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(v0.9.0.9020) as.mo() improvement

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dr. M.S. (Matthijs) Berends
2020-02-09 22:04:29 +01:00
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docs/reference/antibiotics.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
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<p>These data sets are available as 'flat files' for use even without R - you can find the files here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/antibiotics.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/antibiotics.R</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/antivirals.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/antivirals.R</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt</a></p></li>
</ul>

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docs/reference/as.mo.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
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</pre>
<p>Values that cannot be coered will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
<p>Use the <code><a href='mo_property.html'>mo_property_*</a></code> functions to get properties based on the returned code, see Examples.</p>
<p>Use the <code><a href='mo_property.html'>mo_*</a></code> functions to get properties based on the returned code, see Examples.</p>
<p>The algorithm uses data from the Catalogue of Life (see below) and from one other source (see <a href='microorganisms.html'>microorganisms</a>).</p>
<p>The <code>as.mo()</code> function uses several coercion rules for fast and logical results. It assesses the input matching criteria in the following order:</p><ol>
<li><p>Human pathogenic prevalence: the function starts with more prevalent microorganisms, followed by less prevalent ones;</p></li>
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<li><p>Breakdown of input values to identify possible matches.</p></li>
</ol>
<p>This will lead to the effect that e.g. <code>"E. coli"</code> (a highly prevalent microorganism found in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
<p>This will lead to the effect that e.g. <code>"E. coli"</code> (a microorganism highly prevalent in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a microorganism less prevalent in humans), although the latter would alphabetically come first.</p>
<h3>Coping with uncertain results</h3>

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docs/reference/index.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>

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docs/reference/microorganisms.codes.html
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<script src="../extra.js"></script>
<meta property="og:title" content="Translation table for common microorganism codes — microorganisms.codes" />
<meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source()." />
<meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
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</div>
<div class="ref-description">
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href='mo_source.html'>set_mo_source()</a></code>.</p>
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href='mo_source.html'>set_mo_source()</a></code>. They will all be searched when using <code><a href='as.mo.html'>as.mo()</a></code> and consequently all the <code><a href='mo_property.html'>mo_*</a></code> functions.</p>
</div>
<pre class="usage"><span class='no'>microorganisms.codes</span></pre>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 5,433 observations and 2 variables:</p><ul>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 5,450 observations and 2 variables:</p><ul>
<li><p><code>code</code><br /> Commonly used code of a microorganism</p></li>
<li><p><code>mo</code><br /> ID of the microorganism in the <a href='microorganisms.html'>microorganisms</a> data set</p></li>
</ul>

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docs/reference/microorganisms.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
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<p>This data set is available as 'flat file' for use even without R - you can find the file here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/microorganisms.R</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt</a></p></li>
</ul>