<!-- 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=1.0"><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"><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkhref="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css"rel="stylesheet"crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><linkhref="../extra.css"rel="stylesheet"><scriptsrc="../extra.js"></script><metaproperty="og:title"content="Join microorganisms to a Data Set — join"><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"><metaname="twitter:card"content="summary_large_image"><metaname="twitter:creator"content="@msberends"><metaname="twitter:site"content="@univgroningen"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<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>
<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>
<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></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>
<dt>by</dt>
<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>
<dt>suffix</dt>
<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>
<dt>...</dt>
<dd><p>ignored, only in place to allow future extensions</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://rdrr.io/r/base/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>
The <ahref="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>On our website <ahref="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a> you can find <ahref="https://msberends.github.io/AMR/articles/AMR.html">a comprehensive tutorial</a> about how to conduct AMR data analysis, the <ahref="https://msberends.github.io/AMR/reference/">complete documentation of all functions</a> and <ahref="https://msberends.github.io/AMR/articles/WHONET.html">an example analysis using WHONET data</a>.</p>
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>,
by <spanclass="op">=</span><spanclass="fl">1</span><spanclass="op">)</span>,
