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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Join microorganisms to a Data Set — join • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Join microorganisms to a Data Set — join"><meta name="description" content="Join the data set microorganisms easily to an existing data set or to a character vector."><meta property="og:description" content="Join the data set microorganisms easily to an existing data set or to a character vector."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Join microorganisms to a Data Set — join • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Join microorganisms to a Data Set — join"><meta name="description" content="Join the data set microorganisms easily to an existing data set or to a character vector."><meta property="og:description" content="Join the data set microorganisms easily to an existing data set or to a character vector."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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@@ -7,7 +7,7 @@
<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="">3.0.1.9057</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</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">
@@ -94,32 +94,32 @@
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>**Note:** As opposed to the `join()` functions of `dplyr`, [character] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix.</p>
<p>If the `dplyr` package is installed, their join functions will be used. Otherwise, the much slower [merge()] and [interaction()] functions from base <span style="R">R</span> will be used.</p>
<p><strong>Note:</strong> As opposed to the <code>join()</code> functions of <code>dplyr</code>, <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vectors are supported and at default existing columns will get a suffix <code>"2"</code> and the newly joined columns will not get a suffix.</p>
<p>If the <code>dplyr</code> package is installed, their join functions will be used. Otherwise, the much slower <code><a href="https://rdrr.io/pkg/data.table/man/merge.html" class="external-link">merge()</a></code> and <code><a href="https://rdrr.io/r/base/interaction.html" class="external-link">interaction()</a></code> functions from base <span style="R">R</span> will be used.</p>
</div>
<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">left_join_microorganisms</span><span class="op">(</span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 26</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname status 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 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> <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 16 more variables: subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># oxygen_tolerance &lt;chr&gt;, source &lt;chr&gt;, lpsn &lt;chr&gt;, lpsn_parent &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># lpsn_renamed_to &lt;chr&gt;, mycobank &lt;chr&gt;, mycobank_parent &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># mycobank_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;, gbif_parent &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 28</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname status domain kingdom phylum class order family genus</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 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> <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN Klebsiella… accep… Bacte… Pseudo… Pseud… Gamm… Ente… Enter… Kleb…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 18 more variables: species &lt;chr&gt;, subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># oxygen_tolerance &lt;chr&gt;, morphology &lt;chr&gt;, source &lt;chr&gt;, lpsn &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># lpsn_parent &lt;chr&gt;, lpsn_renamed_to &lt;chr&gt;, mycobank &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># mycobank_parent &lt;chr&gt;, mycobank_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># gbif_parent &lt;chr&gt;, gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
<span class="r-in"><span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="st">"B_KLBSL_PNMN"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 26</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname status 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 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> <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 16 more variables: subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># oxygen_tolerance &lt;chr&gt;, source &lt;chr&gt;, lpsn &lt;chr&gt;, lpsn_parent &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># lpsn_renamed_to &lt;chr&gt;, mycobank &lt;chr&gt;, mycobank_parent &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># mycobank_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;, gbif_parent &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 28</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname status domain kingdom phylum class order family genus</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 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> <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN Klebsiella… accep… Bacte… Pseudo… Pseud… Gamm… Ente… Enter… Kleb…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 18 more variables: species &lt;chr&gt;, subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># oxygen_tolerance &lt;chr&gt;, morphology &lt;chr&gt;, source &lt;chr&gt;, lpsn &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># lpsn_parent &lt;chr&gt;, lpsn_renamed_to &lt;chr&gt;, mycobank &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># mycobank_parent &lt;chr&gt;, mycobank_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># gbif_parent &lt;chr&gt;, gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span></span></span>
@@ -139,14 +139,15 @@
<span class="r-in"><span><span class="va">df_joined</span> <span class="op">&lt;-</span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="va">df</span>, <span class="st">"bacteria"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df_joined</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "bacteria" "fullname" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "status" "kingdom" "phylum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "class" "order" "family" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "genus" "species" "subspecies" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "rank" "ref" "oxygen_tolerance" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "source" "lpsn" "lpsn_parent" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "lpsn_renamed_to" "mycobank" "mycobank_parent" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "mycobank_renamed_to" "gbif" "gbif_parent" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "gbif_renamed_to" "prevalence" "snomed" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "status" "domain" "kingdom" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "phylum" "class" "order" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "family" "genus" "species" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "subspecies" "rank" "ref" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "oxygen_tolerance" "morphology" "source" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "lpsn" "lpsn_parent" "lpsn_renamed_to" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "mycobank" "mycobank_parent" "mycobank_renamed_to"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "gbif" "gbif_parent" "gbif_renamed_to" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "prevalence" "snomed" </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -171,14 +172,15 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "IPM" "MEM" "MTR" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "CHL" "COL" "MUP" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "RIF" "fullname" "status" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "kingdom" "phylum" "class" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "order" "family" "genus" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [55] "species" "subspecies" "rank" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [58] "ref" "oxygen_tolerance" "source" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "lpsn" "lpsn_parent" "lpsn_renamed_to" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [64] "mycobank" "mycobank_parent" "mycobank_renamed_to"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [67] "gbif" "gbif_parent" "gbif_renamed_to" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [70] "prevalence" "snomed" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "domain" "kingdom" "phylum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "class" "order" "family" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [55] "genus" "species" "subspecies" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [58] "rank" "ref" "oxygen_tolerance" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "morphology" "source" "lpsn" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [64] "lpsn_parent" "lpsn_renamed_to" "mycobank" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [67] "mycobank_parent" "mycobank_renamed_to" "gbif" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [70] "gbif_parent" "gbif_renamed_to" "prevalence" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] "snomed" </span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>