <li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li> </li>
<<<<<<< HEAD
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let <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> groups of fives and tens end with 100+ instead of 120+</li>
<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 <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> <code>NA</code>
=======
<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><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> for when all values are <code>NA</code>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</li> </li>
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</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> <li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@ -2455,6 +2544,7 @@ frequency tables of function outcomes:</p>
<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">%&gt;%</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">%&gt;%</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_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>
<<<<<<< HEAD
<li><p>Header info is now available as a list, with the <li><p>Header info is now available as a list, with the
<code>header</code> function</p></li> <code>header</code> function</p></li>
<li><p>The argument <code>header</code> is now set to <code>TRUE</code> <li><p>The argument <code>header</code> is now set to <code>TRUE</code>
@ -2473,6 +2563,16 @@ like <code>format</code> defaults to
levels when input is a factor</p></li> levels when input is a factor</p></li>
<li><p>Factor levels will be in header when present in input data <li><p>Factor levels will be in header when present in input data
(maximum of 5)</p></li> (maximum of 5)</p></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>
<li><p>Added header info for class <code>mo</code> to show unique count of families, genera and species</p></li>
<li><p>Now honours the <code>decimal.mark</code> setting, which just like <code>format</code> defaults to <code>getOption("OutDec")</code></p></li>
<li><p>The new <code>big.mark</code> argument will at default be <code>","</code> when <code>decimal.mark = "."</code> and <code>"."</code> otherwise</p></li>
<li><p>Fix for header text where all observations are <code>NA</code></p></li>
<li><p>New argument <code>droplevels</code> to exclude empty factor levels when input is a factor</p></li>
<li><p>Factor levels will be in header when present in input data (maximum of 5)</p></li>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<li><p>Fix for using <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select()</a></code> on frequency tables</p></li> <li><p>Fix for using <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select()</a></code> on frequency tables</p></li>
</ul></li> </ul></li>
<li>Function <code><a href="../reference/ggplot_rsi.html">scale_y_percent()</a></code> now contains the <li>Function <code><a href="../reference/ggplot_rsi.html">scale_y_percent()</a></code> now contains the
@ -2563,6 +2663,7 @@ now supports genus abbreviations with “species” attached</p>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S. spp"</span><span class="op">)</span> <span class="co"># B_STPHY</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S. spp"</span><span class="op">)</span> <span class="co"># B_STPHY</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. species"</span><span class="op">)</span> <span class="co"># "Staphylococcus species"</span></code></pre></div> <span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. species"</span><span class="op">)</span> <span class="co"># "Staphylococcus species"</span></code></pre></div>
</li> </li>
<<<<<<< HEAD
<li><p>Added argument <code>combine_IR</code> (TRUE/FALSE) to functions <li><p>Added argument <code>combine_IR</code> (TRUE/FALSE) to functions
<code>portion_df</code> and <code>count_df</code>, to indicate that all <code>portion_df</code> and <code>count_df</code>, to indicate that all
values of I and R must be merged into one, so the output only consists values of I and R must be merged into one, so the output only consists
@ -2579,6 +2680,13 @@ total available isolate is below argument <code>minimum</code></p></li>
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <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 <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not
set package name as attribute anymore</p></li> set package name as attribute anymore</p></li>
=======
<li><p>Added argument <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</p></li>
<li><p>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</p></li>
<li><p>Added argument <code>also_single_tested</code> for <code>portion_*</code> and <code>count_*</code> functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see <code><a href="../reference/proportion.html">?portion</a></code></p></li>
<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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<li> <li>
<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></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> <ul><li>
@ -2620,12 +2728,18 @@ input when arguments are left blank</p></li>
<code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>)
to comply with CRAN policy to only allow ASCII characters</p></li> 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>mo_property</code> not working properly</p></li>
<<<<<<< HEAD
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would <li><p>Fix for <code>eucast_rules</code> where some Streptococci would
become ceftazidime R in EUCAST rule 4.5</p></li> become ceftazidime R in EUCAST rule 4.5</p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <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> <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 <li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have
<code>breaks</code> argument</p></li> <code>breaks</code> argument</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><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>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
<li> <li>
<p>AI improvements for <code>as.mo</code>:</p> <p>AI improvements for <code>as.mo</code>:</p>
<ul><li> <ul><li>

