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Get Taxonomy of a Microorganism
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Get Properties of an Antibiotic Drug
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Get Properties of an Antiviral Drug
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Changelog
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@@ -195,7 +85,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
</div>
@@ -205,7 +95,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 23 June 2024.</p>
generated on 16 July 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -261,21 +151,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-06-23</td>
<td align="center">2024-07-16</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2024-06-23</td>
<td align="center">2024-07-16</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2024-06-23</td>
<td align="center">2024-07-16</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -318,9 +208,8 @@ have extracted from their laboratory systems:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 E. coli R S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 E. coli S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 S. aureus S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span>
<span></span>
<span><span class="co"># we will use 'our_data' as the data set name for this tutorial</span></span>
<span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">example_isolates_unclean</span></span></code></pre></div>
<p>For AMR data analysis, we would like the microorganism column to
@@ -333,24 +222,21 @@ cleaned as SIR values as well.</p>
<p>With <code><a href="../reference/as.mo.html">as.mo()</a></code>, users can transform arbitrary
microorganism names or codes to current taxonomy. The <code>AMR</code>
package contains up-to-date taxonomic data. To be specific, currently
included data were retrieved on 11 Dec 2022.</p>
included data were retrieved on 24 Jun 2024.</p>
<p>The codes of the AMR packages that come from <code><a href="../reference/as.mo.html">as.mo()</a></code> are
short, but still human readable. More importantly, <code><a href="../reference/as.mo.html">as.mo()</a></code>
supports all kinds of input:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; Class 'mo'</span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span></code></pre></div>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span>
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; Class 'mo'</span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span></code></pre></div>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLEPNE"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span>
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLEPNE"</span><span class="op">)</span></span>
<span><span class="co">#&gt; Class 'mo'</span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span></code></pre></div>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLPN"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span>
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLPN"</span><span class="op">)</span></span>
<span><span class="co">#&gt; Class 'mo'</span></span>
<span><span class="co">#&gt; [1] B_KLBSL_PNMN</span></span></code></pre></div>
<p>The first character in above codes denote their taxonomic kingdom,
@@ -360,58 +246,53 @@ retrieve taxonomic properties, such as the name, genus, species, family,
order, and even Gram-stain. They all start with <code>mo_</code> and
they use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally, so that still any arbitrary
user input can be used:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "Enterobacteriaceae"</span></span></code></pre></div>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "Klebsiella"</span></span></code></pre></div>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "pneumoniae"</span></span></code></pre></div>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; [1] "Enterobacteriaceae"</span></span>
<span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "Klebsiella"</span></span>
<span><span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "pneumoniae"</span></span>
<span></span>
<span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "Gram-negative"</span></span></code></pre></div>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; [1] "Gram-negative"</span></span>
<span></span>
<span><span class="fu"><a href="../reference/mo_property.html">mo_ref</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "Trevisan, 1887"</span></span></code></pre></div>
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; [1] "Trevisan, 1887"</span></span>
<span></span>
<span><span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [[1]]</span></span>
<span><span class="co">#&gt; [1] "1098101000112102" "446870005" "1098201000112108" "409801009" </span></span>
<span><span class="co">#&gt; [5] "56415008" "714315002" "713926009"</span></span></code></pre></div>
<p>Now we can thus clean our data:</p>
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ Microorganism translation was uncertain for four microorganisms. Run</span></span>
<span><span class="co">#&gt; mo_uncertainties() to review these uncertainties, or use</span></span>
<span><span class="co">#&gt; add_custom_microorganisms() to add custom entries.</span></span></code></pre></div>
<p>Apparently, there was some uncertainty about the translation to
taxonomic codes. Let’s check this:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; Matching scores are based on the resemblance between the input and the full</span></span>
<span><span class="co">#&gt; taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
<span><span class="co">#&gt; Also matched: Enterobacter cowanii (0.600), Eubacterium combesii</span></span>
<span><span class="co">#&gt; Also matched: Escherichia coli coli (0.643), Escherichia coli</span></span>
<span><span class="co">#&gt; expressing (0.611), Enterobacter cowanii (0.600), Eubacterium combesii</span></span>
<span><span class="co">#&gt; (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span></span>
<span><span class="co">#&gt; (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span></span>
<span><span class="co">#&gt; (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae</span></span>
<span><span class="co">#&gt; cloacae (0.571), Enterobacter cloacae complex (0.571), and Ehrlichia</span></span>
<span><span class="co">#&gt; canis (0.567)</span></span>
<span><span class="co">#&gt; (0.583), Enterococcus casseliflavus (0.577), and Enterobacter cloacae</span></span>
<span><span class="co">#&gt; cloacae (0.571)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "K. pneumoniae" -&gt; Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
<span><span class="co">#&gt; Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
<span><span class="co">#&gt; pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis</span></span>
<span><span class="co">#&gt; (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500),</span></span>
<span><span class="co">#&gt; Kingella potus (0.400), Kosakonia pseudosacchari (0.361), Kaistella</span></span>
<span><span class="co">#&gt; palustris (0.333), Kocuria palustris (0.333), and Kocuria pelophila</span></span>
<span><span class="co">#&gt; (0.333)</span></span>
<span><span class="co">#&gt; Kingella potus (0.400), Kluyveromyces pseudotropicale (0.386),</span></span>
<span><span class="co">#&gt; Kluyveromyces pseudotropicalis (0.363), Kosakonia pseudosacchari</span></span>
<span><span class="co">#&gt; (0.361), and Kluyveromyces pseudotropicalis pseudotropicalis (0.361)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "S. aureus" -&gt; Staphylococcus aureus (B_STPHY_AURS, 0.690)</span></span>
<span><span class="co">#&gt; Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus</span></span>
@@ -448,7 +329,7 @@ diffusion values, read more about that on the <code><a href="../reference/as.sir
page.</p>
<p>For now, we will just clean the SIR columns in our data using
dplyr:</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># method 1, be explicit about the columns:</span></span>
<span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">:</span><span class="va">GEN</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span>
