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(v0.7.1.9033) 5000 new fungi

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dr. M.S. (Matthijs) Berends
2019-08-09 23:22:10 +02:00
parent 6a349bf757
commit 6598c5615d
31 changed files with 136 additions and 109 deletions
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docs/reference/WHOCC.html
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@ -80,7 +80,7 @@
</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">0.7.1.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>

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docs/reference/antibiotics.html
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@ -80,7 +80,7 @@
</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">0.7.1.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>

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docs/reference/as.ab.html
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@ -80,7 +80,7 @@
</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">0.7.1.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>

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docs/reference/catalogue_of_life.html
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@ -80,7 +80,7 @@
</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">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>
@ -246,10 +246,10 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria and Protozoa</p></li>
<li><p>All ~3,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
<li><p>All ~21,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>All ~61,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa</p></li>
<li><p>All ~8,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Microascales, Mucorales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~150 (sub)species from ~100 other relevant genera from the kingdom of Animalia (like <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
<li><p>All ~23,000 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>

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docs/reference/eucast_rules.html
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@ -80,7 +80,7 @@
</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">0.7.1.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>

5
docs/reference/ggplot_rsi.html
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@ -80,7 +80,7 @@
</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">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>
@ -241,7 +241,8 @@
<span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>S</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>I</span> <span class='kw'>=</span> <span class='st'>"#61f7ff"</span>, <span class='kw'>IR</span> <span class='kw'>=</span>
<span class='st'>"#ff6961"</span>, <span class='kw'>R</span> <span class='kw'>=</span> <span class='st'>"#ff6961"</span>), <span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>2.5</span>,
<span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"gray15"</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>caption</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>y.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
<span class='kw'>caption</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antimicrobial"</span>, <span class='kw'>y.title</span> <span class='kw'>=</span> <span class='st'>"Proportion"</span>,
<span class='no'>...</span>)
<span class='fu'>geom_rsi</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"antibiotic"</span>, <span class='st'>"interpretation"</span>),
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,

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docs/reference/guess_ab_col.html
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@ -80,7 +80,7 @@
</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">0.7.1.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>

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docs/reference/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>
@ -480,7 +480,7 @@
<td>
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
</td>
<td><p>Data set with ~65,000 microorganisms</p></td>
<td><p>Data set with ~70,000 microorganisms</p></td>
</tr><tr>
<td>

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docs/reference/mdro.html
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@ -80,7 +80,7 @@
</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">0.7.1.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>

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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 ~65,000 microorganisms — microorganisms • AMR (for R)</title>
<title>Data set with ~70,000 microorganisms — microorganisms • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -45,7 +45,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with ~65,000 microorganisms — microorganisms" />
<meta property="og:title" content="Data set with ~70,000 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." />
@ -80,7 +80,7 @@
</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">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>
@ -223,7 +223,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with ~65,000 microorganisms</h1>
<h1>Data set with ~70,000 microorganisms</h1>
<div class="hidden name"><code>microorganisms.Rd</code></div>
</div>
@ -238,7 +238,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 68,260 observations and 16 variables:</p><dl class='dl-horizontal'>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 69,854 observations and 16 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd>

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docs/reference/microorganisms.old.html
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@ -80,7 +80,7 @@
</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">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>
@ -238,7 +238,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 21,743 observations and 4 variables:</p><dl class='dl-horizontal'>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 22,932 observations and 4 variables:</p><dl class='dl-horizontal'>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID that was originally given</p></dd>
<dt><code>col_id_new</code></dt><dd><p>New Catalogue of Life ID that responds to an entry in the <code><a href='microorganisms.html'>microorganisms</a></code> data set</p></dd>
<dt><code>fullname</code></dt><dd><p>Old full taxonomic name of the microorganism</p></dd>

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docs/reference/mo_property.html
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@ -80,7 +80,7 @@
</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">0.7.1.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9033</span>
</span>
</div>