<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="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 --><linkrel="icon"type="image/png"sizes="16x16"href="../favicon-16x16.png"><linkrel="icon"type="image/png"sizes="32x32"href="../favicon-32x32.png"><linkrel="apple-touch-icon"type="image/png"sizes="180x180"href="../apple-touch-icon.png"><linkrel="apple-touch-icon"type="image/png"sizes="120x120"href="../apple-touch-icon-120x120.png"><linkrel="apple-touch-icon"type="image/png"sizes="76x76"href="../apple-touch-icon-76x76.png"><linkrel="apple-touch-icon"type="image/png"sizes="60x60"href="../apple-touch-icon-60x60.png"><scriptsrc="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><linkhref="../deps/bootstrap-5.3.1/bootstrap.min.css"rel="stylesheet"><scriptsrc="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><linkhref="../deps/Lato-0.4.9/font.css"rel="stylesheet"><linkhref="../deps/Fira_Code-0.4.9/font.css"rel="stylesheet"><linkhref="../deps/font-awesome-6.4.2/css/all.min.css"rel="stylesheet"><linkhref="../deps/font-awesome-6.4.2/css/v4-shims.min.css"rel="stylesheet"><scriptsrc="../deps/headroom-0.11.0/headroom.min.js"></script><scriptsrc="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><scriptsrc="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><scriptsrc="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><scriptsrc="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><scriptsrc="../deps/search-1.0.0/fuse.min.js"></script><scriptsrc="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><scriptsrc="../pkgdown.js"></script><linkhref="../extra.css"rel="stylesheet"><scriptsrc="../extra.js"></script><metaproperty="og:title"content="Join microorganisms to a Data Set — join"><metaname="description"content="Join the data set microorganisms easily to an existing data set or to a character vector."><metaproperty="og:description"content="Join the data set microorganisms easily to an existing data set or to a character vector."><metaproperty="og:image"content="https://msberends.github.io/AMR/logo.svg"></head><body>
<buttonclass="nav-link dropdown-toggle"type="button"id="dropdown-how-to"data-bs-toggle="dropdown"aria-expanded="false"aria-haspopup="true"><spanclass="fa fa-question-circle"></span> How to</button>
<ulclass="dropdown-menu"aria-labelledby="dropdown-how-to"><li><aclass="dropdown-item"href="../articles/AMR.html"><spanclass="fa fa-directions"></span> Conduct AMR Analysis</a></li>
<p>Join the data set <ahref="microorganisms.html">microorganisms</a> easily to an existing data set or to a <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> vector.</p>
<divclass="sourceCode"><preclass="sourceCode r"><code><span><spanclass="fu">inner_join_microorganisms</span><spanclass="op">(</span><spanclass="va">x</span>, by <spanclass="op">=</span><spanclass="cn">NULL</span>, suffix <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/c.html"class="external-link">c</a></span><spanclass="op">(</span><spanclass="st">"2"</span>, <spanclass="st">""</span><spanclass="op">)</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="fu">left_join_microorganisms</span><spanclass="op">(</span><spanclass="va">x</span>, by <spanclass="op">=</span><spanclass="cn">NULL</span>, suffix <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/c.html"class="external-link">c</a></span><spanclass="op">(</span><spanclass="st">"2"</span>, <spanclass="st">""</span><spanclass="op">)</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="fu">right_join_microorganisms</span><spanclass="op">(</span><spanclass="va">x</span>, by <spanclass="op">=</span><spanclass="cn">NULL</span>, suffix <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/c.html"class="external-link">c</a></span><spanclass="op">(</span><spanclass="st">"2"</span>, <spanclass="st">""</span><spanclass="op">)</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="fu">full_join_microorganisms</span><spanclass="op">(</span><spanclass="va">x</span>, by <spanclass="op">=</span><spanclass="cn">NULL</span>, suffix <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/c.html"class="external-link">c</a></span><spanclass="op">(</span><spanclass="st">"2"</span>, <spanclass="st">""</span><spanclass="op">)</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="fu">semi_join_microorganisms</span><spanclass="op">(</span><spanclass="va">x</span>, by <spanclass="op">=</span><spanclass="cn">NULL</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="fu">anti_join_microorganisms</span><spanclass="op">(</span><spanclass="va">x</span>, by <spanclass="op">=</span><spanclass="cn">NULL</span>, <spanclass="va">...</span><spanclass="op">)</span></span></code></pre></div>
<dd><p>existing data set to join, or <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> vector. In case of a <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> vector, the resulting <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a> will contain a column 'x' with these values.</p></dd>
<dd><p>a variable to join by - if left empty will search for a column with class <code><ahref="as.mo.html">mo</a></code> (created with <code><ahref="as.mo.html">as.mo()</a></code>) or will be <code>"mo"</code> if that column name exists in <code>x</code>, could otherwise be a column name of <code>x</code> with values that exist in <code>microorganisms$mo</code> (such as <code>by = "bacteria_id"</code>), or another column in <ahref="microorganisms.html">microorganisms</a> (but then it should be named, like <code>by = c("bacteria_id" = "fullname")</code>)</p></dd>
<dd><p>if there are non-joined duplicate variables in <code>x</code> and <code>y</code>, these suffixes will be added to the output to disambiguate them. Should be a <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> vector of length 2.</p></dd>
<p><strong>Note:</strong> As opposed to the <code>join()</code> functions of <code>dplyr</code>, <ahref="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><ahref="https://rdatatable.gitlab.io/data.table/reference/merge.html"class="external-link">merge()</a></code> and <code><ahref="https://rdrr.io/r/base/interaction.html"class="external-link">interaction()</a></code> functions from base <spanstyle="R">R</span> will be used.</p>
<spanclass="r-in"><span> date <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/seq.html"class="external-link">seq</a></span><spanclass="op">(</span></span></span>
<spanclass="r-in"><span> from <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/as.Date.html"class="external-link">as.Date</a></span><spanclass="op">(</span><spanclass="st">"2018-01-01"</span><spanclass="op">)</span>,</span></span>
<spanclass="r-in"><span> to <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/as.Date.html"class="external-link">as.Date</a></span><spanclass="op">(</span><spanclass="st">"2018-01-07"</span><spanclass="op">)</span>,</span></span>
<spanclass="r-in"><span> by <spanclass="op">=</span><spanclass="fl">1</span></span></span>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <atarget="_blank"href="https://github.com/msberends/AMR/blob/main/LICENSE"class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