8
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@ -1,4 +1,8 @@
<<<<<<< HEAD
pandoc: 2.17.1.1 pandoc: 2.17.1.1
=======
pandoc: 2.9.2.1
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
pkgdown: 2.0.2 pkgdown: 2.0.2
pkgdown_sha: ~ pkgdown_sha: ~
articles: articles:
@ -12,7 +16,11 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
<<<<<<< HEAD
last_built: 2022-03-14T15:33Z last_built: 2022-03-14T15:33Z
=======
last_built: 2022-03-12T18:42Z
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

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@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>

8
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@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -226,8 +230,12 @@ Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<<<<<<< HEAD
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</footer></div> </footer></div>

4
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@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>

8
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@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -220,8 +224,12 @@ Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<<<<<<< HEAD
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</footer></div> </footer></div>

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@ -275,13 +275,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
docs/reference/ab_property.html
View File

@ -344,13 +344,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
docs/reference/age.html
View File

@ -226,13 +226,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
docs/reference/age_groups.html
View File

@ -250,13 +250,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
docs/reference/antibiotic_class_selectors.html
View File

@ -430,13 +430,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

4
docs/reference/antibiotics.html
View File

@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>

6
docs/reference/as.ab.html
View File

@ -280,13 +280,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
docs/reference/as.disk.html
View File

@ -239,13 +239,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
docs/reference/as.mic.html
View File

@ -273,13 +273,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
docs/reference/as.mo.html
View File

@ -377,13 +377,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

8
docs/reference/as.rsi.html
View File

@ -334,7 +334,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<span class="co"># \donttest{</span> <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://docs.ropensci.org/skimr/" class="external-link">"skimr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</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://docs.ropensci.org/skimr/" class="external-link">"skimr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
<span class="co"># class &lt;rsi&gt; supported in skim() too:</span> <span class="co"># class &lt;rsi&gt; supported in skim() too:</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/skim.html" class="external-link">skim</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span> <span class="fu">skim</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
<span class="op">}</span> <span class="op">}</span>
<span class="co"># }</span> <span class="co"># }</span>
<span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span> <span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span>
@ -423,13 +423,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
docs/reference/atc_online.html
View File

@ -257,13 +257,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
docs/reference/availability.html
View File

@ -216,13 +216,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
docs/reference/bug_drug_combinations.html
View File

@ -265,13 +265,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

4
docs/reference/catalogue_of_life.html
View File

@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>

4
docs/reference/catalogue_of_life_version.html
View File

@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>

6
docs/reference/count.html
View File

@ -358,13 +358,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
docs/reference/custom_eucast_rules.html
View File

@ -301,13 +301,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

8
docs/reference/dosage.html
View File

@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -207,8 +211,12 @@ Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<<<<<<< HEAD
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</footer></div> </footer></div>

6
docs/reference/eucast_rules.html
View File

@ -334,13 +334,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

8
docs/reference/example_isolates.html
View File

@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -204,8 +208,12 @@ Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<<<<<<< HEAD
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</footer></div> </footer></div>

8
docs/reference/example_isolates_unclean.html
View File

@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -199,8 +203,12 @@ Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<<<<<<< HEAD
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</footer></div> </footer></div>

6
docs/reference/first_isolate.html
View File

@ -371,13 +371,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

4
docs/reference/g.test.html
View File

@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>

6
docs/reference/get_episode.html
View File

@ -278,13 +278,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
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@ -304,13 +304,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
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@ -395,13 +395,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
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@ -243,13 +243,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

