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@ -50,7 +50,7 @@
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<meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in dplyrs summarise and support grouped variables, see Examples.
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count_R and count_IR can be used to count resistant isolates, count_S and count_SI can be used to count susceptible isolates." />
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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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="Released version">0.5.0.9008</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9009</span>
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@ -94,12 +94,65 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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Home
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Get Started
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Conduct AMR analysis
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<span class="fa fa-dice"></span>
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Predict antimicrobial resistance
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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Create frequency tables
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Use the G-test
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@ -122,17 +175,17 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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Changelog
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@ -222,79 +275,79 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
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<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='http://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
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<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://www.rdocumentation.org/packages/dplyr/topics/n_distinct'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
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<p><code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
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<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><code><a href='portion.html'>portion</a>_*</code> to calculate microbial resistance and susceptibility.</p></div>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><div class='input'><span class='co'># septic_patients is a data set available in the AMR package. It is true, genuine data.</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'>
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<pre class="examples"><span class='co'># NOT RUN {</span>
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<span class='co'># septic_patients is a data set available in the AMR package. It is true, genuine data.</span>
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?<span class='no'>septic_patients</span>
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<span class='co'># Count resistant isolates</span>
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<span class='fu'>count_R</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 683</div><div class='input'><span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 686</div><div class='input'>
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<span class='fu'>count_R</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='co'># Or susceptible isolates</span>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 486</div><div class='input'><span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 489</div><div class='input'>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='co'># Count all available isolates</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 1172</div><div class='input'><span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 1172</div><div class='input'>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='co'># Since n_rsi counts available isolates, you can</span>
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<span class='co'># calculate back to count e.g. non-susceptible isolates.</span>
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<span class='co'># This results in the same:</span>
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<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 686</div><div class='input'><span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)</div><div class='output co'>#> [1] 686</div><div class='input'>
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<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
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<span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</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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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>cipr</span>),
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/summarise'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>cipr</span>),
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<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>cipr</span>),
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<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>cipr</span>),
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<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>cipr</span>), <span class='co'># the actual total; sum of all three</span>
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<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>cipr</span>), <span class='co'># same - analogous to n_distinct</span>
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<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span></div><div class='output co'>#> <span style='color: #949494;'># A tibble: 4 x 7</span><span>
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#> hospital_id R I S n1 n2 total
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#> </span><span style='color: #949494;font-style: italic;'><fct></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span>
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#> </span><span style='color: #BCBCBC;'>1</span><span> A 26 3 178 207 207 321
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#> </span><span style='color: #BCBCBC;'>2</span><span> B 85 35 379 499 499 663
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#> </span><span style='color: #BCBCBC;'>3</span><span> C 41 22 139 202 202 254
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#> </span><span style='color: #BCBCBC;'>4</span><span> D 76 9 416 501 501 762</div><div class='input'>
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<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/n'>n</a></span>()) <span class='co'># NOT the amount of tested isolates!</span>
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<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
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<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
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<span class='co'># Please mind that `portion_S` calculates percentages right away instead.</span>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># S = 1057 (67.1%)</span></div><div class='output co'>#> [1] 1291</div><div class='input'><span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># n = 1576</span></div><div class='output co'>#> [1] 1828</div><div class='input'>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># S = 1372 (74.0%)</span></div><div class='output co'>#> [1] 1372</div><div class='input'><span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># n = 1855</span></div><div class='output co'>#> [1] 1855</div><div class='input'>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># S = 1057 (67.1%)</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># n = 1576</span>
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<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># S = 1372 (74.0%)</span>
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<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># n = 1855</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
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<span class='fu'>count_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>)) <span class='co'># S = 1396 (92.0%)</span></div><div class='output co'>#> [1] 1609</div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>, <span class='co'># n = 1517</span>
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<span class='fu'>n_rsi</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>))</div><div class='output co'>#> [1] 1747</div><div class='input'>
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<span class='fu'>count_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>)) <span class='co'># S = 1396 (92.0%)</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>, <span class='co'># n = 1517</span>
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<span class='fu'>n_rsi</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>))
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<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
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<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> Interpretation Antibiotic Value
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#> 1 S amox 486
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#> 2 I amox 3
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#> 3 R amox 683
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#> 4 S cipr 1112
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#> 5 I cipr 69
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#> 6 R cipr 228</div><div class='input'>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
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||||
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
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||||
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<span class='co'># It also supports grouping variables</span>
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||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
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||||
<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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||||
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> </span><span style='color: #949494;'># A tibble: 24 x 4</span><span>
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||||
#> Interpretation hospital_id Antibiotic Value
|
||||
#> </span><span style='color: #949494;font-style: italic;'><ord></span><span> </span><span style='color: #949494;font-style: italic;'><fct></span><span> </span><span style='color: #949494;font-style: italic;'><chr></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span>
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||||
#> </span><span style='color: #BCBCBC;'> 1</span><span> S A amox 63
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||||
#> </span><span style='color: #BCBCBC;'> 2</span><span> S B amox 141
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||||
#> </span><span style='color: #BCBCBC;'> 3</span><span> S C amox 59
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||||
#> </span><span style='color: #BCBCBC;'> 4</span><span> S D amox 223
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||||
#> </span><span style='color: #BCBCBC;'> 5</span><span> I A amox 0
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||||
#> </span><span style='color: #BCBCBC;'> 6</span><span> I B amox 1
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||||
#> </span><span style='color: #BCBCBC;'> 7</span><span> I C amox 0
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||||
#> </span><span style='color: #BCBCBC;'> 8</span><span> I D amox 2
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#> </span><span style='color: #BCBCBC;'> 9</span><span> R A amox 87
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#> </span><span style='color: #BCBCBC;'>10</span><span> R B amox 231
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#> </span><span style='color: #949494;'># ... with 14 more rows</span><span></div><div class='input'>
|
||||
</div></span></pre>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/select'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/dplyr/topics/group_by'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
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<h2>Contents</h2>
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@ -307,6 +360,8 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<li><a href="#details">Details</a></li>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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<li><a href="#see-also">See also</a></li>
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<li><a href="#examples">Examples</a></li>
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