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dr. M.S. (Matthijs) Berends
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9101</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9102</span>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9102</span>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9102</span>
</span>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9101</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9102</span>
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9102</span>
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@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9102</span>
</span>
</div>
@ -231,11 +231,11 @@
</div>
<div id="amr-0-7-1-9100" class="section level1">
<div id="amr-0-7-1-9102" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9100" class="anchor"></a>AMR 0.7.1.9100<small> Unreleased </small>
<a href="#amr-0-7-1-9102" class="anchor"></a>AMR 0.7.1.9102<small> Unreleased </small>
</h1>
<p><small>Last updated: 08-Oct-2019</small></p>
<p><small>Last updated: 11-Oct-2019</small></p>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
@ -267,31 +267,32 @@ This is important, because a value like <code>"testvalue"</code> could never be
<a href="#new" class="anchor"></a>New</h3>
<ul>
<li>
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the antimicrobial resistance of any bug-drug combination in a data set. The columns with microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3">x[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, ]</a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co">#&gt; ab mo S I R total</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co">#&gt; 1 AMC CoNS 178 0 132 310</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co">#&gt; 2 AMC E. coli 332 74 61 467</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co">#&gt; 3 AMC K. pneumoniae 49 3 6 58</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co">#&gt; 4 AMC P. aeruginosa 0 0 30 30</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co">#&gt; 5 AMC P. mirabilis 28 7 1 36</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3">x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co">#&gt; mo ab S I R total</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co">#&gt; 1 A. baumannii AMC 0 0 3 3</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co">#&gt; 2 A. baumannii AMK 0 0 0 0</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co">#&gt; 3 A. baumannii AMP 0 0 3 3</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co">#&gt; 4 A. baumannii AMX 0 0 3 3</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># change the transformation with the FUN argument to anything you like:</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates, <span class="dt">FUN =</span> mo_gramstain)</a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14">x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co">#&gt; ab mo S I R total</span></a>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co">#&gt; 1 AMC Gram-negative 469 89 174 732</span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co">#&gt; 2 AMC Gram-positive 873 2 272 1147</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co">#&gt; 3 AMK Gram-negative 251 0 2 253</span></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co">#&gt; 4 AMK Gram-positive 0 0 100 100</span></a></code></pre></div>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co">#&gt; mo ab S I R total</span></a>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co">#&gt; 1 Gram-negative AMC 469 89 174 732</span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co">#&gt; 2 Gram-negative AMK 251 0 2 253</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co">#&gt; 3 Gram-negative AMP 227 0 405 632</span></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co">#&gt; 4 Gram-negative AMX 227 0 405 632</span></a>
<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></a></code></pre></div>
<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/format.html">format</a></span>(x, <span class="dt">combine_IR =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
</li>
<li>
<p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
<p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="co"># --------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># ----------------------- -----------------------</span></a>
@ -377,6 +378,7 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<a href="#other" class="anchor"></a>Other</h4>
<ul>
<li>Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors</li>
<li>Cleaned the coding style of every single syntax line in this package with the help of the <code>lintr</code> package</li>
</ul>
</div>
</div>
@ -1290,7 +1292,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9100">0.7.1.9100</a></li>
<li><a href="#amr-0-7-1-9102">0.7.1.9102</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>

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pandoc: []
pandoc: 2.3.1
pkgdown: 1.4.1
pkgdown_sha: ~
articles:

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9102</span>
</span>
</div>
@ -327,7 +327,7 @@
<pre class="examples"><span class='co'># \donttest{</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>example_isolates</span>)
<span class='no'>x</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='no'>x</span>)
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='no'>x</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name (atc)"</span>)
<span class='co'># Use FUN to change to transformation of microorganism codes</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>example_isolates</span>,

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@ -15,21 +15,25 @@
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
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@ -45,15 +49,15 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Determine first (weighted) isolates — first_isolate" />
<meta property="og:description" content="Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type." />
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@ -64,6 +68,7 @@
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</head>
<body>
@ -80,7 +85,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9067</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9102</span>
</span>
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@ -189,7 +194,6 @@
</a>
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</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
@ -207,7 +211,7 @@
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</ul>
<form class="navbar-form navbar-right" role="search">
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<div class="form-group">
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
</div>
@ -218,6 +222,7 @@
</div><!--/.navbar -->
</header>
<div class="row">
@ -229,9 +234,7 @@
</div>
<div class="ref-description">
<p>Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.</p>
</div>
<pre class="usage"><span class='fu'>first_isolate</span>(<span class='no'>x</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
@ -247,7 +250,7 @@
<span class='fu'>filter_first_weighted_isolate</span>(<span class='no'>x</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
@ -324,15 +327,13 @@
<td><p>parameters passed on to the <code>first_isolate</code> function</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Methodology of this function is based on: <strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Logical vector</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>WHY THIS IS SO IMPORTANT</strong> <br />
@ -351,32 +352,30 @@ To conduct an analysis of antimicrobial resistance, you should only include the
filter(only_weighted_firsts == TRUE) %&gt;%
select(-only_weighted_firsts)
</pre>
<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
<p>There are two ways to determine whether isolates can be included as first <em>weighted</em> isolates which will give generally the same results: <br /></p>
<p>There are two ways to determine whether isolates can be included as first <em>weighted</em> isolates which will give generally the same results: <br /></p>
<p><strong>1. Using</strong> <code>type = "keyantibiotics"</code> <strong>and parameter</strong> <code>ignore_I</code> <br />
Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the <code><a href='key_antibiotics.html'>key_antibiotics</a></code> function. <br /></p>
<p><strong>2. Using</strong> <code>type = "points"</code> <strong>and parameter</strong> <code>points_threshold</code> <br />
A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, which default to <code>2</code>, an isolate will be (re)selected as a first weighted isolate.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='key_antibiotics.html'>key_antibiotics</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># Filter on first isolates:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>,
@ -412,76 +411,44 @@ To conduct an analysis of antimicrobial resistance, you should only include the
<span class='co'>## OTHER EXAMPLES:</span>
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># set key antibiotics to a new variable</span>
<span class='no'>x</span>$<span class='no'>keyab</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='no'>x</span>)
<span class='no'>x</span>$<span class='no'>first_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>)
<span class='no'>x</span>$<span class='no'>first_isolate</span> <span class='kw'>&lt;-</span> <span class='fu'>first_isolate</span>(<span class='no'>x</span>)
<span class='no'>x</span>$<span class='no'>first_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
<span class='no'>x</span>$<span class='no'>first_isolate_weighed</span> <span class='kw'>&lt;-</span> <span class='fu'>first_isolate</span>(<span class='no'>x</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
<span class='no'>x</span>$<span class='no'>first_blood_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Blood'</span>)
<span class='no'>x</span>$<span class='no'>first_blood_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Blood'</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
<span class='no'>x</span>$<span class='no'>first_urine_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Urine'</span>)
<span class='no'>x</span>$<span class='no'>first_urine_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Urine'</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
<span class='no'>x</span>$<span class='no'>first_resp_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Respiratory'</span>)
<span class='no'>x</span>$<span class='no'>first_resp_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Respiratory'</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
<span class='co'># }</span></pre>
<span class='no'>x</span>$<span class='no'>first_blood_isolate</span> <span class='kw'>&lt;-</span> <span class='fu'>first_isolate</span>(<span class='no'>x</span>, <span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>"Blood"</span>)
}</pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#key-antibiotics">Key antibiotics</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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@ -504,6 +471,8 @@ To conduct an analysis of antimicrobial resistance, you should only include the
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@ -84,7 +84,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
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