47
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@ -157,10 +157,7 @@
<table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2"> <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2">
<h2 id="preparing-data-microorganisms">Preparing data: microorganisms <a href="#preparing-data-microorganisms" class="anchor" aria-hidden="true"></a></h2> <h2 id="preparing-data-microorganisms">Preparing data: microorganisms <a href="#preparing-data-microorganisms" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>These functions are meant to get taxonomically valid properties of <p class="section-desc"></p><p>These functions are meant to get taxonomically valid properties of microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach this package how to translate your own codes to valid microorganism codes.</p>
microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach
this package how to translate your own codes to valid microorganism
codes.</p>
</th> </th>
</tr></tbody><tbody><tr><td> </tr></tbody><tbody><tr><td>
<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p> <p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
@ -176,9 +173,7 @@ codes.</p>
<td><p>User-Defined Reference Data Set for Microorganisms</p></td> <td><p>User-Defined Reference Data Set for Microorganisms</p></td>
</tr></tbody><tbody><tr><th colspan="2"> </tr></tbody><tbody><tr><th colspan="2">
<h2 id="preparing-data-antibiotics">Preparing data: antibiotics <a href="#preparing-data-antibiotics" class="anchor" aria-hidden="true"></a></h2> <h2 id="preparing-data-antibiotics">Preparing data: antibiotics <a href="#preparing-data-antibiotics" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>Use these functions to get valid properties of antibiotics from any <p class="section-desc"></p><p>Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p>
input or to clean your input. You can even retrieve drug names and doses
from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p>
</th> </th>
</tr></tbody><tbody><tr><td> </tr></tbody><tbody><tr><td>
<p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p> <p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p>
@ -198,13 +193,7 @@ from clinical text records, using <code><a href="../reference/ab_from_text.html"
<td><p>Get ATC Properties from WHOCC Website</p></td> <td><p>Get ATC Properties from WHOCC Website</p></td>
</tr></tbody><tbody><tr><th colspan="2"> </tr></tbody><tbody><tr><th colspan="2">
<h2 id="preparing-data-antimicrobial-resistance">Preparing data: antimicrobial resistance <a href="#preparing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></a></h2> <h2 id="preparing-data-antimicrobial-resistance">Preparing data: antimicrobial resistance <a href="#preparing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can <p class="section-desc"></p><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p>
transform your raw input to valid MIC or disk diffusion values. Use
<code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”,
“I” and “S”, or to interpret MIC or disk diffusion values as R/SI based
on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend
antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p>
</th> </th>
</tr></tbody><tbody><tr><td> </tr></tbody><tbody><tr><td>
<p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">NA_rsi_</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p> <p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">NA_rsi_</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p>
@ -228,14 +217,7 @@ rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a>
<td><p>Define Custom EUCAST Rules</p></td> <td><p>Define Custom EUCAST Rules</p></td>
</tr></tbody><tbody><tr><th colspan="2"> </tr></tbody><tbody><tr><th colspan="2">
<h2 id="analysing-data-antimicrobial-resistance">Analysing data: antimicrobial resistance <a href="#analysing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></a></h2> <h2 id="analysing-data-antimicrobial-resistance">Analysing data: antimicrobial resistance <a href="#analysing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>Use these function for the analysis part. You can use <p class="section-desc"></p><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
<code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any
antibiotic column. Be sure to first select the isolates that are
appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or
<code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain
resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>,
<code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant
microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
</th> </th>
</tr></tbody><tbody><tr><td> </tr></tbody><tbody><tr><td>
<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p> <p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
@ -287,9 +269,7 @@ microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).
<td><p>Guess Antibiotic Column</p></td> <td><p>Guess Antibiotic Column</p></td>
</tr></tbody><tbody><tr><th colspan="2"> </tr></tbody><tbody><tr><th colspan="2">
<h2 id="background-information-on-included-data">Background information on included data <a href="#background-information-on-included-data" class="anchor" aria-hidden="true"></a></h2> <h2 id="background-information-on-included-data">Background information on included data <a href="#background-information-on-included-data" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>Some pages about our package and its external sources. Be sure to <p class="section-desc"></p><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p>
read our <a href="./../articles/index.html">How To’s</a> for more
information about how to work with functions in this package.</p>
</th> </th>
</tr></tbody><tbody><tr><td> </tr></tbody><tbody><tr><td>
<p><code><a href="AMR.html">AMR</a></code> </p> <p><code><a href="AMR.html">AMR</a></code> </p>
@ -353,9 +333,7 @@ information about how to work with functions in this package.</p>
<td><p>Data Set with 500 Isolates - WHONET Example</p></td> <td><p>Data Set with 500 Isolates - WHONET Example</p></td>
</tr></tbody><tbody><tr><th colspan="2"> </tr></tbody><tbody><tr><th colspan="2">
<h2 id="other-miscellaneous-functions">Other: miscellaneous functions <a href="#other-miscellaneous-functions" class="anchor" aria-hidden="true"></a></h2> <h2 id="other-miscellaneous-functions">Other: miscellaneous functions <a href="#other-miscellaneous-functions" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>These functions are mostly for internal use, but some of them may <p class="section-desc"></p><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p>
also be suitable for your analysis. Especially the ‘like’ function can
be useful: <code>if (x %like% y) {...}</code>.</p>
</th> </th>
</tr></tbody><tbody><tr><td> </tr></tbody><tbody><tr><td>
<p><code><a href="age_groups.html">age_groups()</a></code> </p> <p><code><a href="age_groups.html">age_groups()</a></code> </p>
@ -403,8 +381,7 @@ be useful: <code>if (x %like% y) {...}</code>.</p>
<td><p>Random MIC Values/Disk Zones/RSI Generation</p></td> <td><p>Random MIC Values/Disk Zones/RSI Generation</p></td>
</tr></tbody><tbody><tr><th colspan="2"> </tr></tbody><tbody><tr><th colspan="2">
<h2 id="other-statistical-tests">Other: statistical tests <a href="#other-statistical-tests" class="anchor" aria-hidden="true"></a></h2> <h2 id="other-statistical-tests">Other: statistical tests <a href="#other-statistical-tests" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were <p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p>
added to this package for convenience.</p>
</th> </th>
</tr></tbody><tbody><tr><td> </tr></tbody><tbody><tr><td>
<p><code><a href="g.test.html">g.test()</a></code> </p> <p><code><a href="g.test.html">g.test()</a></code> </p>
@ -420,9 +397,7 @@ added to this package for convenience.</p>
<td><p>Skewness of the Sample</p></td> <td><p>Skewness of the Sample</p></td>
</tr></tbody><tbody><tr><th colspan="2"> </tr></tbody><tbody><tr><th colspan="2">
<h2 id="other-deprecated-functions">Other: deprecated functions <a href="#other-deprecated-functions" class="anchor" aria-hidden="true"></a></h2> <h2 id="other-deprecated-functions">Other: deprecated functions <a href="#other-deprecated-functions" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>These functions are deprecated, meaning that they will still work but <p class="section-desc"></p><p>These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.</p>
show a warning with every use and will be removed in a future
version.</p>
</th> </th>
</tr></tbody><tbody><tr><td> </tr></tbody><tbody><tr><td>
<p><code><a href="AMR-deprecated.html">AMR-deprecated</a></code> </p> <p><code><a href="AMR-deprecated.html">AMR-deprecated</a></code> </p>
@ -437,13 +412,11 @@ version.</p>
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

