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dr. M.S. (Matthijs) Berends
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@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Key antibiotics for first <em>weighted</em> isolates — key_antibiotics • AMR (for R)</title>
<title>Key antibiotics for first weighted isolates — key_antibiotics • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -48,7 +48,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Key antibiotics for first <em>weighted</em> isolates — key_antibiotics" />
<meta property="og:title" content="Key antibiotics for first weighted isolates — key_antibiotics" />
<meta property="og:description" content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first weighted isolates." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
@ -82,7 +82,7 @@
</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">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@ -236,37 +236,37 @@
</div>
<pre class="usage"><span class='fu'>key_antibiotics</span>(
<span class='no'>x</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"amoxicillin"</span>),
<span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"amoxicillin/clavulanic acid"</span>),
<span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"cefuroxime"</span>),
<span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"piperacillin/tazobactam"</span>),
<span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"ciprofloxacin"</span>),
<span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"trimethoprim/sulfamethoxazole"</span>),
<span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"vancomycin"</span>),
<span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"teicoplanin"</span>),
<span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"tetracycline"</span>),
<span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"erythromycin"</span>),
<span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"oxacillin"</span>),
<span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"rifampin"</span>),
<span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"gentamicin"</span>),
<span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"tobramycin"</span>),
<span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"colistin"</span>),
<span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"cefotaxime"</span>),
<span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"ceftazidime"</span>),
<span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"meropenem"</span>),
<span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
col_mo = <span class='kw'>NULL</span>,
universal_1 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"amoxicillin"</span>),
universal_2 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"amoxicillin/clavulanic acid"</span>),
universal_3 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"cefuroxime"</span>),
universal_4 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"piperacillin/tazobactam"</span>),
universal_5 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"ciprofloxacin"</span>),
universal_6 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"trimethoprim/sulfamethoxazole"</span>),
GramPos_1 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"vancomycin"</span>),
GramPos_2 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"teicoplanin"</span>),
GramPos_3 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"tetracycline"</span>),
GramPos_4 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"erythromycin"</span>),
GramPos_5 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"oxacillin"</span>),
GramPos_6 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"rifampin"</span>),
GramNeg_1 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"gentamicin"</span>),
GramNeg_2 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"tobramycin"</span>),
GramNeg_3 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"colistin"</span>),
GramNeg_4 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"cefotaxime"</span>),
GramNeg_5 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"ceftazidime"</span>),
GramNeg_6 = <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='kw'>x</span>, <span class='st'>"meropenem"</span>),
warnings = <span class='fl'>TRUE</span>,
<span class='kw'>...</span>
)
<span class='fu'>key_antibiotics_equal</span>(
<span class='no'>y</span>,
<span class='no'>z</span>,
<span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
<span class='kw'>y</span>,
<span class='kw'>z</span>,
type = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
ignore_I = <span class='fl'>TRUE</span>,
points_threshold = <span class='fl'>2</span>,
info = <span class='fl'>FALSE</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -388,31 +388,31 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
<span class='co'># set key antibiotics to a new variable</span>
<span class='no'>my_patients</span> <span class='kw'>&lt;-</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'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='kw'>my_patients</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(keyab = <span class='fu'>key_antibiotics</span>(<span class='kw'>.</span>)) <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
<span class='co'># now calculate first isolates</span>
<span class='kw'>first_regular</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
first_regular = <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='kw'>.</span>, col_keyantibiotics = <span class='fl'>FALSE</span>),
<span class='co'># and first WEIGHTED isolates</span>
<span class='kw'>first_weighted</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>"keyab"</span>)
first_weighted = <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='kw'>.</span>, col_keyantibiotics = <span class='st'>"keyab"</span>)
)
<span class='co'># Check the difference, in this data set it results in 7% more isolates:</span>
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_regular</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_weighted</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='kw'>my_patients</span><span class='op'>$</span><span class='kw'>first_regular</span>, na.rm = <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='kw'>my_patients</span><span class='op'>$</span><span class='kw'>first_weighted</span>, na.rm = <span class='fl'>TRUE</span>)
}
<span class='co'># output of the `key_antibiotics` function could be like this:</span>
<span class='no'>strainA</span> <span class='kw'>&lt;-</span> <span class='st'>"SSSRR.S.R..S"</span>
<span class='no'>strainB</span> <span class='kw'>&lt;-</span> <span class='st'>"SSSIRSSSRSSS"</span>
<span class='kw'>strainA</span> <span class='op'>&lt;-</span> <span class='st'>"SSSRR.S.R..S"</span>
<span class='kw'>strainB</span> <span class='op'>&lt;-</span> <span class='st'>"SSSIRSSSRSSS"</span>
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>)
<span class='fu'>key_antibiotics_equal</span>(<span class='kw'>strainA</span>, <span class='kw'>strainB</span>)
<span class='co'># TRUE, because I is ignored (as well as missing values)</span>
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>, <span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>key_antibiotics_equal</span>(<span class='kw'>strainA</span>, <span class='kw'>strainB</span>, ignore_I = <span class='fl'>FALSE</span>)
<span class='co'># FALSE, because I is not ignored and so the 4th value differs</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@ -429,7 +429,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
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