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mirror of https://github.com/msberends/AMR.git synced 2025-07-10 12:21:53 +02:00

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

This commit is contained in:
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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@ -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">1.3.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9035</span>
</span>
</div>
@ -424,34 +424,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
NIT = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>32</span>))
<span class='fu'>as.rsi</span>(<span class='kw'>df</span>)
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># the dplyr way</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='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.mic</span>, <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='as.mic.html'>is.mic</a></span>(<span class='kw'>x</span>) <span class='op'>|</span> <span class='fu'><a href='as.disk.html'>is.disk</a></span>(<span class='kw'>x</span>), <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.mic</span>), <span class='kw'>as.rsi</span>))
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>, mo = <span class='st'>"E. coli"</span>)
<span class='co'># to include information about urinary tract infections (UTI)</span>
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(mo = <span class='st'>"E. coli"</span>,
NIT = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&lt;= 2"</span>, <span class='fl'>32</span>),
from_the_bladder = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>TRUE</span>, <span class='fl'>FALSE</span>)) <span class='op'>%&gt;%</span>
<span class='fu'>as.rsi</span>(uti = <span class='st'>"from_the_bladder"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(mo = <span class='st'>"E. coli"</span>,
NIT = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&lt;= 2"</span>, <span class='fl'>32</span>),
specimen = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"urine"</span>, <span class='st'>"blood"</span>)) <span class='op'>%&gt;%</span>
<span class='fu'>as.rsi</span>() <span class='co'># automatically determines urine isolates</span>
<span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>NIT</span>), <span class='kw'>as.rsi</span>, mo = <span class='st'>"E. coli"</span>, uti = <span class='fl'>TRUE</span>)
}
<span class='co'># for single values</span>
<span class='fu'>as.rsi</span>(x = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>2</span>),
mo = <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
@ -463,6 +435,32 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
ab = <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
guideline = <span class='st'>"EUCAST"</span>)
<span class='co'># \donttest{</span>
<span class='co'># the dplyr way</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='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.mic</span>, <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='as.mic.html'>is.mic</a></span>(<span class='kw'>x</span>) <span class='op'>|</span> <span class='fu'><a href='as.disk.html'>is.disk</a></span>(<span class='kw'>x</span>), <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.mic</span>), <span class='kw'>as.rsi</span>))
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>, mo = <span class='st'>"E. coli"</span>)
<span class='co'># to include information about urinary tract infections (UTI)</span>
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(mo = <span class='st'>"E. coli"</span>,
NIT = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&lt;= 2"</span>, <span class='fl'>32</span>),
from_the_bladder = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>TRUE</span>, <span class='fl'>FALSE</span>)) <span class='op'>%&gt;%</span>
<span class='fu'>as.rsi</span>(uti = <span class='st'>"from_the_bladder"</span>)
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(mo = <span class='st'>"E. coli"</span>,
NIT = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"&lt;= 2"</span>, <span class='fl'>32</span>),
specimen = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"urine"</span>, <span class='st'>"blood"</span>)) <span class='op'>%&gt;%</span>
<span class='fu'>as.rsi</span>() <span class='co'># automatically determines urine isolates</span>
<span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>NIT</span>), <span class='kw'>as.rsi</span>, mo = <span class='st'>"E. coli"</span>, uti = <span class='fl'>TRUE</span>)
}
<span class='co'># For CLEANING existing R/SI values ------------------------------------</span>
@ -473,26 +471,23 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>rsi_data</span>) <span class='co'># for percentages</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='kw'>rsi_data</span>) <span class='co'># for frequencies</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='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>PEN</span><span class='op'>:</span><span class='kw'>RIF</span>), <span class='kw'>as.rsi</span>)
<span class='co'># same: </span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>as.rsi</span>(<span class='kw'>PEN</span><span class='op'>:</span><span class='kw'>RIF</span>)
<span class='co'># fastest way to transform all columns with already valid AMR results to class `rsi`:</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.rsi.eligible</span>, <span class='kw'>as.rsi</span>)
<span class='co'># note: from dplyr 1.0.0 on, this will be: </span>
<span class='co'># example_isolates %&gt;%</span>
<span class='co'># mutate(across(is.rsi.eligible, as.rsi))</span>
<span class='co'># default threshold of `is.rsi.eligible` is 5%.</span>
<span class='fu'>is.rsi.eligible</span>(<span class='kw'>WHONET</span><span class='op'>$</span><span class='kw'>`First name`</span>) <span class='co'># fails, &gt;80% is invalid</span>
<span class='fu'>is.rsi.eligible</span>(<span class='kw'>WHONET</span><span class='op'>$</span><span class='kw'>`First name`</span>, threshold = <span class='fl'>0.99</span>) <span class='co'># succeeds</span>
<span class='co'># the dplyr way</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='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>PEN</span><span class='op'>:</span><span class='kw'>RIF</span>), <span class='kw'>as.rsi</span>)
<span class='co'># same: </span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>as.rsi</span>(<span class='kw'>PEN</span><span class='op'>:</span><span class='kw'>RIF</span>)
<span class='co'># fastest way to transform all columns with already valid AMR results to class `rsi`:</span>
<span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.rsi.eligible</span>, <span class='kw'>as.rsi</span>)
<span class='co'># note: from dplyr 1.0.0 on, this will be: </span>
<span class='co'># example_isolates %&gt;%</span>
<span class='co'># mutate(across(is.rsi.eligible, as.rsi))</span>
}
<span class='co'># }</span>
</pre>
</div>
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