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(v0.9.0.9016) Support SNOMED codes

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dr. M.S. (Matthijs) Berends
2020-01-27 19:14:23 +01:00
parent 42b079cdb7
commit a13c62e6e8
31 changed files with 456 additions and 342 deletions
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11
docs/reference/as.mo.html
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@ -85,7 +85,7 @@
</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">0.9.0.9016</span>
</span>
</div>
@ -407,10 +407,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus (MRSA)"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"Zthafilokkoockus oureuz"</span>) <span class='co'># handles incorrect spelling</span>
<span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='fl'>22242419</span>) <span class='co'># Catalogue of Life ID</span>
<span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='fl'>22242419</span>) <span class='co'># Catalogue of Life ID</span>
<span class='fu'>as.mo</span>(<span class='fl'>115329001</span>) <span class='co'># SNOMED CT code</span>
<span class='co'># Dyslexia is no problem - these all work:</span>
<span class='fu'>as.mo</span>(<span class='st'>"Ureaplasma urealyticum"</span>)

2
docs/reference/as.rsi.html
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@ -85,7 +85,7 @@
</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">0.9.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9016</span>
</span>
</div>

4
docs/reference/example_isolates.html
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@ -85,7 +85,7 @@
</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">0.9.0.9016</span>
</span>
</div>
@ -252,7 +252,7 @@
<li><p><code>gender</code><br /> gender of the patient</p></li>
<li><p><code>patient_id</code><br /> ID of the patient</p></li>
<li><p><code>mo</code><br /> ID of microorganism created with <code><a href='as.mo.html'>as.mo()</a></code>, see also <a href='microorganisms.html'>microorganisms</a></p></li>
<li><p><code>PEN:RIF</code><br /> 40 different antibiotics with class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>); these column names occur in <a href='antibiotics.html'>antibiotics</a> data set and can be translated with <code><a href='ab_property.html'>ab_name()</a></code></p></li>
<li><p><code>PEN:RIF</code><br /> 40 different antibiotics with class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>); these column names occur in the <a href='antibiotics.html'>antibiotics</a> data set and can be translated with <code><a href='ab_property.html'>ab_name()</a></code></p></li>
</ul>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

6
docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.9.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9016</span>
</span>
</div>
@ -304,7 +304,7 @@
<td>
<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
</td>
<td><p>Data set for RSI interpretation</p></td>
<td><p>Data set for R/SI interpretation</p></td>
</tr>
</tbody><tbody>
<tr>
@ -364,7 +364,7 @@
</tr><tr>
<td>
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
</td>
<td><p>Property of a microorganism</p></td>
</tr><tr>

5
docs/reference/microorganisms.html
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@ -85,7 +85,7 @@
</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">0.9.0.9016</span>
</span>
</div>
@ -242,7 +242,7 @@
<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 69,447 observations and 16 variables:</p><ul>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 69,447 observations and 17 variables:</p><ul>
<li><p><code>mo</code><br /> ID of microorganism as used by this package</p></li>
<li><p><code>col_id</code><br /> Catalogue of Life ID</p></li>
<li><p><code>fullname</code><br /> Full name, like <code>"Escherichia coli"</code></p></li>
@ -252,6 +252,7 @@
<li><p><code>species_id</code><br /> ID of the species as used by the Catalogue of Life</p></li>
<li><p><code>source</code><br /> Either "CoL", "DSMZ" (see Source) or "manually added"</p></li>
<li><p><code>prevalence</code><br /> Prevalence of the microorganism, see <code><a href='as.mo.html'>as.mo()</a></code></p></li>
<li><p><code>snomed</code><br /> SNOMED code of the microorganism. Use <code><a href='mo_property.html'>mo_snomed()</a></code> to retrieve it quickly, see <code><a href='mo_property.html'>mo_property()</a></code>.</p></li>
</ul>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

8
docs/reference/mo_property.html
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@ -85,7 +85,7 @@
</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">0.9.0.9016</span>
</span>
</div>
@ -263,6 +263,8 @@
<span class='fu'>mo_gramstain</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_snomed</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_ref</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_authors</span>(<span class='no'>x</span>, <span class='no'>...</span>)
@ -313,6 +315,7 @@
<li><p>An <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code> in case of <code>mo_year()</code></p></li>
<li><p>A <code><a href='https://rdrr.io/r/base/list.html'>list</a></code> in case of <code>mo_taxonomy()</code> and <code>mo_info()</code></p></li>
<li><p>A named <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> in case of <code>mo_url()</code></p></li>
<li><p>A <code><a href='https://rdrr.io/r/base/double.html'>double</a></code> in case of <code>mo_snomed()</code></p></li>
<li><p>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> in all other cases</p></li>
</ul>
@ -367,11 +370,12 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='co'># colloquial properties ----------------------------------------------------</span>
<span class='fu'>mo_name</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli"</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli", same as mo_name()</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli" - same as mo_name()</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "E. coli"</span>
<span class='co'># other properties ---------------------------------------------------------</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gram-negative"</span>
<span class='fu'>mo_snomed</span>(<span class='st'>"E. coli"</span>) <span class='co'># 112283007, 116395006, ... (SNOMED codes)</span>
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom, but may be translated)</span>
<span class='fu'>mo_rank</span>(<span class='st'>"E. coli"</span>) <span class='co'># "species"</span>
<span class='fu'>mo_url</span>(<span class='st'>"E. coli"</span>) <span class='co'># get the direct url to the online database entry</span>

16
docs/reference/rsi_translation.html
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@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Data set for RSI interpretation — rsi_translation • AMR (for R)</title>
<title>Data set for R/SI interpretation — rsi_translation • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -50,8 +50,8 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Data set for RSI interpretation — rsi_translation" />
<meta property="og:description" content="Data set to interpret MIC and disk diffusion to RSI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use as.rsi() to transform MICs or disks measurements to RSI values." />
<meta property="og:title" content="Data set for R/SI interpretation — rsi_translation" />
<meta property="og:description" content="Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use as.rsi() to transform MICs or disks measurements to R/SI values." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -85,7 +85,7 @@
</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">0.9.0.9016</span>
</span>
</div>
@ -228,13 +228,13 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set for RSI interpretation</h1>
<h1>Data set for R/SI interpretation</h1>
<div class="hidden name"><code>rsi_translation.Rd</code></div>
</div>
<div class="ref-description">
<p>Data set to interpret MIC and disk diffusion to RSI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to RSI values.</p>
<p>Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
</div>
<pre class="usage"><span class='no'>rsi_translation</span></pre>
@ -253,6 +253,9 @@
<li><p><code>breakpoint_S</code><br /> Lowest MIC value or highest number of millimeters that leads to "S"</p></li>
<li><p><code>breakpoint_R</code><br /> Highest MIC value or lowest number of millimeters that leads to "R"</p></li>
</ul>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This file <strong>allows for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -264,6 +267,7 @@
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#format">Format</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>