(v1.7.1.9068) new logo, unit tests

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.7.1.9067
+Version: 1.7.1.9068
 Date: 2021-12-12
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# `AMR` 1.7.1.9067
+# `AMR` 1.7.1.9068
 ## <small>Last updated: 12 December 2021</small>
 
 ### Breaking changes

R/first_isolate.R

@@ -490,8 +490,6 @@ first_isolate <- function(x = NULL,
                                          FALSE)
   } else {
     # no key antibiotics
-    x1 <<- x$other_pat_or_mo
-    x2 <<- x$more_than_episode_ago
     x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start &
                                            x$newvar_row_index_sorted <= row.end &
                                            x$newvar_genus_species != "" & 

R/translate.R

@@ -133,7 +133,7 @@ coerce_language_setting <- function(lang) {
     "fr"
   } else if (grepl("^(Portuguese|Portugu.+s|pt_|PT_)", lang, ignore.case = FALSE, perl = TRUE)) {
     "pt"
-  } else if (grepl("^(Russian|русс|ru_|RU_)", lang, ignore.case = FALSE, perl = TRUE)) {
+  } else if (grepl("^(Russian|pycc|ru_|RU_)", lang, ignore.case = FALSE, perl = TRUE)) {
     "ru"
   } else if (grepl("^(Swedish|Svenskt|sv_|SV_)", lang, ignore.case = FALSE, perl = TRUE)) {
     "sv"

README.md

@@ -6,7 +6,7 @@
 [![CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr)
 [![Codecov](https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=main)
 
-<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
+<img src="https://msberends.github.io/AMR/AMR_intro.svg" align="center" height="300px" />
 
 The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](https://github.com/msberends/AMR/tree/main/data-raw).
 

data-raw/_internals.R

@@ -69,8 +69,8 @@ TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv",
 
 # for checking input in `language` argument in e.g. mo_*() and ab_*() functions
 LANGUAGES_SUPPORTED <- c(Danish = "da",
-                         English = "en",
                          German = "de",
+                         English = "en",
                          Spanish = "es",
                          French = "fr",
                          Italian = "it",

docs/404.html

@@ -19,7 +19,7 @@
 <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="https://msberends.github.io/AMR/pkgdown.css" rel="stylesheet">
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 <script src="https://msberends.github.io/AMR/extra.js"></script><meta property="og:title" content="Page not found (404)">
-<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
 <meta name="twitter:card" content="summary_large_image">
 <meta name="twitter:creator" content="@msberends">
 <meta name="twitter:site" content="@univgroningen">
@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>License • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet"><script src="extra.js"></script><meta property="og:title" content="License"><meta property="og:image" content="https://msberends.github.io/AMR/logo.png"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>License • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><link href="extra.css" rel="stylesheet"><script src="extra.js"></script><meta property="og:title" content="License"><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
       </span>
     </div>
 

docs/articles/AMR.html

@@ -20,7 +20,7 @@
 <script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
 <script src="../extra.js"></script><meta property="og:title" content="How to conduct AMR data analysis">
 <meta property="og:description" content="AMR">
-<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
 <meta name="twitter:card" content="summary_large_image">
 <meta name="twitter:creator" content="@msberends">
 <meta name="twitter:site" content="@univgroningen">
@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9064</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9068</span>
       </span>
     </div>
 
@@ -191,7 +191,7 @@
       <h1 data-toc-skip>How to conduct AMR data analysis</h1>
                         <h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
             
-            <h4 data-toc-skip class="date">11 December 2021</h4>
+            <h4 data-toc-skip class="date">12 December 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
       <div class="hidden name"><code>AMR.Rmd</code></div>
@@ -200,7 +200,7 @@
 
     
     
