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(v1.1.0.9020) updated taxonomy

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dr. M.S. (Matthijs) Berends
2020-05-27 16:37:49 +02:00
parent ae1969b941
commit 86d44054f0
55 changed files with 68063 additions and 70233 deletions
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2
docs/reference/as.disk.html
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@ -82,7 +82,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9020</span>
</span>
</div>

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docs/reference/as.mic.html
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@ -82,7 +82,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9020</span>
</span>
</div>

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docs/reference/as.mo.html
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@ -82,7 +82,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9020</span>
</span>
</div>
@ -399,7 +399,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<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>

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docs/reference/as.rsi.html
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@ -82,7 +82,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9020</span>
</span>
</div>

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docs/reference/catalogue_of_life.html
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@ -82,7 +82,7 @@
</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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9020</span>
</span>
</div>
@ -275,9 +275,9 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
<span class='co'># Get a note when a species was renamed</span>
<span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='st'>"Chlamydia psittaci"</span>)
<span class='co'># Note: 'Chlamydia psittaci' (Page, 1968) was renamed</span>
<span class='co'># 'Chlamydophila psittaci' (Everett et al., 1999)</span>
<span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='st'>"Chlamydophila psittaci"</span>)
<span class='co'># Note: 'Chlamydophila psittaci' (Everett et al., 1999) was renamed back to</span>
<span class='co'># 'Chlamydia psittaci' (Page, 1968)</span>
<span class='co'># [1] "C. psittaci"</span>
<span class='co'># Get any property from the entire taxonomic tree for all included species</span>
@ -295,9 +295,9 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
<span class='co'># Do not get mistaken - this package is about microorganisms</span>
<span class='fu'><a href='mo_property.html'>mo_kingdom</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Bacteria" # Bacteria?!</span>
<span class='co'># [1] "Fungi" # Fungi?!</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Chroococcus limneticus elegans" # Because a microorganism was found</span></pre>
<span class='co'># [1] "Cladosporium elegans" # Because a microorganism was found</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -313,7 +313,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

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docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9020</span>
</span>
</div>
@ -472,7 +472,7 @@
<td>
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
</td>
<td><p>Data set with 69,447 microorganisms</p></td>
<td><p>Data set with 67,107 microorganisms</p></td>
</tr><tr>
<td>
@ -502,7 +502,7 @@
<td>
<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
</td>
<td><p>Translation table for common microorganism codes</p></td>
<td><p>Translation table with 5,582 common microorganism codes</p></td>
</tr><tr>
<td>

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docs/reference/microorganisms.codes.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>Translation table for common microorganism codes — microorganisms.codes • AMR (for R)</title>
<title>Translation table with 5,582 common microorganism codes — microorganisms.codes • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Translation table for common microorganism codes — microorganisms.codes" />
<meta property="og:title" content="Translation table with 5,582 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(). 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.svg" />
@ -82,7 +82,7 @@
</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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9020</span>
</span>
</div>
@ -226,7 +226,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Translation table for common microorganism codes</h1>
<h1>Translation table with 5,582 common microorganism codes</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
</div>
@ -240,7 +240,7 @@
<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 5,585 observations and 2 variables:</p><ul>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 5,582 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>
@ -276,7 +276,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>

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docs/reference/microorganisms.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 with 69,447 microorganisms — microorganisms • AMR (for R)</title>
<title>Data set with 67,107 microorganisms — microorganisms • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with 69,447 microorganisms — microorganisms" />
<meta property="og:title" content="Data set with 67,107 microorganisms — microorganisms" />
<meta property="og:description" content="A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using as.mo()." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</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">1.1.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9020</span>
</span>
</div>
@ -226,7 +226,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with 69,447 microorganisms</h1>
<h1>Data set with 67,107 microorganisms</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.Rd</code></div>
</div>
@ -240,9 +240,8 @@
<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 17 variables:</p><ul>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 67,107 observations and 16 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>
<li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br /> Taxonomic rank of the microorganism</p></li>
<li><p><code>rank</code><br /> Text of the taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></li>
@ -256,6 +255,7 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
<p>Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786</p>
<p>Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <a href='https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date'>https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date</a> (check included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@ -266,7 +266,7 @@
<li><p>1 entry of <em>Blastocystis</em> (<em>Blastocystis hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
<li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
<li><p>6 families under the Enterobacterales order, according to Adeolu <em>et al.</em> (2016, PMID 27620848), that are not (yet) in the Catalogue of Life</p></li>
<li><p>12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
<li><p>7,368 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
</ul>
<h3>Direct download</h3>

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docs/reference/microorganisms.old.html
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@ -82,7 +82,7 @@
</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">1.1.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9020</span>
</span>
</div>
@ -240,10 +240,9 @@
<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 24,253 observations and 5 variables:</p><ul>
<li><p><code>col_id</code><br /> Catalogue of Life ID that was originally given</p></li>
<li><p><code>col_id_new</code><br /> New Catalogue of Life ID that responds to an entry in the <a href='microorganisms.html'>microorganisms</a> data set</p></li>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 12,709 observations and 4 variables:</p><ul>
<li><p><code>fullname</code><br /> Old full taxonomic name of the microorganism</p></li>
<li><p><code>fullname_new</code><br /> New full taxonomic name of the microorganism</p></li>
<li><p><code>ref</code><br /> Author(s) and year of concerning scientific publication</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>
</ul>
@ -251,6 +250,7 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
<p>Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786</p>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
@ -282,7 +282,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>
</footer>