@@ -516,7 +397,7 @@ analysis, but the default phenotype-based method is in any case the
method to properly correct for most duplicate isolates. Read more about
the methods on the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> page.</p>
<p>The outcome of the function can easily be added to our data:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ Determining first isolates using an episode length of 365 days</span></span>
@@ -530,16 +411,16 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
<p>So only 90% is suitable for resistance analysis! We can now filter on
it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
<p>For future use, the above two syntaxes can be shortened:</p>
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op">&lt;-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 2 712 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 9</span></span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
@@ -564,7 +445,7 @@ like:</p>
<p>The base R <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> function gives a good first
impression, as it comes with support for the new <code>mo</code> and
<code>sir</code> classes that we now have in our data set:</p>
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
<span><span class="co">#&gt; patient_id hospital date </span></span>
<span><span class="co">#&gt; Length:2712 Length:2712 Min. :2011-01-01 </span></span>
@@ -586,9 +467,8 @@ impression, as it comes with support for the new <code>mo</code> and
<span><span class="co">#&gt; %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; %I : 6.6% (n=178) %I : 3.1% (n=85) </span></span>
<span><span class="co">#&gt; %R :42.0% (n=1138) %R :37.3% (n=1011) </span></span>
<span><span class="co">#&gt; %NI : 0.0% (n=0) %NI : 0.0% (n=0)</span></span></code></pre></div>
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; %NI : 0.0% (n=0) %NI : 0.0% (n=0)</span></span>
<span></span>
<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">our_data_1st</span><span class="op">)</span></span>
<span><span class="co">#&gt; Rows: 2,712</span></span>
<span><span class="co">#&gt; Columns: 9</span></span>
@@ -600,9 +480,8 @@ impression, as it comes with support for the new <code>mo</code> and
<span><span class="co">#&gt; $ AMC <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> I, I, I, S, S, S, S, S, S, S, S, S, I, S, S, S, S, R, S, S,…</span></span>
<span><span class="co">#&gt; $ CIP <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S, S,…</span></span>
<span><span class="co">#&gt; $ GEN <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S, S,…</span></span>
<span><span class="co">#&gt; $ first <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…</span></span></code></pre></div>
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; $ first <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…</span></span>
<span></span>
<span><span class="co"># number of unique values per column:</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">our_data_1st</span>, <span class="va">n_distinct</span><span class="op">)</span></span>
<span><span class="co">#&gt; patient_id hospital date bacteria AMX AMC CIP </span></span>
@@ -615,7 +494,7 @@ impression, as it comes with support for the new <code>mo</code> and
<p>To just get an idea how the species are distributed, create a
frequency table with <code><a href="../reference/count.html">count()</a></code> based on the name of the
microorganisms:</p>
<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/count.html">count</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">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
@@ -624,9 +503,8 @@ microorganisms:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>518</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 730</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 426</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 326</span></span></code></pre></div>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 326</span></span>
<span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/count.html">count</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">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
@@ -643,7 +521,7 @@ microorganisms:</p>
<p>Using so-called antibiotic class selectors, you can select or filter
columns based on the antibiotic class that your antibiotic results are
in:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<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">date</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span>
@@ -660,9 +538,8 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2015-04-27 S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2011-06-21 S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2014-09-05 S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span></code></pre></div>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
<span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<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">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
@@ -680,9 +557,8 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_ESCHR_COLI S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span></code></pre></div>
<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
<span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<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="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,712 × 5</span></span></span>
@@ -698,9 +574,8 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> B_ESCHR_COLI S S S S </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span></code></pre></div>
<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,702 more rows</span></span></span>
<span></span>
<span><span class="co"># filtering using AB selectors is also possible:</span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
@@ -718,9 +593,8 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,001 more rows</span></span></span></code></pre></div>
<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,001 more rows</span></span></span>
<span></span>
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
@@ -738,9 +612,8 @@ in:</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 473 more rows</span></span></span></code></pre></div>
<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 473 more rows</span></span></span>
<span></span>
<span><span class="co"># even works in base R (since R 3.0):</span></span>
<span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span>
<span><span class="co">#&gt; ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC'</span></span>
@@ -793,7 +666,7 @@ failure</li>
function to create any of the above antibiogram types. For starters,
this is what the included <code>example_isolates</code> data set looks
like:</p>
<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">example_isolates</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
<span><span class="co">#&gt; date patient age gender ward mo PEN OXA FLC AMX </span></span>
@@ -822,7 +695,7 @@ like:</p>
should be used. The <code>antibiotics</code> argument in the
<code><a href="../reference/antibiogram.html">antibiogram()</a></code> function supports any (combination) of the
previously mentioned antibiotic class selectors:</p>
<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <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="../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><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
@@ -949,7 +822,7 @@ Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian,
Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish,
Swedish, Turkish, or Ukrainian. In this next example, we force the
language to be Spanish using the <code>language</code> argument:</p>
<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
<span> antibiotics <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>
@@ -995,7 +868,7 @@ language to be Spanish using the <code>language</code> argument:</p>
</h4>
<p>To create a combined antibiogram, use antibiotic codes or names with
a plus <code>+</code> character like this:</p>
<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<table class="table">
@@ -1077,7 +950,7 @@ a plus <code>+</code> character like this:</p>
