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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 70,764 Microorganisms</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="d-none name"><code>microorganisms.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>A data set containing the full microbial taxonomy (<strong>last updated: 5 October 2021</strong>) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">microorganisms</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<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>
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<li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code></p></li>
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<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>
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<li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></li>
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<li><p><code>ref</code><br> Author(s) and year of concerning scientific publication</p></li>
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<li><p><code>species_id</code><br> ID of the species as used by the Catalogue of Life</p></li>
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<li><p><code>source</code><br> Either "CoL", "LPSN" or "manually added" (see <em>Source</em>)</p></li>
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<li><p><code>prevalence</code><br> Prevalence of the microorganism, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
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<li><p><code>snomed</code><br> Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, according to the US Edition of SNOMED CT from 1 September 2020 (see <em>Source</em>). 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>
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</ul></div>
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<div class="section level2">
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<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
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<p>Catalogue of Life: 2019 Annual Checklist as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Annual Checklist (public online taxonomic database), <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a></p></li>
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</ul><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a></p></li>
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<li><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; <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">doi:10.1099/ijsem.0.002786</a></p></li>
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<li><p>Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; <a href="https://doi.org/10.1093/nar/gkt1111" class="external-link">doi:10.1093/nar/gkt1111</a></p></li>
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<li><p>Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; <a href="https://doi.org/10.1099/00207713-47-2-590" class="external-link">doi:10.1099/00207713-47-2-590</a></p></li>
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</ul><p>US Edition of SNOMED CT from 1 September 2020 as currently implemented in this <code>AMR</code> package:</p><ul><li><p>Retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.</p>
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<p>For example, <em>Staphylococcus pettenkoferi</em> was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (<a href="https://doi.org/10.1016/s0732-8893%2802%2900399-1" class="external-link">doi:10.1016/s0732-8893(02)00399-1</a>
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), but it was not before 2007 that a publication in IJSEM followed (<a href="https://doi.org/10.1099/ijs.0.64381-0" class="external-link">doi:10.1099/ijs.0.64381-0</a>
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). Consequently, the <code>AMR</code> package returns 2007 for <code>mo_year("S. pettenkoferi")</code>.</p><div class="section">
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<h3 id="manual-additions">Manual additions<a class="anchor" aria-label="anchor" href="#manual-additions"></a></h3>
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<p>For convenience, some entries were added manually:</p><ul><li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li>
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<li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative (CoNS) and coagulase-positive (CoPS))</p></li>
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<li><p>3 entries of <em>Trichomonas</em> (<em>T. vaginalis</em>, and its family and genus)</p></li>
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<li><p>4 entries of <em>Toxoplasma</em> (<em>T. gondii</em>, and its order, family and genus)</p></li>
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<li><p>1 entry of <em>Candida</em> (<em>C. krusei</em>), that is not (yet) in the Catalogue of Life</p></li>
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<li><p>1 entry of <em>Blastocystis</em> (<em>B. hominis</em>), although it officially does not exist (Noel <em>et al.</em> 2005, PMID 15634993)</p></li>
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<li><p>1 entry of <em>Moraxella</em> (<em>M. catarrhalis</em>), which was formally named <em>Branhamella catarrhalis</em> (Catlin, 1970) though this change was never accepted within the field of clinical microbiology</p></li>
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<li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
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<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>
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</ul></div>
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<div class="section">
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<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
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<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>
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<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>
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</div>
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</div>
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<div class="section level2">
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<h2 id="about-the-records-from-lpsn-see-source-">About the Records from LPSN (see <em>Source</em>)<a class="anchor" aria-label="anchor" href="#about-the-records-from-lpsn-see-source-"></a></h2>
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<p>The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes. LPSN is a free to use service founded by Jean P. Euzeby in 1997 and later on maintained by Aidan C. Parte.</p>
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<p>As of February 2020, the regularly augmented LPSN database at DSMZ is the basis of the new LPSN service. The new database was implemented for the Type-Strain Genome Server and augmented in 2018 to store all kinds of nomenclatural information. Data from the previous version of LPSN and from the Prokaryotic Nomenclature Up-to-date (PNU) service were imported into the new system. PNU had been established in 1993 as a service of the Leibniz Institute DSMZ, and was curated by Norbert Weiss, Manfred Kracht and Dorothea Gleim.</p>
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</div>
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<div class="section level2">
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<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
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<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
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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>
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<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>
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</div>
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<div class="section level2">
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<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>
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</div>
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<div class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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<div class="dont-index"><p><code><a href="as.mo.html">as.mo()</a></code>, <code><a href="mo_property.html">mo_property()</a></code>, <a href="microorganisms.codes.html">microorganisms.codes</a>, <a href="intrinsic_resistant.html">intrinsic_resistant</a></p></div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> mo fullname kingdom phylum</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 F_FUNGUS (unknown fungus) Fungi (unknown phylum)</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B_GRAMN (unknown Gram-negatives) Bacteria (unknown phylum)</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B_GRAMP (unknown Gram-positives) Bacteria (unknown phylum)</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 UNKNOWN (unknown name) (unknown kingdom) (unknown phylum)</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F_YEAST (unknown yeast) Fungi (unknown phylum)</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 B_[FAM]_ABDTBCTR Abditibacteriaceae Bacteria Abditibacteriota</span>
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<span class="r-out co"><span class="r-pr">#></span> class order family genus</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 (unknown class) (unknown order) (unknown family) (unknown genus)</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 (unknown class) (unknown order) (unknown family) (unknown Gram-negatives)</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 (unknown class) (unknown order) (unknown family) (unknown Gram-positives)</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 (unknown class) (unknown order) (unknown family) (unknown genus)</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 (unknown class) (unknown order) (unknown family) (unknown genus)</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 Abditibacteria Abditibacteriales Abditibacteriaceae </span>
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<span class="r-out co"><span class="r-pr">#></span> species subspecies rank ref species_id</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 (unknown species) (unknown subspecies) species <NA> NA</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 (unknown species) (unknown subspecies) species <NA> NA</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 (unknown species) (unknown subspecies) species <NA> NA</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 (unknown species) (unknown subspecies) (unknown rank) <NA> NA</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 (unknown species) (unknown subspecies) species <NA> NA</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 family <NA> NA</span>
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<span class="r-out co"><span class="r-pr">#></span> source prevalence snomed</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 manually added 3 </span>
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<span class="r-out co"><span class="r-pr">#></span> 2 manually added 3 </span>
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<span class="r-out co"><span class="r-pr">#></span> 3 manually added 3 </span>
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<span class="r-out co"><span class="r-pr">#></span> 4 manually added 3 </span>
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<span class="r-out co"><span class="r-pr">#></span> 5 manually added 3 </span>
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<span class="r-out co"><span class="r-pr">#></span> 6 CoL 2 </span>
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</code></pre></div>
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</div>
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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