8
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@ -17,7 +17,11 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<<<<<<< HEAD
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -215,8 +219,12 @@ Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<<<<<<< HEAD
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p> 2.0.2.</p>
=======
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</div> </div>
</footer></div> </footer></div>

6
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@ -221,13 +221,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
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@ -242,13 +242,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
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@ -308,13 +308,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
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@ -210,13 +210,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
</div> </div>
</footer></div> </footer></div>

6
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@ -211,13 +211,11 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
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</footer></div> </footer></div>

6
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@ -260,13 +260,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<footer><div class="copyright"> <footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
Erwin E. A. Hassing.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
2.0.2.</p>
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</footer></div> </footer></div>

6
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@ -352,13 +352,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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docs/reference/microorganisms.codes.html
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@ -17,7 +17,11 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
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docs/reference/microorganisms.html
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@ -17,7 +17,11 @@
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=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>

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docs/reference/microorganisms.old.html
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=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>

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docs/reference/mo_matching_score.html
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@ -231,13 +231,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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6
docs/reference/mo_property.html
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@ -433,13 +433,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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6
docs/reference/mo_source.html
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@ -267,13 +267,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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6
docs/reference/pca.html
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@ -266,13 +266,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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6
docs/reference/plot.html
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@ -332,13 +332,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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6
docs/reference/proportion.html
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@ -381,13 +381,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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6
docs/reference/random.html
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@ -232,13 +232,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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docs/reference/resistance_predict.html
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@ -358,13 +358,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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8
docs/reference/rsi_translation.html
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@ -17,7 +17,11 @@
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=======
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
</span> </span>
</div> </div>
@ -213,8 +217,12 @@ Erwin E. A. Hassing.</p>
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=======
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
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6
docs/reference/skewness.html
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@ -210,13 +210,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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docs/reference/translate.html
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@ -237,13 +237,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
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