-<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 11 December 2021.</p>
+<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 12 December 2021.</p>
 <div class="section level1">
 <h1 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h1>
@@ -231,21 +231,21 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2021-12-11</td>
+<td align="center">2021-12-12</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
 <tr class="even">
-<td align="center">2021-12-11</td>
+<td align="center">2021-12-12</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 </tr>
 <tr class="odd">
-<td align="center">2021-12-11</td>
+<td align="center">2021-12-12</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -342,67 +342,67 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2011-06-27</td>
-<td align="center">V5</td>
-<td align="center">Hospital B</td>
+<td align="center">2014-11-21</td>
+<td align="center">L5</td>
+<td align="center">Hospital C</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">F</td>
+<td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2015-07-06</td>
-<td align="center">O8</td>
+<td align="center">2015-03-18</td>
+<td align="center">G9</td>
 <td align="center">Hospital D</td>
 <td align="center">Staphylococcus aureus</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">F</td>
+<td align="center">M</td>
 </tr>
 <tr class="odd">
-<td align="center">2013-08-29</td>
-<td align="center">Q6</td>
+<td align="center">2011-10-31</td>
+<td align="center">Z3</td>
 <td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2012-05-28</td>
-<td align="center">S1</td>
+<td align="center">2017-05-24</td>
+<td align="center">A3</td>
 <td align="center">Hospital A</td>
-<td align="center">Klebsiella pneumoniae</td>
-<td align="center">R</td>
+<td align="center">Staphylococcus aureus</td>
+<td align="center">S</td>
 <td align="center">I</td>
 <td align="center">R</td>
-<td align="center">S</td>
-<td align="center">F</td>
+<td align="center">R</td>
+<td align="center">M</td>
 </tr>
 <tr class="odd">
-<td align="center">2015-10-19</td>
-<td align="center">Q1</td>
-<td align="center">Hospital B</td>
-<td align="center">Staphylococcus aureus</td>
-<td align="center">S</td>
+<td align="center">2013-01-31</td>
+<td align="center">Y10</td>
+<td align="center">Hospital C</td>
+<td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2011-12-02</td>
-<td align="center">E2</td>
-<td align="center">Hospital D</td>
-<td align="center">Escherichia coli</td>
-<td align="center">S</td>
+<td align="center">2013-04-13</td>
+<td align="center">L6</td>
+<td align="center">Hospital B</td>
+<td align="center">Klebsiella pneumoniae</td>
 <td align="center">S</td>
+<td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
@@ -439,16 +439,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,551</td>
-<td align="right">52.76%</td>
-<td align="right">10,551</td>
-<td align="right">52.76%</td>
+<td align="right">10,451</td>
+<td align="right">52.26%</td>
+<td align="right">10,451</td>
+<td align="right">52.26%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,449</td>
-<td align="right">47.25%</td>
+<td align="right">9,549</td>
+<td align="right">47.75%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -502,9 +502,9 @@ Longest: 1</p>
 <span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
 <span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
 <span class="co"># 2</span>
-<span class="co"># =&gt; Found 10,742 'phenotype-based' first isolates (53.7% of total where a</span>
+<span class="co"># =&gt; Found 10,684 'phenotype-based' first isolates (53.4% of total where a</span>
 <span class="co">#    microbial ID was available)</span></code></pre></div>
-<p>So only 53.7% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
+<p>So only 53.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
@@ -512,10 +512,10 @@ Longest: 1</p>
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
-<p>So we end up with 10,742 isolates for analysis. Now our data looks like:</p>
+<p>So we end up with 10,684 isolates for analysis. Now our data looks like:</p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
-<table class="table">
+<table style="width:100%;" class="table">
 <colgroup>
 <col width="2%">
 <col width="9%">
@@ -528,7 +528,7 @@ Longest: 1</p>
 <col width="3%">
 <col width="6%">
 <col width="11%">
-<col width="11%">
+<col width="12%">
 <col width="9%">
 <col width="5%">
 </colgroup>
@@ -550,30 +550,46 @@ Longest: 1</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">1</td>
-<td align="center">2011-06-27</td>
-<td align="center">V5</td>
-<td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="left">2</td>
+<td align="center">2015-03-18</td>
+<td align="center">G9</td>
+<td align="center">Hospital D</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
+<td align="center">M</td>
+<td align="center">Gram-positive</td>
+<td align="center">Staphylococcus</td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">3</td>
-<td align="center">2013-08-29</td>
-<td align="center">Q6</td>
+<td align="left">4</td>
+<td align="center">2017-05-24</td>
+<td align="center">A3</td>
 <td align="center">Hospital A</td>
-<td align="center">B_ESCHR_COLI</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
+<td align="center">M</td>
+<td align="center">Gram-positive</td>
+<td align="center">Staphylococcus</td>
+<td align="center">aureus</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="odd">
+<td align="left">5</td>
+<td align="center">2013-01-31</td>
+<td align="center">Y10</td>
+<td align="center">Hospital C</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">S</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
@@ -581,30 +597,30 @@ Longest: 1</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="odd">
-<td align="left">4</td>
-<td align="center">2012-05-28</td>
-<td align="center">S1</td>
-<td align="center">Hospital A</td>
-<td align="center">B_KLBSL_PNMN</td>
+<tr class="even">
+<td align="left">10</td>
