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<img src="../logo.svg" class="logo" alt=""><h1>User-Defined Reference Data Set for Microorganisms</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/mo_source.R" class="external-link"><code>R/mo_source.R</code></a></small>
<div class="d-none name"><code>mo_source.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>These functions can be used to predefine your own reference to be used in <code><a href="as.mo.html">as.mo()</a></code> and consequently all <code><a href="mo_property.html">mo_*</a></code> functions (such as <code><a href="mo_property.html">mo_genus()</a></code> and <code><a href="mo_property.html">mo_gramstain()</a></code>).</p>
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">set_mo_source</span><span class="op">(</span></span>
<span> <span class="va">path</span>,</span>
<span> destination <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_mo_source"</span>, <span class="st">"~/mo_source.rds"</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">get_mo_source</span><span class="op">(</span>destination <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_mo_source"</span>, <span class="st">"~/mo_source.rds"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>path</dt>
<dd><p>location of your reference file, this can be any text file (comma-, tab- or pipe-separated) or an Excel file (see <em>Details</em>). Can also be <code>""</code>, <code>NULL</code> or <code>FALSE</code> to delete the reference file.</p></dd>
<dt>destination</dt>
<dd><p>destination of the compressed data file - the default is the user's home directory.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an <span style="R">R</span> object file (extension '.rds'). To use an Excel file, you will need to have the <code>readxl</code> package installed.</p>
<p><code>set_mo_source()</code> will check the file for validity: it must be a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href="microorganisms.html">microorganisms$mo</a></code> or <code><a href="microorganisms.html">microorganisms$fullname</a></code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source()</code> will read the file into <span style="R">R</span> and will ask to export it to <code>"~/mo_source.rds"</code>. The CRAN policy disallows packages to write to the file system, although '<em>exceptions may be allowed in interactive sessions if the package obtains confirmation from the user</em>'. For this reason, this function only works in interactive sessions so that the user can <strong>specifically confirm and allow</strong> that this file will be created. The destination of this file can be set with the <code>destination</code> argument and defaults to the user's home directory. It can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_mo_source</a></code>, e.g. <code>options(AMR_mo_source = "my/location/file.rds")</code>.</p>
<p>The created compressed data file <code>"mo_source.rds"</code> will be used at default for MO determination (function <code><a href="as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href="mo_property.html">mo_genus()</a></code> and <code><a href="mo_property.html">mo_gramstain()</a></code>). The location and timestamp of the original file will be saved as an <a href="https://rdrr.io/r/base/attributes.html" class="external-link">attribute</a> to the compressed data file.</p>
<p>The function <code>get_mo_source()</code> will return the data set by reading <code>"mo_source.rds"</code> with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>. If the original file has changed (by checking the location and timestamp of the original file), it will call <code>set_mo_source()</code> to update the data file automatically if used in an interactive session.</p>
<p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file created with <code>set_mo_source()</code> will then have a size of 0.1 kB and can be read by <code>get_mo_source()</code> in only a couple of microseconds (millionths of a second).</p>
</div>
<div class="section level2">
<h2 id="how-to-setup">How to Setup<a class="anchor" aria-label="anchor" href="#how-to-setup"></a></h2>
<p>Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="sc">|</span> A <span class="sc">|</span> B <span class="sc">|</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="sc">--</span><span class="er">|</span><span class="sc">--------------------</span><span class="er">|</span><span class="sc">-----------------------</span><span class="er">|</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="dv">1</span> <span class="sc">|</span> Organisation XYZ <span class="sc">|</span> mo <span class="sc">|</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="dv">2</span> <span class="sc">|</span> lab_mo_ecoli <span class="sc">|</span> Escherichia coli <span class="sc">|</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="dv">3</span> <span class="sc">|</span> lab_mo_kpneumoniae <span class="sc">|</span> Klebsiella pneumoniae <span class="sc">|</span></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="dv">4</span> <span class="sc">|</span> <span class="er">|</span> <span class="er">|</span></span></code></pre><p></p></div>
<p>We save it as <code>"home/me/ourcodes.xlsx"</code>. Now we have to set it as a source:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">set_mo_source</span>(<span class="st">"home/me/ourcodes.xlsx"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="co">#&gt; "Organisation XYZ" and "mo"</span></span></code></pre><p></p></div>
<p>It has now created a file <code>"~/mo_source.rds"</code> with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.</p>
<p>And now we can use it in our functions:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">as.mo</span>(<span class="st">"lab_mo_ecoli"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; Class 'mo'</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; [1] B_ESCHR_COLI</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="fu">mo_genus</span>(<span class="st">"lab_mo_kpneumoniae"</span>)</span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="co">#&gt; [1] "Klebsiella"</span></span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a></span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a><span class="co"># other input values still work too</span></span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a><span class="fu">as.mo</span>(<span class="fu">c</span>(<span class="st">"Escherichia coli"</span>, <span class="st">"E. coli"</span>, <span class="st">"lab_mo_ecoli"</span>))</span>
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Translation to one microorganism was guessed with uncertainty.</span></span>
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a><span class="co">#&gt; Use mo_uncertainties() to review it.</span></span>
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a><span class="co">#&gt; Class 'mo'</span></span>
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a><span class="co">#&gt; [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI</span></span></code></pre><p></p></div>
<p>If we edit the Excel file by, let's say, adding row 4 like this:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="sc">|</span> A <span class="sc">|</span> B <span class="sc">|</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="sc">--</span><span class="er">|</span><span class="sc">--------------------</span><span class="er">|</span><span class="sc">-----------------------</span><span class="er">|</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="dv">1</span> <span class="sc">|</span> Organisation XYZ <span class="sc">|</span> mo <span class="sc">|</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="dv">2</span> <span class="sc">|</span> lab_mo_ecoli <span class="sc">|</span> Escherichia coli <span class="sc">|</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="dv">3</span> <span class="sc">|</span> lab_mo_kpneumoniae <span class="sc">|</span> Klebsiella pneumoniae <span class="sc">|</span></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="dv">4</span> <span class="sc">|</span> lab_Staph_aureus <span class="sc">|</span> Staphylococcus aureus <span class="sc">|</span></span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a><span class="dv">5</span> <span class="sc">|</span> <span class="er">|</span> <span class="er">|</span></span></code></pre><p></p></div>
<p>...any new usage of an MO function in this package will update your data file:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">as.mo</span>(<span class="st">"lab_mo_ecoli"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#&gt; '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="co">#&gt; "Organisation XYZ" and "mo"</span></span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="co">#&gt; Class 'mo'</span></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="co">#&gt; [1] B_ESCHR_COLI</span></span>
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a></span>
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a><span class="fu">mo_genus</span>(<span class="st">"lab_Staph_aureus"</span>)</span>
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a><span class="co">#&gt; [1] "Staphylococcus"</span></span></code></pre><p></p></div>
<p>To delete the reference data file, just use <code>""</code>, <code>NULL</code> or <code>FALSE</code> as input for <code>set_mo_source()</code>:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">set_mo_source</span>(<span class="cn">NULL</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="co">#&gt; Removed mo_source file '/Users/me/mo_source.rds'</span></span></code></pre><p></p></div>
<p>If the original file (in the previous case an Excel file) is moved or deleted, the <code>mo_source.rds</code> file will be removed upon the next use of <code><a href="as.mo.html">as.mo()</a></code> or any <code><a href="mo_property.html">mo_*</a></code> function.</p>
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