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(v1.4.0.9000) more extensive unit tests

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dr. M.S. (Matthijs) Berends
2020-10-15 09:46:41 +02:00
parent 28e77680c5
commit 833a1be36d
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docs/reference/as.rsi.html
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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">1.4.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
</span>
</div>
@ -242,45 +242,45 @@
<p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S &lt; I &lt; R</code>. Values that cannot be interpreted will be returned as <code>NA</code> with a warning.</p>
</div>
<pre class="usage"><span class='fu'>as.rsi</span>(<span class='kw'>x</span>, <span class='kw'>...</span>)
<pre class="usage"><span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>is.rsi</span>(<span class='kw'>x</span>)
<span class='fu'>is.rsi</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
<span class='fu'>is.rsi.eligible</span>(<span class='kw'>x</span>, threshold = <span class='fl'>0.05</span>)
<span class='fu'>is.rsi.eligible</span><span class='op'>(</span><span class='va'>x</span>, threshold <span class='op'>=</span> <span class='fl'>0.05</span><span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'>as.rsi</span>(
<span class='kw'>x</span>,
mo = <span class='kw'>NULL</span>,
ab = <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>)),
guideline = <span class='st'>"EUCAST"</span>,
uti = <span class='fl'>FALSE</span>,
conserve_capped_values = <span class='fl'>FALSE</span>,
add_intrinsic_resistance = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)
<span class='fu'>as.rsi</span><span class='op'>(</span>
<span class='va'>x</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
uti <span class='op'>=</span> <span class='cn'>FALSE</span>,
conserve_capped_values <span class='op'>=</span> <span class='cn'>FALSE</span>,
add_intrinsic_resistance <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'>as.rsi</span>(
<span class='kw'>x</span>,
mo = <span class='kw'>NULL</span>,
ab = <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>)),
guideline = <span class='st'>"EUCAST"</span>,
uti = <span class='fl'>FALSE</span>,
add_intrinsic_resistance = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)
<span class='fu'>as.rsi</span><span class='op'>(</span>
<span class='va'>x</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
uti <span class='op'>=</span> <span class='cn'>FALSE</span>,
add_intrinsic_resistance <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for data.frame</span>
<span class='fu'>as.rsi</span>(
<span class='kw'>x</span>,
<span class='kw'>...</span>,
col_mo = <span class='kw'>NULL</span>,
guideline = <span class='st'>"EUCAST"</span>,
uti = <span class='kw'>NULL</span>,
conserve_capped_values = <span class='fl'>FALSE</span>,
add_intrinsic_resistance = <span class='fl'>FALSE</span>
)</pre>
<span class='fu'>as.rsi</span><span class='op'>(</span>
<span class='va'>x</span>,
<span class='va'>...</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
uti <span class='op'>=</span> <span class='cn'>NULL</span>,
conserve_capped_values <span class='op'>=</span> <span class='cn'>FALSE</span>,
add_intrinsic_resistance <span class='op'>=</span> <span class='cn'>FALSE</span>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -334,43 +334,43 @@ list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST In
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<h3>How it works</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>How it works</h3>
<p>The <code>as.rsi()</code> function works in four ways:</p><ol>
<li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='kw'>your_data</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='co'># until dplyr 1.0.0</span>
<span class='kw'>your_data</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='co'># since dplyr 1.0.0</span>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</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='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
</pre></li>
<li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
</ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='kw'>your_data</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.disk</span>, <span class='kw'>as.rsi</span>) <span class='co'># until dplyr 1.0.0</span>
<span class='kw'>your_data</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.disk</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</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='op'>(</span><span class='va'>is.disk</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.disk</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
</pre></li>
</ul></li>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(data)</code>.</p></li>
</ol>
<h3>Supported guidelines</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Supported guidelines</h3>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
<h3>After interpretation</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>After interpretation</h3>
<p>After using <code>as.rsi()</code>, you can use the <code><a href='eucast_rules.html'>eucast_rules()</a></code> defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<h3>Machine readable interpretation guidelines</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Machine readable interpretation guidelines</h3>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<h3>Other</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Other</h3>
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
@ -411,87 +411,87 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code>, <code><a href='as.disk.html'>as.disk()</a></code>, <code><a href='as.mo.html'>as.mo()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='kw'>example_isolates</span>) <span class='co'># see all R/SI results at a glance</span>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># see all R/SI results at a glance</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://docs.ropensci.org/skimr'>"skimr"</a></span>)) {
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://docs.ropensci.org/skimr'>"skimr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># support for skim() too:</span>
<span class='fu'><a href='https://docs.ropensci.org/skimr/reference/skim.html'>skim</a></span>(<span class='kw'>example_isolates</span>)
}
<span class='fu'><a href='https://docs.ropensci.org/skimr/reference/skim.html'>skim</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># For INTERPRETING disk diffusion and MIC values -----------------------</span>
<span class='co'># a whole data set, even with combined MIC values and disk zones</span>
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(microorganism = <span class='st'>"E. coli"</span>,
AMP = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>8</span>),
CIP = <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>0.256</span>),
GEN = <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>),
TOB = <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>16</span>),
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='va'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>microorganism <span class='op'>=</span> <span class='st'>"E. coli"</span>,
AMP <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>8</span><span class='op'>)</span>,