<p>To create a syndromic antibiogram, the <code>syndromic_group</code>
argument must be used. This can be any column in the data, or e.g. an
<code><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse()</a></code> with calculations based on certain columns:</p>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <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="../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>,</span>
<span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span>
@@ -1271,7 +1144,7 @@ Antibiogram) in which cases are predefined based on clinical or
demographic characteristics (e.g., endocarditis in 75+ females). This
next example is a simplification without clinical characteristics, but
just gives an idea of how a WISCA can be created:</p>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">wisca</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC+CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
@@ -1339,7 +1212,7 @@ just gives an idea of how a WISCA can be created:</p>
<p>Antibiograms can be plotted using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> from the
<code>ggplot2</code> packages, since this <code>AMR</code> package
provides an extension to that function:</p>
<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">wisca</span><span class="op">)</span></span></code></pre></div>
<p><img src="AMR_files/figure-html/unnamed-chunk-10-1.png" width="720"></p>
<p>To calculate antimicrobial resistance in a more sensible way, also by
@@ -1368,12 +1241,12 @@ proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a>
I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to
<code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their
own:</p>
<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] 0.4288348</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
<code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span><span class="op">)</span></span>
@@ -1387,7 +1260,7 @@ own:</p>
<p><em>Author: Dr. Matthijs Berends, 26th Feb 2023</em></p>
</div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside>
</div>
@@ -1404,9 +1277,9 @@ own:</p>
</footer>
</div>
</body>
</html>

208
articles/EUCAST.html
View File

@@ -5,7 +5,6 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="AMR">
<title>How to apply EUCAST rules • AMR (for R)</title>
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
@@ -17,31 +16,22 @@
<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet">
<link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet">
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@@ -195,7 +85,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to apply EUCAST rules</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
<div class="d-none name"><code>EUCAST.Rmd</code></div>
</div>
@@ -248,9 +138,8 @@ be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</
<span><span class="va">oops</span></span>
<span><span class="co">#&gt; mo ampicillin</span></span>
<span><span class="co">#&gt; 1 Klebsiella S</span></span>
<span><span class="co">#&gt; 2 Escherichia S</span></span></code></pre></div>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; 2 Escherichia S</span></span>
<span></span>
<span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">oops</span>, info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span><span class="co">#&gt; mo ampicillin</span></span>
<span><span class="co">#&gt; 1 Klebsiella R</span></span>
@@ -259,14 +148,13 @@ be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</
<code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline,
but allows to check for one or more specific microorganisms or
antibiotics:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,</span>
<span> <span class="st">"ampicillin"</span></span>
<span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] TRUE FALSE</span></span></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; [1] TRUE FALSE</span></span>
<span></span>
<span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span></span>
<span> <span class="st">"Klebsiella"</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span></span>
@@ -277,7 +165,7 @@ used for filling in known resistance and susceptibility based on results
of other antimicrobials drugs. This process is called <em>interpretive
reading</em>, is basically a form of imputation, and is part of the
<code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
<span> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span>
<span> <span class="st">"Staphylococcus aureus"</span>,</span>
@@ -295,7 +183,7 @@ reading</em>, is basically a form of imputation, and is part of the
<span> FOX <span class="op">=</span> <span class="st">"S"</span>, <span class="co"># Cefoxitin</span></span>
<span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span></code></pre></div>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
@@ -361,7 +249,7 @@ reading</em>, is basically a form of imputation, and is part of the
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
@@ -428,7 +316,7 @@ reading</em>, is basically a form of imputation, and is part of the
</tbody>
</table>
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@@ -445,9 +333,9 @@ reading</em>, is basically a form of imputation, and is part of the
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@@ -5,7 +5,6 @@
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@@ -195,7 +85,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to determine multi-drug resistance (MDR)</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
<div class="d-none name"><code>MDR.Rmd</code></div>
</div>
@@ -495,7 +385,7 @@ Unique: 5</p>
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@@ -512,9 +402,9 @@ Unique: 5</p>
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190
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@@ -5,7 +5,6 @@
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@@ -49,141 +39,41 @@
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Conduct AMR Analysis
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Generate Antibiogram (Trad./Syndromic/WISCA)
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Predict Antimicrobial Resistance
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Download Data Sets for Own Use
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Set User- Or Team-specific Package Settings
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Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
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Determine Multi-Drug Resistance (MDR)
</a>
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Work with WHONET Data
</a>
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Apply Eucast Rules
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Get Taxonomy of a Microorganism
</a>
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Get Properties of an Antibiotic Drug
</a>
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Get Properties of an Antiviral Drug
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<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
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<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
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AMR &amp; data.table
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AMR &amp; tidymodels
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<li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="fa far fa-newspaper"></span> Changelog</a></li>
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/msberends/AMR"><span class="fa fab fa-github"></span> Source Code</a></li>
</ul>
</div>
</div>
</nav><div class="container template-article">
@@ -195,7 +85,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct principal component analysis (PCA) for AMR</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
<div class="d-none name"><code>PCA.Rmd</code></div>
</div>
@@ -337,7 +227,7 @@ automatically adds the right labels and even groups:</p>
<span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"An AMR/PCA biplot!"</span><span class="op">)</span></span></code></pre></div>
<p><img src="PCA_files/figure-html/unnamed-chunk-7-1.png" width="750"></p>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside>
