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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9006</small>
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</nav><div class="container template-reference-topic">
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<div class="row">
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 52 149 Microorganisms</h1>
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 52 151 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="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://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 52 149 observations and 22 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
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<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 52 151 observations and 22 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>. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.</p></li>
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<li><p><code>status</code> <br> Status of the taxon, either "accepted" or "synonym"</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>2 entries of <em>Staphylococcus</em> (coagulase-negative (CoNS) and coagulase-positive (CoPS))</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>6 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast, unknown fungus, and unknown anaerobic bacteria)</p></li>
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<li><p>8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)</p></li>
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</ul><p>The syntax used to transform the original data to a cleansed <span style="R">R</span> format, can be found here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R</a>.</p>
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</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="va">microorganisms</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 52,149 × 22</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo fullname status kingdom phylum class order family genus</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_ANAER (unknown ana… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> F_FUNGUS (unknown fun… accep… Fungi (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_GRAMN (unknown Gra… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B_GRAMP (unknown Gra… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> UNKNOWN (unknown nam… accep… (unkno… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> F_YEAST (unknown yea… accep… Fungi (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B_[FAM]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">""</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B_[ORD]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_[CLS]_ADTBCTRA Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B_[PHL]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 52,139 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 13 more variables: species <chr>, subspecies <chr>, rank <chr>, ref <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># source <chr>, lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif <chr>, gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># snomed <list></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 52,151 × 22</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo fullname status kingdom phylum class order family genus species</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_ANAER (unknow… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_ANAER-NEG (unknow… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_ANAER-POS (unknow… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> F_FUNGUS (unknow… accep… 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">#></span> <span style="color: #BCBCBC;"> 5</span> B_GRAMN (unknow… accep… 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">#></span> <span style="color: #BCBCBC;"> 6</span> B_GRAMP (unknow… accep… 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">#></span> <span style="color: #BCBCBC;"> 7</span> UNKNOWN (unknow… accep… (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">#></span> <span style="color: #BCBCBC;"> 8</span> F_YEAST (unknow… accep… 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">#></span> <span style="color: #BCBCBC;"> 9</span> B_[FAM]_ABDT… Abditib… accep… 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">#></span> <span style="color: #BCBCBC;">10</span> B_[ORD]_ABDT… Abditib… accep… 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">#></span> <span style="color: #949494;"># ℹ 52,141 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 12 more variables: subspecies <chr>, rank <chr>, ref <chr>, source <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>, gbif <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>, snomed <list></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
Reference in New Issue
Block a user