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<h1>Key antibiotics for first <em>weighted</em> isolates</h1>
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<div class="hidden name"><code>key_antibiotics.Rd</code></div>
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</div>
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<div class="ref-description">
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<p>These function can be used to determine first isolates (see <code><a href='first_isolate.html'>first_isolate</a></code>). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first <em>weighted</em> isolates.</p>
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<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>tbl</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='st'>"amox"</span>,
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<span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='st'>"amcl"</span>, <span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='st'>"cfur"</span>, <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='st'>"pita"</span>,
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<span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='st'>"cipr"</span>, <span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='st'>"trsu"</span>, <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='st'>"vanc"</span>,
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<span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='st'>"teic"</span>, <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='st'>"tetr"</span>, <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='st'>"eryt"</span>,
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<span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='st'>"oxac"</span>, <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='st'>"rifa"</span>, <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='st'>"gent"</span>,
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<span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='st'>"tobr"</span>, <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='st'>"coli"</span>, <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='st'>"cfot"</span>,
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<span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='st'>"cfta"</span>, <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='st'>"mero"</span>, <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
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<span class='fu'>key_antibiotics_equal</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
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<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>)</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>tbl</th>
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<td><p>table with antibiotics coloms, like <code>amox</code> and <code>amcl</code>.</p></td>
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</tr>
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<tr>
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<th>col_mo</th>
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<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
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</tr>
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<tr>
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<th>universal_1, universal_2, universal_3, universal_4, universal_5, universal_6</th>
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<td><p>column names of <strong>broad-spectrum</strong> antibiotics, case-insensitive</p></td>
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</tr>
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<tr>
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<th>GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6</th>
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<td><p>column names of antibiotics for <strong>Gram positives</strong>, case-insensitive</p></td>
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</tr>
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<tr>
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<th>GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6</th>
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<td><p>column names of antibiotics for <strong>Gram negatives</strong>, case-insensitive</p></td>
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</tr>
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<tr>
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<th>warnings</th>
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<td><p>give warning about missing antibiotic columns, they will anyway be ignored</p></td>
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</tr>
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<tr>
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<th>...</th>
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<td><p>other parameters passed on to function</p></td>
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</tr>
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<tr>
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<th>x, y</th>
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<td><p>characters to compare</p></td>
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</tr>
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<tr>
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<th>type</th>
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<td><p>type to determine weighed isolates; can be <code>"keyantibiotics"</code> or <code>"points"</code>, see Details</p></td>
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</tr>
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<tr>
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<th>ignore_I</th>
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<td><p>logical to determine whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantibiotics"</code>, see Details</p></td>
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</tr>
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<tr>
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<th>points_threshold</th>
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<td><p>points until the comparison of key antibiotics will lead to inclusion of an isolate when <code>type = "points"</code>, see Details</p></td>
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</tr>
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<tr>
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<th>info</th>
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<td><p>print progress</p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>The function <code>key_antibiotics</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>). The <code><a href='first_isolate.html'>first_isolate</a></code> function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) found within the same episode (see <code>episode</code> parameter of <code><a href='first_isolate.html'>first_isolate</a></code>). Without key antibiotic comparison it wouldn't.</p>
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<p>At default, the antibiotics that are used for <strong>Gram positive bacteria</strong> are (colum names): <br />
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<code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"vanc"</code>, <code>"teic"</code>, <code>"tetr"</code>, <code>"eryt"</code>, <code>"oxac"</code>, <code>"rifa"</code>.</p>
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<p>At default, the antibiotics that are used for <strong>Gram negative bacteria</strong> are (colum names): <br />
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<code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"gent"</code>, <code>"tobr"</code>, <code>"coli"</code>, <code>"cfot"</code>, <code>"cfta"</code>, <code>"mero"</code>.</p>
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<p>The function <code>key_antibiotics_equal</code> checks the characters returned by <code>key_antibiotics</code> for equality, and returns a logical vector.</p>
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<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
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<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>
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<p><strong>1. Using</strong> <code>type = "keyantibiotics"</code> <strong>and parameter</strong> <code>ignore_I</code> <br />
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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. <br /></p>
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<p><strong>2. Using</strong> <code>type = "points"</code> <strong>and parameter</strong> <code>points_threshold</code> <br />
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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>, an isolate will be (re)selected as a first weighted isolate.</p>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate</a></code></p></div>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># NOT RUN {</span>
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<span class='co'># septic_patients is a dataset available in the AMR package</span>
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?<span class='no'>septic_patients</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='co'># set key antibiotics to a new variable</span>
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<span class='no'>my_patients</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://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'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(
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<span class='co'># now calculate first isolates</span>
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<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>),
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<span class='co'># and first WEIGHTED isolates</span>
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<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>)
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)
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<span class='co'># Check the difference, in this data set it results in 7% more isolates:</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_regular</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_weighted</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
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<span class='co'># output of the `key_antibiotics` function could be like this:</span>
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<span class='no'>strainA</span> <span class='kw'><-</span> <span class='st'>"SSSRR.S.R..S"</span>
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<span class='no'>strainB</span> <span class='kw'><-</span> <span class='st'>"SSSIRSSSRSSS"</span>
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<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>)
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<span class='co'># TRUE, because I is ignored (as well as missing values)</span>
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<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>)
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<span class='co'># FALSE, because I is not ignored and so the 4th value differs</span>
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<span class='co'># }</span></pre>
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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="#details">Details</a></li>
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<li><a href="#key-antibiotics">Key antibiotics</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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