CIP <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>0.256</span><span class='op'>)</span>,
GEN <span class='op'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span><span class='op'>(</span><span class='fl'>18</span><span class='op'>)</span>,
TOB <span class='op'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span><span class='op'>(</span><span class='fl'>16</span><span class='op'>)</span>,
NIT <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>32</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>df</span><span class='op'>)</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>),
ab = <span class='st'>"AMP"</span>,
guideline = <span class='st'>"EUCAST"</span>)
<span class='fu'>as.rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span>,
mo <span class='op'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"S. pneumoniae"</span><span class='op'>)</span>,
ab <span class='op'>=</span> <span class='st'>"AMP"</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</span>
<span class='fu'>as.rsi</span>(x = <span class='fu'><a href='as.disk.html'>as.disk</a></span>(<span class='fl'>18</span>),
mo = <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
ab = <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
guideline = <span class='st'>"EUCAST"</span>)
<span class='fu'>as.rsi</span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span><span class='op'>(</span><span class='fl'>18</span><span class='op'>)</span>,
mo <span class='op'>=</span> <span class='st'>"Strep pneu"</span>, <span class='co'># `mo` will be coerced with as.mo()</span>
ab <span class='op'>=</span> <span class='st'>"ampicillin"</span>, <span class='co'># and `ab` with as.ab()</span>
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span><span class='op'>)</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'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>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='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span>
<span class='va'>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='op'>(</span><span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='as.mic.html'>is.mic</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='op'>|</span> <span class='fu'><a href='as.disk.html'>is.disk</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span>
<span class='va'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>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='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>TOB</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span>
<span class='va'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>TOB</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</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='va'>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='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>TOB</span><span class='op'>)</span>, <span class='va'>as.rsi</span>, mo <span class='op'>=</span> <span class='st'>"E. coli"</span><span class='op'>)</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><span class='op'>(</span>mo <span class='op'>=</span> <span class='st'>"E. coli"</span>,
NIT <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"&lt;= 2"</span>, <span class='fl'>32</span><span class='op'>)</span>,
from_the_bladder <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='cn'>TRUE</span>, <span class='cn'>FALSE</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>as.rsi</span><span class='op'>(</span>uti <span class='op'>=</span> <span class='st'>"from_the_bladder"</span><span class='op'>)</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='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='st'>"E. coli"</span>,
NIT <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"&lt;= 2"</span>, <span class='fl'>32</span><span class='op'>)</span>,
specimen <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"urine"</span>, <span class='st'>"blood"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'>as.rsi</span><span class='op'>(</span><span class='op'>)</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='va'>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='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>NIT</span><span class='op'>)</span>, <span class='va'>as.rsi</span>, mo <span class='op'>=</span> <span class='st'>"E. coli"</span>, uti <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># For CLEANING existing R/SI values ------------------------------------</span>
<span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"S"</span>, <span class='st'>"I"</span>, <span class='st'>"R"</span>, <span class='st'>"A"</span>, <span class='st'>"B"</span>, <span class='st'>"C"</span>))
<span class='fu'>as.rsi</span>(<span class='st'>"&lt;= 0.002; S"</span>) <span class='co'># will return "S"</span>
<span class='kw'>rsi_data</span> <span class='op'>&lt;-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>)))
<span class='fu'>is.rsi</span>(<span class='kw'>rsi_data</span>)
<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='fu'>as.rsi</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"S"</span>, <span class='st'>"I"</span>, <span class='st'>"R"</span>, <span class='st'>"A"</span>, <span class='st'>"B"</span>, <span class='st'>"C"</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>as.rsi</span><span class='op'>(</span><span class='st'>"&lt;= 0.002; S"</span><span class='op'>)</span> <span class='co'># will return "S"</span>
<span class='va'>rsi_data</span> <span class='op'>&lt;-</span> <span class='fu'>as.rsi</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='st'>"S"</span>, <span class='fl'>474</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='st'>"I"</span>, <span class='fl'>36</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='st'>"R"</span>, <span class='fl'>370</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'>is.rsi</span><span class='op'>(</span><span class='va'>rsi_data</span><span class='op'>)</span>
<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>rsi_data</span><span class='op'>)</span> <span class='co'># for percentages</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span><span class='op'>(</span><span class='va'>rsi_data</span><span class='op'>)</span> <span class='co'># for frequencies</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='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>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='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span><span class='op'>(</span><span class='va'>PEN</span><span class='op'>:</span><span class='va'>RIF</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</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='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>PEN</span><span class='op'>:</span><span class='va'>RIF</span><span class='op'>)</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='va'>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='op'>(</span><span class='va'>is.rsi.eligible</span>, <span class='va'>as.rsi</span><span class='op'>)</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(where(is.rsi.eligible), as.rsi))</span>
}
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</div>
@ -509,7 +509,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
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