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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -138,7 +138,7 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 70,764 observations and 16 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
<p>A [tibble<a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a> with 70,764 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>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>
@ -181,8 +181,7 @@
<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
<p>This data set is available as 'flat file' for use even without <span style="R">R</span> - you can find the file here: <a href="https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt" class="external-link">https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt</a>.</p>
<p>The file in <span style="R">R</span> format (with preserved data structure) can be found here: <a href="https://github.com/msberends/AMR/raw/main/data/microorganisms.rda" class="external-link">https://github.com/msberends/AMR/raw/main/data/microorganisms.rda</a>.</p>
<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
</div>
@ -200,12 +199,6 @@
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
@ -214,35 +207,22 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">microorganisms</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname kingdom phylum</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 F_FUNGUS (unknown fungus) Fungi (unknown phylum)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B_GRAMN (unknown Gram-negatives) Bacteria (unknown phylum)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 B_GRAMP (unknown Gram-positives) Bacteria (unknown phylum)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 UNKNOWN (unknown name) (unknown kingdom) (unknown phylum)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 F_YEAST (unknown yeast) Fungi (unknown phylum)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 B_[FAM]_ABDTBCTR Abditibacteriaceae Bacteria Abditibacteriota</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> class order family genus</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 (unknown class) (unknown order) (unknown family) (unknown genus)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 (unknown class) (unknown order) (unknown family) (unknown Gram-negatives)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 (unknown class) (unknown order) (unknown family) (unknown Gram-positives)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 (unknown class) (unknown order) (unknown family) (unknown genus)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 (unknown class) (unknown order) (unknown family) (unknown genus)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 Abditibacteria Abditibacteriales Abditibacteriaceae </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> species subspecies rank ref species_id</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 (unknown species) (unknown subspecies) species &lt;NA&gt; NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 (unknown species) (unknown subspecies) species &lt;NA&gt; NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 (unknown species) (unknown subspecies) species &lt;NA&gt; NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 (unknown species) (unknown subspecies) (unknown rank) &lt;NA&gt; NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 (unknown species) (unknown subspecies) species &lt;NA&gt; NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 family &lt;NA&gt; NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> source prevalence snomed</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 manually added 3 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 manually added 3 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 manually added 3 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 manually added 3 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 manually added 3 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 CoL 2 </span>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 70,764 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname kingdom phylum class order family genus species</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> F_FUNGUS (unknown fu… Fungi (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_GRAMN (unknown Gr… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_GRAMP (unknown Gr… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> UNKNOWN (unknown na… (unkno… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> F_YEAST (unknown ye… Fungi (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_[FAM]_ABDTBCTR Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_[ORD]_ABDTBCTR Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ABDTB Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ABDTB_UTST Abditibacte… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>utste…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> C_ABDTD Abditodentr… Chromi… Foram… Glob… Rota… <span style="color: #949494;">"</span>Boli… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 70,754 more rows, and 7 more variables: subspecies &lt;chr&gt;, rank &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ref &lt;chr&gt;, species_id &lt;dbl&gt;, source &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
</code></pre></div>
</div>
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