+<td align="center">2014-07-29</td>
+<td align="center">G3</td>
+<td align="center">Hospital D</td>
+<td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
-<td align="center">I</td>
 <td align="center">R</td>
-<td align="center">S</td>
-<td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Klebsiella</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">M</td>
+<td align="center">Gram-positive</td>
+<td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
-<td align="left">6</td>
-<td align="center">2011-12-02</td>
-<td align="center">E2</td>
-<td align="center">Hospital D</td>
+<tr class="odd">
+<td align="left">11</td>
+<td align="center">2010-12-28</td>
+<td align="center">G5</td>
+<td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
@@ -613,36 +629,20 @@ Longest: 1</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="odd">
-<td align="left">8</td>
-<td align="center">2010-05-20</td>
-<td align="center">X1</td>
+<tr class="even">
+<td align="left">14</td>
+<td align="center">2015-01-05</td>
+<td align="center">A8</td>
 <td align="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">R</td>
+<td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
-<td align="center">F</td>
-<td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="left">11</td>
-<td align="center">2013-03-04</td>
-<td align="center">T9</td>
-<td align="center">Hospital C</td>
-<td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">F</td>
+<td align="center">M</td>
 <td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</td>
+<td align="center">Staphylococcus</td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@@ -666,8 +666,8 @@ Longest: 1</p>
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 10,742<br>
-Available: 10,742 (100.0%, NA: 0 = 0.0%)<br>
+Length: 10,684<br>
+Available: 10,684 (100.0%, NA: 0 = 0.0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@@ -684,33 +684,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,726</td>
-<td align="right">44.00%</td>
-<td align="right">4,726</td>
-<td align="right">44.00%</td>
+<td align="right">4,660</td>
+<td align="right">43.62%</td>
+<td align="right">4,660</td>
+<td align="right">43.62%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,781</td>
-<td align="right">25.89%</td>
-<td align="right">7,507</td>
-<td align="right">69.88%</td>
+<td align="right">2,727</td>
+<td align="right">25.52%</td>
+<td align="right">7,387</td>
+<td align="right">69.14%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,090</td>
-<td align="right">19.46%</td>
-<td align="right">9,597</td>
-<td align="right">89.34%</td>
+<td align="right">2,106</td>
+<td align="right">19.71%</td>
+<td align="right">9,493</td>
+<td align="right">88.85%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,145</td>
-<td align="right">10.66%</td>
-<td align="right">10,742</td>
+<td align="right">1,191</td>
+<td align="right">11.15%</td>
+<td align="right">10,684</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@@ -729,14 +729,14 @@ Longest: 24</p>
 <col width="9%">
 <col width="9%">
 <col width="9%">
-<col width="11%">
+<col width="10%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="6%">
 <col width="11%">
-<col width="11%">
+<col width="12%">
 <col width="9%">
 <col width="5%">
 </colgroup>
@@ -757,93 +757,93 @@ Longest: 24</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2010-05-20</td>
-<td align="center">X1</td>
+<td align="center">2017-05-24</td>
+<td align="center">A3</td>
 <td align="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">F</td>
+<td align="center">R</td>
+<td align="center">M</td>
 <td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</td>
+<td align="center">Staphylococcus</td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2013-03-04</td>
-<td align="center">T9</td>
-<td align="center">Hospital C</td>
+<td align="center">2014-07-29</td>
+<td align="center">G3</td>
+<td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
-<td align="center">F</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2011-04-02</td>
-<td align="center">K4</td>
-<td align="center">Hospital B</td>
+<td align="center">2014-10-24</td>
+<td align="center">S9</td>
+<td align="center">Hospital A</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">M</td>
+<td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2016-11-29</td>
-<td align="center">X8</td>
-<td align="center">Hospital D</td>
+<td align="center">2012-08-31</td>
+<td align="center">A1</td>
+<td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
+<td align="center">S</td>
 <td align="center">R</td>
-<td align="center">R</td>
-<td align="center">F</td>
+<td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2014-06-19</td>
-<td align="center">V9</td>
-<td align="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</td>
+<td align="center">2016-04-25</td>
+<td align="center">Z10</td>
+<td align="center">Hospital C</td>
+<td align="center">B_KLBSL_PNMN</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">R</td>
 <td align="center">F</td>
-<td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
+<td align="center">Gram-negative</td>
+<td align="center">Klebsiella</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2015-11-16</td>
-<td align="center">M7</td>
-<td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</td>
+<td align="center">2011-04-30</td>
+<td align="center">J10</td>
+<td align="center">Hospital D</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">R</td>
 <td align="center">M</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
+<td align="center">Gram-positive</td>
+<td align="center">Staphylococcus</td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@@ -853,6 +853,7 @@ Longest: 24</p>
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show first 6 rows</span></code></pre></div>
+<pre><code><span class="co"># ℹ Using column 'bacteria' as input for `col_mo`.</span></code></pre>
 <table class="table">
 <thead><tr class="header">
