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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="">1.8.2.9032</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9033</small>
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</nav><div class="container template-reference-topic">
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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 48,787 Microorganisms</h1>
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 48,788 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 48,787 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 48,788 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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<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: 48,787 × 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> 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;"> 2</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;"> 3</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;"> 4</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;"> 5</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;"> 6</span> B_[CLS]_ABDTBCTR Abditibacter… accep… Bacter… Armat… <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;"> 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;"># … with 48,777 more rows, and 13 more variables: species <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># subspecies <chr>, rank <chr>, ref <chr>, source <chr>, lpsn <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># lpsn_parent <chr>, lpsn_renamed_to <chr>, gbif <chr>, gbif_parent <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># gbif_renamed_to <chr>, prevalence <dbl>, snomed <list></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 48,788 × 22</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo fulln…¹ status kingdom phylum class order family genus species subsp…²</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 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_ANA… (unkno… accep… Bacter… (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn… <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> F_FUN… (unkno… accep… Fungi (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn… <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_GRA… (unkno… accep… Bacter… (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn… <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> B_GRA… (unkno… accep… Bacter… (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn… <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;"> 5</span> UNKNO… (unkno… accep… (unkno… (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn… <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;"> 6</span> F_YEA… (unkno… accep… Fungi (unkn… (unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unkn… <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;"> 7</span> B_[CL… Abditi… accep… Bacter… Armat… Abdi… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <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: #BCBCBC;"> 8</span> B_[FA… Abditi… accep… Bacter… Abdit… Abdi… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>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: #BCBCBC;"> 9</span> B_[OR… Abditi… accep… Bacter… Abdit… Abdi… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span> <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: #BCBCBC;">10</span> B_[CL… Abditi… accep… Bacter… Abdit… Abdi… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <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;"># … with 48,778 more rows, 11 more variables: rank <chr>, ref <chr>,</span></span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># snomed <list>, and abbreviated variable names ¹fullname, ²subspecies</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