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<img src="../logo.svg" class="logo" alt=""><h1>Add Custom Microorganisms</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/custom_microorganisms.R" class="external-link"><code>R/custom_microorganisms.R</code></a></small>
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<div class="d-none name"><code>add_custom_microorganisms.Rd</code></div>
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<div class="ref-description section level2">
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<p>With <code>add_custom_microorganisms()</code> you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_custom_microorganisms</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">clear_custom_microorganisms</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> resembling the <a href="microorganisms.html">microorganisms</a> data set, at least containing column "genus" (case-insensitive)</p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see <em>Examples</em>.</p>
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<p><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_microorganisms()</code> function has to be run in every <span style="R">R</span> session - added microorganisms are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p>
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<p>There are two ways to circumvent this and automate the process of adding microorganisms:</p>
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<p><strong>Method 1:</strong> Using the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_mo</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="microorganisms.html">microorganisms</a> data set (containing at the very least column "genus") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_mo.rds"</code>, or any remote location.</p></li>
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<li><p>Set the file location to the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_mo</a></code>: <code>options(AMR_custom_mo = "~/my_custom_mo.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p>
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<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom microorganism codes:</span></span>
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<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_custom_mo <span class="op">=</span> <span class="st">"~/my_custom_mo.rds"</span><span class="op">)</span></span></code></pre><p></p></div>
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<p>Upon package load, this file will be loaded and run through the <code>add_custom_microorganisms()</code> function.</p></li>
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</ol><p><strong>Method 2:</strong> Loading the microorganism directly from your <code>.Rprofile</code> file. Note that the definitions will be stored in a user-specific <span style="R">R</span> file, which is a suboptimal workflow. To use this method:</p><ol><li><p>Edit the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>.</p></li>
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<li><p>Add a text like below and save the file:</p>
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<p></p><div class="sourceCode r"><pre><code><span> <span class="co"># Add custom antibiotic drug codes:</span></span>
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<span> <span class="fu">AMR</span><span class="fu">::</span><span class="fu"><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms</a></span><span class="op">(</span></span>
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<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>genus <span class="op">=</span> <span class="st">"Enterobacter"</span>,</span>
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<span> species <span class="op">=</span> <span class="st">"asburiae/cloacae"</span><span class="op">)</span></span>
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<span> <span class="op">)</span></span></code></pre><p></p></div></li>
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</ol><p>Use <code>clear_custom_microorganisms()</code> to clear the previously added microorganisms.</p>
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</div>
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<div class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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<div class="dont-index"><p><code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> to add custom antimicrobials.</p></div>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="co"># a combination of species is not formal taxonomy, so</span></span></span>
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<span class="r-in"><span><span class="co"># this will result in "Enterobacter cloacae cloacae",</span></span></span>
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<span class="r-in"><span><span class="co"># since it resembles the input best:</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacter cloacae cloacae"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.mo() and</span></span></span>
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<span class="r-in"><span><span class="co"># all mo_*() functions</span></span></span>
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<span class="r-in"><span><span class="fu">add_custom_microorganisms</span><span class="op">(</span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> genus <span class="op">=</span> <span class="st">"Enterobacter"</span>,</span></span>
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<span class="r-in"><span> species <span class="op">=</span> <span class="st">"asburiae/cloacae"</span></span></span>
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<span class="r-in"><span> <span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Added Enterobacter asburiae/cloacae to the internal microorganisms data</span>
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<span class="r-msg co"><span class="r-pr">#></span> set.</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># E. asburiae/cloacae is now a new microorganism:</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacter asburiae/cloacae"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># its code:</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] CUSTOM1_ENTRB_ASB/</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># all internal algorithms will work as well:</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Ent asburia cloacae"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacter asburiae/cloacae"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># and even the taxonomy was added based on the genus!</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"E. asburiae/cloacae"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacteriaceae"</span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative"</span>
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<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_info</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $mo</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "CUSTOM1_ENTRB_ASB/"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $kingdom</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $phylum</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Pseudomonadota"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $class</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gammaproteobacteria"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $order</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacterales"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $family</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacteriaceae"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $genus</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacter"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $species</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "asburiae/cloacae"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $subspecies</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] ""</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $status</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "accepted"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $synonyms</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> NULL</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $gramstain</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $oxygen_tolerance</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $url</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] ""</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $ref</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Self-added, 2023"</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $snomed</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $lpsn</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> $gbif</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] NA</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># the function tries to be forgiving:</span></span></span>
|
||
<span class="r-in"><span><span class="fu">add_custom_microorganisms</span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> GENUS <span class="op">=</span> <span class="st">"BACTEROIDES / PARABACTEROIDES SLASHLINE"</span>,</span></span>
|
||
<span class="r-in"><span> SPECIES <span class="op">=</span> <span class="st">"SPECIES"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Added Bacteroides/Parabacteroides to the internal microorganisms data</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> set.</span>
|
||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"BACTEROIDES / PARABACTEROIDES"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteroides/Parabacteroides"</span>
|
||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_rank</a></span><span class="op">(</span><span class="st">"BACTEROIDES / PARABACTEROIDES"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "genus"</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># taxonomy still works, even though a slashline genus was given as input:</span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"Bacteroides/Parabacteroides"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteroidaceae"</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># for groups and complexes, set them as species or subspecies:</span></span></span>
|
||
<span class="r-in"><span><span class="fu">add_custom_microorganisms</span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> genus <span class="op">=</span> <span class="st">"Citrobacter"</span>,</span></span>
|
||
<span class="r-in"><span> species <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">"freundii"</span>, <span class="st">"braakii complex"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> subspecies <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">"complex"</span>, <span class="st">""</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Added Citrobacter braakii complex and Citrobacter freundii complex to the</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> internal microorganisms data set.</span>
|
||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Citrobacter freundii complex" "Citrobacter braakii complex" </span>
|
||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_species</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "freundii complex" "braakii complex" </span>
|
||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative" "Gram-negative"</span>
|
||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||
</code></pre></div>
|
||
</div>
|
||
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||
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|
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||
|
||
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|
||
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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|
||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
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