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reference/add_custom_antimicrobials.html

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     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
     <p><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_antimicrobials()</code> function has to be run in every <span style="R">R</span> session - added antimicrobials are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p>
-<p>There are two ways to automate this process:</p>
+<p>There are two ways to circumvent this and automate the process of adding antimicrobials:</p>
 <p><strong>Method 1:</strong> Using the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_ab</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="antibiotics.html">antibiotics</a> data set (containing at the very least columns "ab" and "name") 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_ab.rds"</code>, or any remote location.</p></li>
 <li><p>Set the file location to the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_ab</a></code>: <code>options(AMR_custom_ab = "~/my_custom_ab.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>
 <p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom antimicrobial codes:</span></span>
 <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_ab <span class="op">=</span> <span class="st">"~/my_custom_ab.rds"</span><span class="op">)</span></span></code></pre><p></p></div>
 <p>Upon package load, this file will be loaded and run through the <code>add_custom_antimicrobials()</code> function.</p></li>
-</ol><p><strong>Method 2:</strong> Loading the antimicrobial additions directly from your <code>.Rprofile</code> file. An important downside is that this requires the <code>AMR</code> package to be installed or else this method will fail. 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>
+</ol><p><strong>Method 2:</strong> Loading the antimicrobial additions 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>
 <li><p>Add a text like below and save the file:</p>
 <p></p><div class="sourceCode r"><pre><code><span> <span class="co"># Add custom antibiotic drug codes:</span></span>
 <span> <span class="fu">AMR</span><span class="fu">::</span><span class="fu"><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials</a></span><span class="op">(</span></span>