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@ -45,15 +49,15 @@
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<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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<![endif]-->
</head>
<body>
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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">0.7.1.9067</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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</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
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</li>
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<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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</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>
</div>
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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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