 <th align="center">mo</th>
@@ -866,58 +867,59 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2242</td>
-<td align="center">112</td>
-<td align="center">2372</td>
-<td align="center">4726</td>
+<td align="center">2148</td>
+<td align="center">144</td>
+<td align="center">2368</td>
+<td align="center">4660</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">3500</td>
-<td align="center">154</td>
-<td align="center">1072</td>
-<td align="center">4726</td>
+<td align="center">3418</td>
+<td align="center">162</td>
+<td align="center">1080</td>
+<td align="center">4660</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3435</td>
+<td align="center">3376</td>
 <td align="center">0</td>
-<td align="center">1291</td>
-<td align="center">4726</td>
+<td align="center">1284</td>
+<td align="center">4660</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4126</td>
+<td align="center">4068</td>
 <td align="center">0</td>
-<td align="center">600</td>
-<td align="center">4726</td>
+<td align="center">592</td>
+<td align="center">4660</td>
 </tr>
 <tr class="odd">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMX</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1145</td>
-<td align="center">1145</td>
+<td align="center">1191</td>
+<td align="center">1191</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">902</td>
-<td align="center">39</td>
-<td align="center">204</td>
-<td align="center">1145</td>
+<td align="center">947</td>
+<td align="center">46</td>
+<td align="center">198</td>
+<td align="center">1191</td>
 </tr>
 </tbody>
 </table>
-<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
-<pre><code><span class="co"># ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)</span></code></pre>
+<pre><code><span class="co"># ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)</span>
+<span class="co"># ℹ Using column 'bacteria' as input for `col_mo`.</span></code></pre>
 <table class="table">
 <thead><tr class="header">
 <th align="center">mo</th>
@@ -931,34 +933,34 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4126</td>
+<td align="center">4068</td>
 <td align="center">0</td>
-<td align="center">600</td>
-<td align="center">4726</td>
+<td align="center">592</td>
+<td align="center">4660</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1049</td>
+<td align="center">1062</td>
 <td align="center">0</td>
-<td align="center">96</td>
-<td align="center">1145</td>
+<td align="center">129</td>
+<td align="center">1191</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2469</td>
+<td align="center">2401</td>
 <td align="center">0</td>
-<td align="center">312</td>
-<td align="center">2781</td>
+<td align="center">326</td>
+<td align="center">2727</td>
 </tr>
 <tr class="even">
 <td align="center">S. pneumoniae</td>
 <td align="center">GEN</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">2090</td>
-<td align="center">2090</td>
+<td align="center">2106</td>
+<td align="center">2106</td>
 </tr>
 </tbody>
 </table>
@@ -970,11 +972,11 @@ Longest: 24</p>
 <p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</p>
 <p>All these functions contain a <code>minimum</code> argument, denoting the minimum required number of test results for returning a value. These functions will otherwise return <code>NA</code>. The default is <code>minimum = 30</code>, following the <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">CLSI M39-A4 guideline</a> for applying microbial epidemiology.</p>
 <p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
-<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
-<span class="co"># [1] 0.5448706</span></code></pre></div>
+<span class="co"># [1] 0.5497005</span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
-<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span><span class="op">)</span></code></pre></div>
@@ -986,24 +988,24 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5393604</td>
+<td align="center">0.5528455</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5352956</td>
+<td align="center">0.5463890</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5694087</td>
+<td align="center">0.5533333</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5527446</td>
+<td align="center">0.5482679</td>
 </tr>
 </tbody>
 </table>
 <p>Of course it would be very convenient to know the number of isolates responsible for the percentages. For that purpose the <code><a href="../reference/count.html">n_rsi()</a></code> can be used, which works exactly like <code><a href="https://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct()</a></code> from the <code>dplyr</code> package. It counts all isolates available for every group (i.e. values S, I or R):</p>
-<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>,
@@ -1017,28 +1019,28 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5393604</td>
-<td align="center">3252</td>
+<td align="center">0.5528455</td>
+<td align="center">3075</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5352956</td>
-<td align="center">3839</td>
+<td align="center">0.5463890</td>
+<td align="center">3794</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5694087</td>
-<td align="center">1556</td>
+<td align="center">0.5533333</td>
+<td align="center">1650</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5527446</td>
-<td align="center">2095</td>
+<td align="center">0.5482679</td>
+<td align="center">2165</td>
 </tr>
 </tbody>
 </table>
 <p>These functions can also be used to get the proportion of multiple antibiotics, to calculate empiric susceptibility of combination therapies very easily:</p>
-<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>amoxiclav <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">susceptibility</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span>,
@@ -1054,32 +1056,32 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7731697</td>
-<td align="center">0.8730427</td>
-<td align="center">0.9769361</td>
+<td align="center">0.7682403</td>