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@@ -354,9 +244,9 @@ automatically adds the right labels and even groups:</p>
</footer>
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</html>

190
articles/WHONET.html
View File

@@ -5,7 +5,6 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<title>How to work with WHONET data • AMR (for R)</title>
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<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
@@ -17,31 +16,22 @@
<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet">
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
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<script src="../extra.js"></script><meta property="og:title" content="How to work with WHONET data">
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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<span class="navbar-toggler-icon"></span>
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@@ -49,141 +39,41 @@
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto">
<li class="active nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--how-to">
<span class="fa fa-question-circle"></span>
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../reference/antibiogram.html">
<span class="fa fa-file-prescription"></span>
Generate Antibiogram (Trad./Syndromic/WISCA)
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict Antimicrobial Resistance
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<span class="fa fa-database"></span>
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
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Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
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Work with WHONET Data
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Apply Eucast Rules
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Get Taxonomy of a Microorganism
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Get Properties of an Antibiotic Drug
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Get Properties of an Antiviral Drug
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<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
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<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
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<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
</ul>
</li>
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<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
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<span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse
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<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; data.table
</a>
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<span class="fa fa-layer-group"></span>
AMR &amp; tidymodels
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; base R
</a>
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Manual
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<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs">
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; dplyr/tidyverse</a></li>
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; data.table</a></li>
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; tidymodels</a></li>
<li><a class="dropdown-item" href="../articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; base R</a></li>
</ul>
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<li class="nav-item"><a class="nav-link" href="../reference/index.html"><span class="fa fa-book-open"></span> Manual</a></li>
<li class="nav-item"><a class="nav-link" href="../authors.html"><span class="fa fa-users"></span> Authors</a></li>
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<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
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@@ -195,7 +85,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to work with WHONET data</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/WHONET.Rmd" class="external-link"><code>vignettes/WHONET.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/WHONET.Rmd" class="external-link"><code>vignettes/WHONET.Rmd</code></a></small>
<div class="d-none name"><code>WHONET.Rmd</code></div>
</div>
@@ -427,7 +317,7 @@ using the included <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a>
<span> <span class="fu"><a href="../reference/ggplot_sir.html">ggplot_sir</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">"ab"</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside>
</div>
@@ -444,9 +334,9 @@ using the included <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a>
</footer>
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341
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@@ -5,7 +5,6 @@
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<title>Data sets for download / own use • AMR (for R)</title>
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@@ -17,31 +16,22 @@
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<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet">
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@@ -49,141 +39,41 @@
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AMR &amp; tidymodels
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@@ -194,9 +84,9 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">23 June 2024</h4>
<h4 data-toc-skip class="date">16 July 2024</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
</div>
@@ -215,43 +105,44 @@ of the data sets look like.</p>
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 52 171 rows and 23 columns, containing the following
<p>A data set with 70 547 rows and 26 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</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>oxygen_tolerance</em>, <em>source</em>, <em>lpsn</em>,
<em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>,
<em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>mycobank</em>,
<em>mycobank_parent</em>, <em>mycobank_renamed_to</em>, <em>gbif</em>,
<em>gbif_parent</em>, <em>gbif_renamed_to</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 14 July 2023 08:49:06 UTC. Find more info
<p>It was last updated on 16 July 2024 12:51:57 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>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original
R Data Structure (RDS) file</a> (1.2 MB)<br>
R Data Structure (RDS) file</a> (1.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated
text file</a> (11.7 MB)<br>
text file</a> (15.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft
Excel workbook</a> (5.2 MB)<br>
Excel workbook</a> (7.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache
Feather file</a> (5.5 MB)<br>
Feather file</a> (19 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache
Parquet file</a> (2.6 MB)<br>
Parquet file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xpt" class="external-link">SAS
transport (XPT) file</a> (48.6 MB)<br>
transport (XPT) file</a> (69.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM
SPSS Statistics data file</a> (17.8 MB)<br>
SPSS Statistics data file</a> (24.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
DTA file</a> (48.6 MB)</li>
DTA file</a> (69.5 MB)</li>
</ul>
<p><strong>NOTE: The exported files for SAS, SPSS and Stata contain only
the first 50 SNOMED codes per record, as their file size would otherwise
@@ -263,16 +154,16 @@ all SNOMED codes as comma separated values.</p>
<div class="section level3">
<h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
</h3>
<p>This data set contains the full microbial taxonomy of five kingdoms
<p>This data set contains the full microbial taxonomy of six kingdoms
from the List of Prokaryotic names with Standing in Nomenclature (LPSN)
and the Global Biodiversity Information Facility (GBIF):</p>
<ul>
<li>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names
with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong>
International Journal of Systematic and Evolutionary Microbiology, 70,
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on December 11th, 2022.</li>
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on June 24th, 2024.</li>
<li>GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset .
