(v1.8.1.9001) update unit tests, fixes #53

2024-12-26 07:26:13 +01:00 · 2022-04-08 11:02:45 +02:00 · 2022-04-08 11:02:45 +02:00 · 4754848e96
commit 4754848e96
parent 641b88c814
13 changed files with 2409 additions and 818 deletions
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@ -57,8 +57,8 @@ jobs:
          - {os: macOS-latest,   r: '3.6',     allowfail: false}
          - {os: macOS-latest,   r: '3.5',     allowfail: false}
          - {os: macOS-latest,   r: '3.4',     allowfail: false}
-          - {os: macOS-latest,   r: '3.3',     allowfail: false}
+          # - {os: macOS-latest,   r: '3.3',     allowfail: false}
-          - {os: macOS-latest,   r: '3.2',     allowfail: false}
+          # - {os: macOS-latest,   r: '3.2',     allowfail: false}
          # - {os: macOS-latest,   r: '3.1',     allowfail: true}
          # - {os: macOS-latest,   r: '3.0',     allowfail: true}
          - {os: ubuntu-20.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
@ -77,7 +77,7 @@ jobs:
          - {os: windows-latest, r: '3.6',     allowfail: false}
          - {os: windows-latest, r: '3.5',     allowfail: false}
          - {os: windows-latest, r: '3.4',     allowfail: false}
-          - {os: windows-latest, r: '3.3',     allowfail: false}
+          # - {os: windows-latest, r: '3.3',     allowfail: false}
          # - {os: windows-latest, r: '3.2',     allowfail: true}
          # - {os: windows-latest, r: '3.1',     allowfail: true}
          # - {os: windows-latest, r: '3.0',     allowfail: true}
--- a/4
+++ b/4
@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.1
+Version: 1.8.1.9001
-Date: 2022-03-17
+Date: 2022-04-08
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
    data analysis and to work with microbial and antimicrobial properties by
--- a/NEWS.md
+++ b/NEWS.md
@ -1,8 +1,12 @@
 # `AMR` 1.8.1.9001
 ## <small>Last updated:  8 April 2022</small>
 ### Changed
 * Small fix for using `ab_from_text()`
 # `AMR` 1.8.1
 All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
 ### Changed
 * Fix for using `as.rsi()` on values containing capped values (such as `>=`), sometimes leading to `NA`
 * Support for antibiotic interpretations of the MIPS laboratory system: `"U"` for S ('susceptible urine'), `"D"` for I ('susceptible dose-dependent')
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@ -638,7 +638,7 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
  if (isTRUE(initial_captital)) {
    v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE)
  }
-  if (length(v) == 1) {
+  if (length(v) <= 1) {
    return(paste0(quotes, v, quotes))
  }
  if (identical(v, c("I", "R", "S"))) {
--- a/data-raw/AMR_latest.tar.gz
+++ b/data-raw/AMR_latest.tar.gz
--- a/docs/404.html
+++ b/docs/404.html
@ -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">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9001</span>
      </span>
    </div>
@ -57,7 +57,7 @@
  </a>
 </li>
 <li class="dropdown">
-  <a href="https://msberends.github.io/AMR/#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="https://msberends.github.io/AMR/#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    <span class="fa fa-question-circle"></span>
    How to
@ -205,12 +205,14 @@ Content not found. Please use links in the navbar.
      <footer><div class="copyright">
  <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
 Erwin E. A. Hassing.</p>
 </div>
 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
 2.0.2.</p>
 </div>
      </footer>
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@ -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">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9001</span>
      </span>
    </div>
@ -30,7 +30,7 @@
  </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    <span class="fa fa-question-circle"></span>
    How to
@ -416,11 +416,13 @@ END OF TERMS AND CONDITIONS
      <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
 Erwin E. A. Hassing.</p>
 </div>
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
 2.0.2.</p>
 </div>
      </footer></div>
--- a/docs/articles/datasets.html
+++ b/docs/articles/datasets.html
@ -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">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9001</span>
      </span>
    </div>
@ -58,7 +58,7 @@
  </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    <span class="fa fa-question-circle"></span>
    How to
@ -185,12 +185,12 @@
-      </header><script src="datasets_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+      </header><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Data sets for download / own use</h1>
-            <h4 data-toc-skip class="date">27 March 2022</h4>
+            <h4 data-toc-skip class="date">08 April 2022</h4>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="hidden name"><code>datasets.Rmd</code></div>
@ -199,42 +199,71 @@
-<p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply tab separated files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
+<p>All reference data (about microorganisms, antibiotics, R/SI
-<p>On this page, we explain how to download them and how the structure of the data sets look like.</p>
+interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
 reliable, up-to-date and freely available. We continually export our
 data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also
 supply tab separated files that are machine-readable and suitable for
 input in any software program, such as laboratory information
 systems.</p>
 <p>On this page, we explain how to download them and how the structure
 of the data sets look like.</p>
 <p class="dataset-within-r">
-If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.
+If you are reading this page from within R, please
 <a href="https://msberends.github.io/AMR/articles/datasets.html">visit
 our website</a>, which is automatically updated with every code change.
