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(v1.3.0.9004) data sets, as.disk() improvement
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@ -82,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9004</span>
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</span>
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</div>
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@ -118,6 +118,13 @@
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Predict antimicrobial resistance
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</a>
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</li>
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<li>
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<a href="../articles/datasets.html">
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<span class="fa fa-database"></span>
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Download our free data sets
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</a>
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</li>
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<li>
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<a href="../articles/PCA.html">
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<span class="fa fa-compress"></span>
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@ -249,6 +256,7 @@
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guideline = <span class='st'>"EUCAST"</span>,
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uti = <span class='fl'>FALSE</span>,
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conserve_capped_values = <span class='fl'>FALSE</span>,
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add_intrinsic_resistance = <span class='fl'>FALSE</span>,
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<span class='kw'>...</span>
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)
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@ -259,6 +267,7 @@
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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>)),
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guideline = <span class='st'>"EUCAST"</span>,
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uti = <span class='fl'>FALSE</span>,
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add_intrinsic_resistance = <span class='fl'>FALSE</span>,
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<span class='kw'>...</span>
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)
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@ -269,6 +278,7 @@
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guideline = <span class='st'>"EUCAST"</span>,
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uti = <span class='kw'>NULL</span>,
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conserve_capped_values = <span class='fl'>FALSE</span>,
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add_intrinsic_resistance = <span class='fl'>FALSE</span>,
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<span class='kw'>...</span>
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)</pre>
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@ -307,6 +317,10 @@
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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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</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 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.</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 IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo()</a></code>), defaults to the first column of class <code><a href='as.mo.html'>mo</a></code>. Values will be coerced using <code><a href='as.mo.html'>as.mo()</a></code>.</p></td>
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@ -406,6 +420,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='co'># the dplyr way</span>
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<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>)
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<span class='kw'>df</span> <span class='op'>%>%</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>)
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<span class='kw'>df</span> <span class='op'>%>%</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>)
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<span class='kw'>df</span> <span class='op'>%>%</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>))
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<span class='kw'>df</span> <span class='op'>%>%</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>)
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<span class='kw'>df</span> <span class='op'>%>%</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>)
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