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on January 8th, 2024.</li>
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on June 24th, 2024.</li>
<li>Public Health Information Network Vocabulary Access and Distribution
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value
Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>
@@ -295,52 +186,55 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
</tr>
<tr class="even">
<td align="center">Animalia</td>
<td align="center">1 379</td>
<td align="center">1 713</td>
</tr>
<tr class="odd">
<td align="center">Archaea</td>
<td align="center">1 314</td>
<td align="center">1 418</td>
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">36 501</td>
<td align="center">39 238</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>
<td align="center">7 905</td>
<td align="center">Chromista</td>
<td align="center">164</td>
</tr>
<tr class="even">
<td align="center">Protozoa</td>
<td align="center">5 071</td>
<td align="center">Fungi</td>
<td align="center">19 878</td>
</tr>
</tbody>
</table>
<p>Example rows when filtering on genus <em>Escherichia</em>:</p>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="3%">
<col width="7%">
<col width="2%">
<col width="2%">
<col width="4%">
<col width="5%">
<col width="4%">
<col width="5%">
<col width="3%">
<col width="4%">
<col width="3%">
<col width="2%">
<col width="6%">
<col width="7%">
<col width="2%">
<col width="2%">
<col width="3%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="2%">
<col width="5%">
<col width="6%">
<col width="1%">
<col width="1%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="3%">
<col width="4%">
<col width="2%">
<col width="2%">
<col width="3%">
<col width="11%">
<col width="2%">
<col width="10%">
</colgroup>
<thead><tr class="header">
<th align="center">mo</th>
@@ -361,6 +255,9 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<th align="center">lpsn</th>
<th align="center">lpsn_parent</th>
<th align="center">lpsn_renamed_to</th>
<th align="center">mycobank</th>
<th align="center">mycobank_parent</th>
<th align="center">mycobank_renamed_to</th>
<th align="center">gbif</th>
<th align="center">gbif_parent</th>
<th align="center">gbif_renamed_to</th>
@@ -387,7 +284,10 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center">515602</td>
<td align="center">482</td>
<td align="center"></td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">11158430</td>
<td align="center"></td>
<td align="center">1.0</td>
@@ -407,7 +307,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center"></td>
<td align="center">species</td>
<td align="center">Leclerc, 1962</td>
<td align="center">aerobe</td>
<td align="center">likely facultative anaerobe</td>
<td align="center">LPSN</td>
<td align="center">776052</td>
<td align="center">515602</td>
@@ -415,6 +315,9 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center"></td>
</tr>
@@ -432,13 +335,16 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center"></td>
<td align="center">species</td>
<td align="center">Huys et al., 2003</td>
<td align="center">aerobe</td>
<td align="center">facultative anaerobe</td>
<td align="center">LPSN</td>
<td align="center">776053</td>
<td align="center">515602</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">5427575</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">419388003</td>
@@ -465,6 +371,9 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.5</td>
<td align="center"></td>
</tr>
@@ -487,15 +396,18 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center">776057</td>
<td align="center">515602</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">11286021</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">1095001000112106, 715307006, 737528008, …</td>
</tr>
<tr class="even">
<td align="center">B_ESCHR_DYSN</td>
<td align="center">Escherichia dysenteriae</td>
<td align="center">B_ESCHR_COLI_COLI</td>
<td align="center">Escherichia coli coli</td>
<td align="center">accepted</td>
<td align="center">Bacteria</td>
<td align="center">Pseudomonadota</td>
@@ -503,19 +415,22 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">dysenteriae</td>
<td align="center">coli</td>
<td align="center">coli</td>
<td align="center">subspecies</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center"></td>
<td align="center">likely facultative anaerobe</td>
<td align="center">GBIF</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">10862979</td>
<td align="center">3221780</td>
<td align="center"></td>
<td align="center">1.5</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">12233256</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center"></td>
</tr>
</tbody>
@@ -912,7 +827,7 @@ column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</e
<em>breakpoint_R</em>, <em>uti</em>, and <em>is_SDD</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 June 2024 13:08:23 UTC. Find more info
<p>It was last updated on 16 July 2024 12:51:57 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@@ -923,7 +838,7 @@ R Data Structure (RDS) file</a> (70 kB)<br>
text file</a> (3.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
Excel workbook</a> (1.7 MB)<br>
Excel workbook</a> (2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class="external-link">Apache
Feather file</a> (4.9 MB)<br>
@@ -1125,37 +1040,37 @@ use.</p>
<code>intrinsic_resistant</code>: Intrinsic Bacterial
Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
</h2>
<p>A data set with 134 634 rows and 2 columns, containing the following
<p>A data set with 340 804 rows and 2 columns, containing the following
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>It was last updated on 16 December 2022 15:10:43 UTC. Find more info
<p>It was last updated on 16 July 2024 12:51:57 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>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original
R Data Structure (RDS) file</a> (78 kB)<br>
R Data Structure (RDS) file</a> (0.1 MB)<br>
</li>
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</ul>
<div class="section level3">
<h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
@@ -2188,7 +2103,7 @@ which are used in the <code>clinical_breakpoints</code> data set.</p>
column names:<br><em>code</em> and <em>mo</em>.</p>
<p>This data set is in R available as <code>microorganisms.codes</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 16 June 2024 09:28:56 UTC. Find more info
