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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># NOT RUN {</span>
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<span class='co'># septic_patients is a dataset available in the AMR package</span>
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?<span class='no'>septic_patients</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<pre class="examples"><div class='input'><span class='co'># septic_patients is a dataset available in the AMR package</span>
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?<span class='no'>septic_patients</span></div><div class='output co'>#> <span class='message'>Rendering development documentation for 'septic_patients'</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='co'># set key antibiotics to a new variable</span>
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<span class='no'>my_patients</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%>%</span>
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@ -267,23 +265,18 @@
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<span class='kw'>first_regular</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
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<span class='co'># and first WEIGHTED isolates</span>
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<span class='kw'>first_weighted</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>"keyab"</span>)
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)
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)</div><div class='output co'>#> <span class='message'><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>mo</span><span style='color: #0000BB;'>` as input for `col_mo`.</span><span></span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>mo</span><span style='color: #0000BB;'>` as input for `col_mo`.</span><span></span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>date</span><span style='color: #0000BB;'>` as input for `col_date`.</span><span></span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>patient_id</span><span style='color: #0000BB;'>` as input for `col_patient_id`.</span><span></span></div><div class='output co'>#> <span class='message'>=> Found </span><span style='font-weight: bold;'>1,317 first isolates</span><span> (65.9% of total)</span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>mo</span><span style='color: #0000BB;'>` as input for `col_mo`.</span><span></span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>date</span><span style='color: #0000BB;'>` as input for `col_date`.</span><span></span></div><div class='output co'>#> <span class='message'></span><span style='color: #0000BB;'>NOTE: Using column `</span><span style='color: #0000BB;font-weight: bold;'>patient_id</span><span style='color: #0000BB;'>` as input for `col_patient_id`.</span><span></span></div><div class='output co'>#> [Criterion] Inclusion based on key antibiotics, ignoring I.</div><div class='output co'>#> <span class='message'>=> Found </span><span style='font-weight: bold;'>1,413 first weighted isolates</span><span> (70.7% of total)</span></div><div class='input'>
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<span class='co'># Check the difference, in this data set it results in 7% more isolates:</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_regular</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_weighted</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_regular</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> [1] 1317</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_weighted</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> [1] 1413</div><div class='input'>
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<span class='co'># output of the `key_antibiotics` function could be like this:</span>
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<span class='no'>strainA</span> <span class='kw'><-</span> <span class='st'>"SSSRR.S.R..S"</span>
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<span class='no'>strainB</span> <span class='kw'><-</span> <span class='st'>"SSSIRSSSRSSS"</span>
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<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>)
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<span class='co'># TRUE, because I is ignored (as well as missing values)</span>
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<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>)</div><div class='output co'>#> [1] TRUE</div><div class='input'><span class='co'># TRUE, because I is ignored (as well as missing values)</span>
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<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>, <span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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<span class='co'># FALSE, because I is not ignored and so the 4th value differs</span>
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<span class='co'># }</span></pre>
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<span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>, <span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> [1] FALSE</div><div class='input'># FALSE, because I is not ignored and so the 4th value differs
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</div></span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<h2>Contents</h2>
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