P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 15:47:54 +02:00
Code Releases Activity

Built site for AMR@2.1.1.9186: f793828

Browse Source
This commit is contained in:
github-actions
2025-03-07 19:50:52 +00:00
parent a4384adaa6
commit 8a29e934c9
83 changed files with 607 additions and 598 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
reference/count.html
View File

@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9183</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9186</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -88,7 +88,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<dt id="arg-only-all-tested">only_all_tested<a class="anchor" aria-label="anchor" href="#arg-only-all-tested"></a></dt>
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antibiotics, see section <em>Combination Therapy</em> below</p></dd>
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see section <em>Combination Therapy</em> below</p></dd>
<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
@ -96,7 +96,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dd><p>a column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
@ -115,7 +115,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>These functions are meant to count isolates. Use the <code><a href="proportion.html">resistance()</a></code>/<code><a href="proportion.html">susceptibility()</a></code> functions to calculate microbial resistance/susceptibility.</p>
<p>The function <code>count_resistant()</code> is equal to the function <code>count_R()</code>. The function <code>count_susceptible()</code> is equal to the function <code>count_SI()</code>.</p>
<p>The function <code>n_sir()</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://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct()</a></code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p>
<p>The function <code>n_sir()</code> is an alias of <code>count_all()</code>. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to <code><a href="https://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct()</a></code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p>
<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code><a href="as.sir.html">sir</a></code> class (created with <code><a href="as.sir.html">as.sir()</a></code>) and counts the number of S's, I's and R's. It also supports grouped variables. The function <code><a href="proportion.html">sir_df()</a></code> works exactly like <code>count_df()</code>, but adds the percentage of S, I and R.</p>
</div>
<div class="section level2">
@ -135,7 +135,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<h2 id="combination-therapy">Combination Therapy<a class="anchor" aria-label="anchor" href="#combination-therapy"></a></h2>
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href="proportion.html">susceptibility()</a></code> works to calculate the %SI:</p>
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antimicrobials, Drug A and Drug B, about how <code><a href="proportion.html">susceptibility()</a></code> works to calculate the %SI:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="sc">-----------------------</span> <span class="sc">-----------------------</span></span>