<p>It was last updated on 16 July 2024 12:51:57 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@@ -2199,7 +2114,7 @@ R Data Structure (RDS) file</a> (22 kB)<br>
text file</a> (0.1 MB)<br>
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<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.xlsx" class="external-link">Microsoft
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<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.feather" class="external-link">Apache
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@@ -2259,7 +2174,7 @@ laboratory systems and <a href="https://whonet.org" class="external-link">WHONET
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@@ -220,9 +110,9 @@ used to working in <code>dplyr</code> or other tidyverse packages.</p>
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@@ -195,7 +85,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to predict antimicrobial resistance</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/resistance_predict.Rmd" class="external-link"><code>vignettes/resistance_predict.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/resistance_predict.Rmd" class="external-link"><code>vignettes/resistance_predict.Rmd</code></a></small>
<div class="d-none name"><code>resistance_predict.Rmd</code></div>
</div>
@@ -362,16 +252,15 @@ model might be more appropriate:</p>
<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">family</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Family: binomial </span></span>
<span><span class="co">#&gt; Link function: logit</span></span></code></pre></div>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="co">#&gt; Link function: logit</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">$</span><span class="va">coefficients</span></span>
<span><span class="co">#&gt; Estimate Std. Error z value Pr(&gt;|z|)</span></span>
<span><span class="co">#&gt; (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05</span></span>
<span><span class="co">#&gt; year 0.09883005 0.02295317 4.305725 1.664395e-05</span></span></code></pre></div>
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@@ -388,9 +277,9 @@ model might be more appropriate:</p>
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@@ -5,7 +5,6 @@
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@@ -49,141 +39,41 @@
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Conduct AMR Analysis
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<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
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AMR &amp; data.table
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@@ -195,7 +85,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>Welcome to the `AMR` package</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/welcome_to_AMR.Rmd" class="external-link"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/welcome_to_AMR.Rmd" class="external-link"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
<div class="d-none name"><code>welcome_to_AMR.Rmd</code></div>
</div>
@@ -222,7 +112,7 @@ this a successful and durable project!</p>
10.18637/jss.v104.i03</a>) and 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>).</p>
<p>After installing this package, R knows ~52 000 distinct microbial
<p>After installing this package, R knows ~71 000 distinct microbial
species and all ~600 antibiotic, antimycotic and antiviral drugs by name
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid SIR and MIC values. The integral
@@ -313,9 +203,9 @@ included with the package. </small></p>
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<li><a class="dropdown-item" href="articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
<li><a class="dropdown-item" href="reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
<li><a class="dropdown-item" href="reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
<li><a class="dropdown-item" href="reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
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@@ -157,9 +51,9 @@
<img src="logo.svg" class="logo" alt=""><h1>Authors and Citation</h1>
</div>
<div class="section level2 citation">
<div class="section level2">
<h2>Authors</h2>
<ul class="list-unstyled"><li>
<p><strong>Matthijs S. Berends</strong>. Author, maintainer. <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>
@@ -169,7 +63,7 @@
</p>
</li>
<li>
<p><strong>Erwin E. A. Hassing</strong>. Author, contributor.
<p><strong>Erwin E. A. Hassing</strong>. Author, contributor.
</p>
</li>
<li>
@@ -181,7 +75,7 @@
</p>
</li>
<li>
<p><strong>Judith M. Fonville</strong>. Contributor.
<p><strong>Judith M. Fonville</strong>. Contributor.
</p>
</li>
<li>
@@ -193,7 +87,7 @@
</p>
</li>
<li>
<p><strong>Eric H. L. C. M. Hazenberg</strong>. Contributor.
<p><strong>Eric H. L. C. M. Hazenberg</strong>. Contributor.
</p>
</li>
<li>
@@ -209,15 +103,15 @@
</p>
</li>
<li>
<p><strong>Bart C. Meijer</strong>. Contributor.
<p><strong>Bart C. Meijer</strong>. Contributor.
</p>
</li>
<li>
<p><strong>Dmytro Mykhailenko</strong>. Contributor.
<p><strong>Dmytro Mykhailenko</strong>. Contributor.
</p>
</li>
<li>
<p><strong>Anton Mymrikov</strong>. Contributor.
<p><strong>Anton Mymrikov</strong>. Contributor.
</p>
</li>
<li>
@@ -229,11 +123,11 @@
</p>
</li>
<li>
<p><strong>Matthew Saab</strong>. Contributor.
<p><strong>Matthew Saab</strong>. Contributor.
</p>
</li>
<li>
<p><strong>Jonas Salm</strong>. Contributor.
<p><strong>Jonas Salm</strong>. Contributor.
</p>
</li>
<li>
@@ -241,7 +135,7 @@
</p>
</li>
<li>
<p><strong>Rogier P. Schade</strong>. Contributor.
<p><strong>Rogier P. Schade</strong>. Contributor.
</p>
</li>
<li>
@@ -262,14 +156,14 @@
</li>
</ul></div>
<div class="section level2 citation">
<div class="section level2">
<h2 id="citation">Citation</h2>
<p><small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/inst/CITATION" class="external-link"><code>inst/CITATION</code></a></small></p>
<p><small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/inst/CITATION" class="external-link"><code>inst/CITATION</code></a></small></p>
<p>Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022).
“AMR: An R Package for Working with Antimicrobial Resistance Data.”
<em>Journal of Statistical Software</em>, <b>104</b>(3), 1–31.
<a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a>.
<a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a>.
