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<p>With <code>add_custom_microorganisms()</code> you can add your own custom microorganisms to the <code>AMR</code> package, such the non-taxonomic outcome of laboratory analysis.</p>
<dd><p>a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a> resembling the <ahref="microorganisms.html">microorganisms</a> data set, at least containing columns "genus" and "species"</p></dd>
<p>This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see <em>Examples</em>.</p>
<p><strong>Important:</strong> Due to how <spanstyle="R">R</span> works, the <code>add_custom_microorganisms()</code> function has to be run in every <spanstyle="R">R</span> session - added microorganisms are not stored between sessions and are thus lost when <spanstyle="R">R</span> is exited.</p>
<p>There are two ways to automate this process:</p>
<p><strong>Method 1:</strong> Save the microorganisms to a local or remote file (can even be the internet). To use this method:</p><ol><li><p>Create a data set in the structure of the <ahref="microorganisms.html">microorganisms</a> data set (containing at the very least columns "genus" and "species") and save it with <code><ahref="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>
<li><p>Set the file location to the <code>AMR_custom_mo</code><spanstyle="R">R</span> option: <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 <spanstyle="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will loaded on start-up of <spanstyle="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>
<p>Upon package load, this file will be loaded and run through the <code>add_custom_microorganisms()</code> function.</p></li>
</ol><p><strong>Method 2:</strong> Save the microorganism directly to your <code>.Rprofile</code> file. An important downside is that this requires to load the <code>AMR</code> package at every start-up. 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>
<li><p>Add a text like below and save the file:</p>
<p></p><divclass="sourceCode r"><pre><code><span><spanclass="co"># Add custom antibiotic drug codes:</span></span>
<divclass="dont-index"><p><code><ahref="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> to add custom antimicrobials to this package.</p></div>
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<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <atarget="_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 <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
