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(v1.6.0.9021) join functions update
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@ -49,7 +49,7 @@
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<meta property="og:title" content="Interpret MIC and Disk Values, or Clean Raw R/SI Data — as.rsi" />
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<meta property="og:description" content="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 rsi, which is an ordered factor with levels S &lt; I &lt; R. Values that cannot be interpreted will be returned as NA with a warning." />
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<meta property="og:description" content="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 rsi, which is an ordered factor with levels S &lt; I &lt; R." />
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9021</span>
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Get properties of an antibiotic
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@ -239,7 +239,7 @@
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</div>
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<div class="ref-description">
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<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 < I < R</code>. Values that cannot be interpreted will be returned as <code>NA</code> with a warning.</p>
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<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 <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <code>S < I < R</code>.</p>
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</div>
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<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>
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@ -290,7 +290,7 @@
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>x</th>
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<td><p>vector of values (for class <code><a href='as.mic.html'>mic</a></code>: an MIC value in mg/L, for class <code><a href='as.disk.html'>disk</a></code>: a disk diffusion radius in millimetres)</p></td>
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<td><p>vector of values (for class <code><a href='as.mic.html'>mic</a></code>: MIC values in mg/L, for class <code><a href='as.disk.html'>disk</a></code>: a disk diffusion radius in millimetres)</p></td>
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</tr>
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<tr>
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<th>...</th>
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@ -302,7 +302,7 @@
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</tr>
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<tr>
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<th>mo</th>
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<td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code>, can be left empty to determine it automatically</p></td>
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<td><p>any (vector of) text that can be coerced to valid microorganism codes with <code><a href='as.mo.html'>as.mo()</a></code>, can be left empty to determine it automatically</p></td>
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</tr>
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<tr>
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<th>ab</th>
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@ -314,15 +314,15 @@
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</tr>
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<tr>
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<th>uti</th>
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<td><p>(Urinary Tract Infection) A vector with <a href='https://rdrr.io/r/base/logical.html'>logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.rsi()</code> on a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, this can also be a column containing <a href='https://rdrr.io/r/base/logical.html'>logical</a>s or when left blank, the data set will be searched for a 'specimen' and rows containing 'urin' (such as 'urine', 'urina') in that column will be regarded isolates from a UTI. See <em>Examples</em>.</p></td>
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<td><p>(Urinary Tract Infection) A vector with <a href='https://rdrr.io/r/base/logical.html'>logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.rsi()</code> on a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, this can also be a column containing <a href='https://rdrr.io/r/base/logical.html'>logical</a>s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See <em>Examples</em>.</p></td>
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</tr>
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<tr>
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<th>conserve_capped_values</th>
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<td><p>a logical to indicate that MIC values starting with <code>">"</code> (but not <code>">="</code>) must always return "R" , and that MIC values starting with <code>"<"</code> (but not <code>"<="</code>) must always return "S"</p></td>
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<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate that MIC values starting with <code>">"</code> (but not <code>">="</code>) must always return "R" , and that MIC values starting with <code>"<"</code> (but not <code>"<="</code>) must always return "S"</p></td>
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</tr>
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<tr>
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<th>add_intrinsic_resistance</th>
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<td><p><em>(only useful when using a EUCAST guideline)</em> a logical to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, that itself is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020).</p></td>
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<td><p><em>(only useful when using a EUCAST guideline)</em> a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, that itself is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020).</p></td>
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</tr>
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<tr>
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<th>reference_data</th>
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@ -336,7 +336,7 @@
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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<p>Ordered factor with new class <code><rsi></code></p>
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<p>Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with new class <code><rsi></code></p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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@ -346,14 +346,14 @@
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<p>The <code>as.rsi()</code> function works in four ways:</p><ol>
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<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>"<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>
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<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> argument.</p><ul>
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<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'>%>%</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>
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<span class='va'>your_data</span> <span class='op'>%>%</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='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>
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<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'>%>%</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>
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<span class='va'>your_data</span> <span class='op'>%>%</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>
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</pre></li>
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<li><p>Operators like "<=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=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 ">2" to be lower than ">=4" and might in this case return "S" or "I".</p></li>
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</ul></li>
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<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> argument.</p><ul>
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<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'>%>%</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>
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<span class='va'>your_data</span> <span class='op'>%>%</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='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>
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<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'>%>%</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>
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<span class='va'>your_data</span> <span class='op'>%>%</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>
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</pre></li>
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</ul></li>
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<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>
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@ -363,7 +363,7 @@
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<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Supported Guidelines</h3>
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<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
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<p>For interpreting MIC values as well as disk diffusion diameters, currently supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
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<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
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<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>After Interpretation</h3>
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<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Other</h3>
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<p>The function <code>is.rsi()</code> detects if the input contains class <code><rsi></code>. If the input is a data.frame, it iterates over all columns and returns a logical vector.</p>
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<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> argument. If the input is a data.frame, it iterates over all columns and returns a logical vector.</p>
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<p>The function <code>is.rsi()</code> detects if the input contains class <code><rsi></code>. If the input is a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, it iterates over all columns and returns a <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector.</p>
|
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<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> argument. If the input is a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, it iterates over all columns and returns a <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
|
||||
|
||||
@ -420,7 +420,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<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='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='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='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'># class <rsi> supported in skim() too:</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>
|
||||
|
||||
Reference in New Issue
Block a user