</p>
<pre>@Article{,
title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},
@@ -282,7 +176,8 @@
doi = {10.18637/jss.v104.i03},
}</pre>
</div>
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@@ -296,9 +191,9 @@
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# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #

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# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #

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<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in &lt;doi:10.18637/jss.v104.i03&gt;.">
<title>Antimicrobial Resistance Data Analysis • AMR (for R)</title>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9061</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9063</small>
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@@ -49,141 +45,41 @@
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto">
<li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--how-to">
<span class="fa fa-question-circle"></span>
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="reference/antibiogram.html">
<span class="fa fa-file-prescription"></span>
Generate Antibiogram (Trad./Syndromic/WISCA)
</a>
<a class="dropdown-item" href="articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict Antimicrobial Resistance
</a>
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<span class="fa fa-database"></span>
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET Data
</a>
<a class="dropdown-item" href="articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply Eucast Rules
</a>
<a class="dropdown-item" href="reference/mo_property.html">
<span class="fa fa-bug"></span>
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="reference/av_property.html">
<span class="fa fa-capsules"></span>
Get Properties of an Antiviral Drug
</a>
</div>
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
<ul class="dropdown-menu" aria-labelledby="dropdown-how-to">
<li><a class="dropdown-item" href="articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
<li><a class="dropdown-item" href="reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
<li><a class="dropdown-item" href="articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
<li><a class="dropdown-item" href="reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
<li><a class="dropdown-item" href="articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
<li><a class="dropdown-item" href="articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
<li><a class="dropdown-item" href="reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
<li><a class="dropdown-item" href="reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
<li><a class="dropdown-item" href="reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
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</li>
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With other pkgs
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<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse
</a>
<a class="dropdown-item" href="articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; data.table
</a>
<a class="dropdown-item" href="articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; tidymodels
</a>
<a class="dropdown-item" href="articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; base R
</a>
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<a class="nav-link" href="reference/index.html">
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Manual
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Authors
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<ul class="dropdown-menu" aria-labelledby="dropdown-with-other-pkgs">
<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; dplyr/tidyverse</a></li>
<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; data.table</a></li>
<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; tidymodels</a></li>
<li><a class="dropdown-item" href="articles/other_pkg.html"><span class="fa fa-layer-group"></span> AMR &amp; base R</a></li>
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</div>
</div>
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14
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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/*!
* Color mode toggler for Bootstrap's docs (https://getbootstrap.com/)
* Copyright 2011-2023 The Bootstrap Authors
* Licensed under the Creative Commons Attribution 3.0 Unported License.
* Updates for {pkgdown} by the {bslib} authors, also licensed under CC-BY-3.0.
*/
const getStoredTheme = () => localStorage.getItem('theme')
const setStoredTheme = theme => localStorage.setItem('theme', theme)
const getPreferredTheme = () => {
const storedTheme = getStoredTheme()
if (storedTheme) {
return storedTheme
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'use strict'
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setTheme(getPreferredTheme())
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})
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showActiveTheme(getPreferredTheme())
document
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setTheme(theme)
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})
})
})
}
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<img src="../logo.svg" class="logo" alt=""><h1>Changelog</h1>
<small>Source: <a href="https://github.com/msberends/AMR/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
<small>Source: <a href="https://github.com/msberends/AMR/blob/main/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9061" id="amr-2119061">AMR 2.1.1.9061<a class="anchor" aria-label="anchor" href="#amr-2119061"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9063" id="amr-2119063">AMR 2.1.1.9063<a class="anchor" aria-label="anchor" href="#amr-2119063"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9061">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9061"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9063">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9063"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9061">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9061"></a></h3>
<h3 id="breaking-2-1-1-9063">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9063"></a></h3>
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
</ul></div>
<div class="section level3">
<h3 id="new-2-1-1-9061">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9061"></a></h3>
<h3 id="new-2-1-1-9063">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9063"></a></h3>
<ul><li>One Health implementation
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for animal breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li>
@@ -186,15 +80,24 @@
<code><a href="../reference/as.sir.html">as.sir()</a></code> now brings additional factor levels: “NI” for non-interpretable and “SDD” for susceptible dose-dependent. Currently, the <code>clinical_breakpoints</code> data set contains 24 breakpoints that can return the value “SDD” instead of “I”.</li>
</ul></li>
<li>MIC plotting and transforming
<ul><li>The function group <code>scale_*_mic()</code>, namely: <code><a href="../reference/plot.html">scale_x_mic()</a></code>, <code><a href="../reference/plot.html">scale_y_mic()</a></code>, <code><a href="../reference/plot.html">scale_colour_mic()</a></code> and <code><a href="../reference/plot.html">scale_fill_mic()</a></code>. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.</li>
<li>Function <code><a href="../reference/as.mic.html">rescale_mic()</a></code>, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.</li>
<ul><li>New function group <code>scale_*_mic()</code>, namely: <code><a href="../reference/plot.html">scale_x_mic()</a></code>, <code><a href="../reference/plot.html">scale_y_mic()</a></code>, <code><a href="../reference/plot.html">scale_colour_mic()</a></code> and <code><a href="../reference/plot.html">scale_fill_mic()</a></code>. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.</li>
<li>New function <code><a href="../reference/as.mic.html">rescale_mic()</a></code>, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.</li>
</ul></li>
<li>Microbiological taxonomy (<code>microorganisms</code> data set) updated to June 2024, with some exciting new features:
<ul><li>Added MycoBank as the primary taxonomic source for fungi
<ul><li>The <code>microorganisms</code> data set now contains additional columns <code>mycobank</code>, <code>mycobank_parent</code>, and <code>mycobank_renamed_to</code>
</li>
<li>New function <code><a href="../reference/mo_property.html">mo_mycobank()</a></code> to get the MycoBank record number, analogous to existing functions <code><a href="../reference/mo_property.html">mo_lpsn()</a></code> and <code><a href="../reference/mo_property.html">mo_gbif()</a></code>
</li>
</ul></li>
<li>We’ve welcomed over 2,000 records from 2023, over 900 from 2024, and many thousands of new fungi</li>
</ul></li>
<li>Other
