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@ -24,16 +24,20 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- pkgdown -->
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@ -46,7 +50,7 @@
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<meta property="og:title" content="Determine first (weighted) isolates — first_isolate" />
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<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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<meta property="og:image" content="/logo.svg" />
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<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
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@ -64,7 +68,7 @@
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</head>
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<body>
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<body data-spy="scroll" data-target="#toc">
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<header>
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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@ -78,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
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</span>
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</div>
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@ -223,7 +227,7 @@
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<div class="col-md-9 contents">
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<div class="page-header">
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<h1>Determine first (weighted) isolates</h1>
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<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/first_isolate.R'><code>R/first_isolate.R</code></a></small>
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<div class="hidden name"><code>first_isolate.Rd</code></div>
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</div>
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@ -404,19 +408,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='co'># Filter on first isolates:</span>
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<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<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>,
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<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
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<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
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<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%>%</span>
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<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>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>)
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<span class='co'># Which can be shortened to:</span>
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<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<span class='fu'>filter_first_isolate</span>()
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<span class='co'># or for first weighted isolates:</span>
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<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<span class='fu'>filter_first_weighted_isolate</span>()
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<span class='co'># Now let's see if first isolates matter:</span>
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<span class='no'>A</span> <span class='kw'><-</span> <span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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@ -430,8 +424,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='proportion.html'>resistance</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
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<span class='co'># Have a look at A and B.</span>
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<span class='co'># B is more reliable because every isolate is only counted once.</span>
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<span class='co'># Gentamicin resitance in hospital D appears to be 3.1% higher than</span>
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<span class='co'># B is more reliable because every isolate is counted only once.</span>
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<span class='co'># Gentamicin resitance in hospital D appears to be 3.7% higher than</span>
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<span class='co'># when you (erroneously) would have used all isolates for analysis.</span>
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@ -439,6 +433,14 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
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<span class='co'># Short-hand versions:</span>
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<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<span class='fu'>filter_first_isolate</span>()
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<span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<span class='fu'>filter_first_weighted_isolate</span>()
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<span class='co'># set key antibiotics to a new variable</span>
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<span class='no'>x</span>$<span class='no'>keyab</span> <span class='kw'><-</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='no'>x</span>)
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@ -450,19 +452,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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}</pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#arguments">Arguments</a></li>
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<li><a href="#source">Source</a></li>
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<li><a href="#value">Value</a></li>
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<li><a href="#details">Details</a></li>
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<li><a href="#key-antibiotics">Key antibiotics</a></li>
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<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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<li><a href="#see-also">See also</a></li>
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<li><a href="#examples">Examples</a></li>
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</ul>
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<nav id="toc" data-toggle="toc" class="sticky-top">
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<h2 data-toc-skip>Contents</h2>
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</nav>
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</div>
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</div>
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@ -473,7 +465,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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</div>
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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