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(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup

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dr. M.S. (Matthijs) Berends
2020-09-29 23:35:46 +02:00
parent 68e6e1e329
commit 4e0374af29
94 changed files with 1143 additions and 1165 deletions
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docs/reference/key_antibiotics.html
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@ -50,7 +50,7 @@
<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" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -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">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9035</span>
</span>
</div>
@ -395,32 +395,35 @@ 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='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='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>
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>
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='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='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='co'># can those strings can be compared with:</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='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>
<span class='co'># FALSE, because I is not ignored and so the 4th value differs</span>
<span class='co'># \donttest{</span>
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
<span class='co'># set key antibiotics to a new variable</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>
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>
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='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'># }</span>
</pre>
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