<ul><li>Function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that are in that group.</li>
<ul><li>New function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that are in that group.</li>
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9061">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9061"></a></h3>
<h3 id="changed-2-1-1-9063">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9063"></a></h3>
<ul><li>SIR interpretation
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@@ -231,9 +134,10 @@
<li>Improved overall algorithm of <code><a href="../reference/as.ab.html">as.ab()</a></code> for better performance and accuracy</li>
<li>Improved overall algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code> for better performance and accuracy. Specifically, more weight is given to genus and species combinations in cases where the subspecies is miswritten, so that the result will be the correct genus and species.</li>
<li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
<li>Fixed a bug for when <code><a href="../reference/antibiogram.html">antibiogram()</a></code> returns an empty data set</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9061">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9061"></a></h3>
<h3 id="other-2-1-1-9063">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9063"></a></h3>
<ul><li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
</ul></div>
</div>
@@ -455,7 +359,7 @@
</ul><hr><p>This changelog only contains changes from AMR v2.0 (January 2023) and later. For prior versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our archive</a>.</p>
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last_built: 2024-07-16T12:57Z
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Conduct AMR Analysis
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Generate Antibiogram (Trad./Syndromic/WISCA)
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Predict Antimicrobial Resistance
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Conduct Principal Component Analysis for AMR
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Determine Multi-Drug Resistance (MDR)
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Work with WHONET Data
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Apply Eucast Rules
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Get Taxonomy of a Microorganism
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<ul class="dropdown-menu" aria-labelledby="dropdown-how-to"><li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
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<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
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AMR &amp; data.table
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<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Options for the AMR package</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/aa_options.R" class="external-link"><code>R/aa_options.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/aa_options.R" class="external-link"><code>R/aa_options.R</code></a></small>
<div class="d-none name"><code>AMR-options.Rd</code></div>
</div>
@@ -166,7 +60,7 @@
<div class="section level2">
<h2 id="options">Options<a class="anchor" aria-label="anchor" href="#options"></a></h2>
<ul><li><p><code>AMR_breakpoint_type</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".</p></li>
<li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li>
@@ -183,7 +77,7 @@
</ul></div>
<div class="section level2">
<h2 id="saving-settings-between-sessions">Saving Settings Between Sessions<a class="anchor" aria-label="anchor" href="#saving-settings-between-sessions"></a></h2>
<p>Settings in <span style="R">R</span> are not saved globally and are thus lost when <span style="R">R</span> is exited. You can save your options to your own <code>.Rprofile</code> file, which is a user-specific file. You can edit it using:</p>
<p></p><div class="sourceCode r"><pre><code><span> <span class="fu">utils</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/utils/file.edit.html" class="external-link">file.edit</a></span><span class="op">(</span><span class="st">"~/.Rprofile"</span><span class="op">)</span></span></code></pre><p></p></div>
@@ -203,7 +97,7 @@
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside></div>
@@ -217,9 +111,9 @@
</footer></div>
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8
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@@ -0,0 +1,8 @@
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@@ -1,175 +1,69 @@
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Welcome to the AMR package.
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>The AMR Package — AMR • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="The AMR Package — AMR"><meta name="description" content="Welcome to the AMR package.
The AMR package is a free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. Many different researchers from around the globe are continually helping us to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~52 000 microorganisms (updated January 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><title>The AMR Package — AMR • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="The AMR Package — AMR"><meta property="og:description" content="Welcome to the AMR package.
After installing this package, R knows ~71 000 microorganisms (updated June 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:description" content="Welcome to the AMR package.
The AMR package is a free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. Many different researchers from around the globe are continually helping us to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~52 000 microorganisms (updated January 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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After installing this package, R knows ~71 000 microorganisms (updated June 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"></head><body>
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<img src="../logo.svg" class="logo" alt=""><h1>The <code>AMR</code> Package</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/aa_amr-package.R" class="external-link"><code>R/aa_amr-package.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/aa_amr-package.R" class="external-link"><code>R/aa_amr-package.R</code></a></small>
<div class="d-none name"><code>AMR.Rd</code></div>
</div>
@@ -180,7 +74,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
) and 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>
).</p>
<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~52 000 microorganisms</strong></a> (updated January 2024) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package 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 public <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>.</p>
<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~71 000 microorganisms</strong></a> (updated June 2024) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package 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 public <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>.</p>
<p>The <code>AMR</code> package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
</div>
@@ -206,7 +100,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
@@ -246,7 +140,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<li><p>Anita Williams (<a href="https://orcid.org/0000-0002-5295-8451" class="external-link">ORCID</a>) [contributor]</p></li>
</ul></div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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<img src="../logo.svg" class="logo" alt=""><h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/whocc.R" class="external-link"><code>R/whocc.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/whocc.R" class="external-link"><code>R/whocc.R</code></a></small>
<div class="d-none name"><code>WHOCC.Rd</code></div>
</div>
@@ -166,7 +60,7 @@
<div class="section level2">
<h2 id="whocc">WHOCC<a class="anchor" aria-label="anchor" href="#whocc"></a></h2>
<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) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://atcddd.fhi.no" class="external-link">https://atcddd.fhi.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
@@ -189,7 +83,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "flucloxacillinum" "fluorochloroxacillin" "staphylex" </span>
</code></pre></div>
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@@ -203,9 +97,9 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 500 Isolates - WHONET Example</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>WHONET.Rd</code></div>
</div>
@@ -227,7 +121,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Carbapenemase &lt;lgl&gt;, `MRSA screening test` &lt;lgl&gt;, …</span></span>
</code></pre></div>
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