 </p>
 <div class="section level2">
 <h2 id="microorganisms-currently-accepted-names">Microorganisms (currently accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-currently-accepted-names"></a>
 </h2>
-<p>A data set with 70,760 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
+<p>A data set with 70,760 rows and 16 columns, containing the following
-<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>,
-<p>It was last updated on 1 February 2022 22:08:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+<em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>,
 <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>,
 <em>species_id</em>, <em>source</em>, <em>prevalence</em> and
 <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after
 you load the <code>AMR</code> package.</p>
 <p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (1.3 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R
 file</a> (1.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel file</a> (6.4 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel
 file</a> (6.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain text file</a> (13.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain
 text file</a> (13.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS file</a> (30.7 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS
 file</a> (30.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS file</a> (16.3 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS
 file</a> (16.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata file</a> (27.5 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
 file</a> (27.5 MB)</li>
 </ul>
-<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
+<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not
 contain SNOMED codes, as their file size would exceed 100 MB; the file
 size limit of GitHub.</strong> Advice? Use R instead.</p>
 <div class="section level3">
 <h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
 </h3>
-<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
+<p>Our full taxonomy of microorganisms is based on the authoritative and
 comprehensive:</p>
 <ul>
 <li>
-<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
+<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a>
 (included version: 2019)</li>
 <li>
-<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
+<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with
-<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
+Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
 <li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public
 Health Information Network Vocabulary Access and Distribution System
 (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
 </ul>
 </div>
 <div class="section level3">
@ -427,40 +456,64 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="microorganisms-previously-accepted-names">Microorganisms (previously accepted names)<a class="anchor" aria-label="anchor" href="#microorganisms-previously-accepted-names"></a>
 </h2>
-<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
+<p>A data set with 14,338 rows and 4 columns, containing the following
-<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
+column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and
-<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
+<em>prevalence</em>.</p>
-<p>It was last updated on 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
+<p><strong>Note:</strong> remember that the ‘ref’ columns contains the
 scientific reference to the old taxonomic entries, i.e. of column
 <em>‘fullname’</em>. For the scientific reference of the new names,
 i.e. of column <em>‘fullname_new’</em>, see the
 <code>microorganisms</code> data set.</p>
 <p>This data set is in R available as <code>microorganisms.old</code>,
 after you load the <code>AMR</code> package.</p>
 <p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R
 file</a> (0.2 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel file</a> (0.5 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel
 file</a> (0.5 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain text file</a> (1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain
 text file</a> (1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS file</a> (2.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS
 file</a> (2.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS file</a> (1.3 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS
 file</a> (1.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata file</a> (2 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata
 file</a> (2 MB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
 </h3>
-<p>This data set contains old, previously accepted taxonomic names. The data sources are the same as the <code>microorganisms</code> data set:</p>
+<p>This data set contains old, previously accepted taxonomic names. The
 data sources are the same as the <code>microorganisms</code> data
 set:</p>
 <ul>
 <li>
-<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
+<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a>
 (included version: 2019)</li>
 <li>
-<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
+<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with
 Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
 </ul>
 </div>
 <div class="section level3">
 <h3 id="example-content-1">Example content<a class="anchor" aria-label="anchor" href="#example-content-1"></a>
 </h3>
 <p>Example rows when filtering on <em>Escherichia</em>:</p>
-<table class="table">
+<table style="width:100%;" class="table">
 <colgroup>
 <col width="31%">
 <col width="30%">
 <col width="24%">
 <col width="13%">
 </colgroup>
 <thead><tr class="header">
 <th align="center">fullname</th>
 <th align="center">fullname_new</th>
@ -493,31 +546,50 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="antibiotic-agents">Antibiotic agents<a class="anchor" aria-label="anchor" href="#antibiotic-agents"></a>
 </h2>
-<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
+<p>A data set with 464 rows and 14 columns, containing the following
-<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
-<p>It was last updated on 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
 <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
 <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antibiotics</code>, after
 you load the <code>AMR</code> package.</p>
 <p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (33 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R
 file</a> (33 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel file</a> (65 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel
 file</a> (65 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain text file</a> (0.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain
 text file</a> (0.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS file</a> (1.8 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS
 file</a> (1.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS file</a> (0.3 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS
 file</a> (0.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata file</a> (0.3 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata
 file</a> (0.3 MB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
 </h3>
-<p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
+<p>This data set contains all EARS-Net and ATC codes gathered from WHO
 and WHONET, and all compound IDs from PubChem. It also contains all
 brand names (synonyms) as found on PubChem and Defined Daily Doses
 (DDDs) for oral and parenteral administration.</p>
 <ul>
 <li>
-<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
+<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO
-<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
+Collaborating Centre for Drug Statistics Methodology</a> (note: this may
 not be used for commercial purposes, but is freely available from the
 WHO CC website for personal use)</li>
 <li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
 National Library of Medicine</a></li>
 <li><a href="https://whonet.org" class="external-link">WHONET software 2019</a></li>
 </ul>
 </div>
@ -597,7 +669,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <td align="center">Beta-lactams/penicillins</td>
 <td align="center">J01CR02</td>
 <td align="center">Beta-lactam antibacterials, penicillins</td>
-<td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td>
+<td align="center">Combinations of penicillins, incl. beta-lactamase
 inhibitors</td>
 <td align="center">a/c, amcl, aml, …</td>
 <td align="center">amocla, amoclan, amoclav, …</td>
 <td align="center">1.5</td>
@ -661,31 +734,49 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="antiviral-agents">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents"></a>
 </h2>
-<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
+<p>A data set with 102 rows and 9 columns, containing the following
-<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>,
-<p>It was last updated on 23 July 2021 20:35:47 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
 <em>iv_ddd</em> and <em>iv_units</em>.</p>
 <p>This data set is in R available as <code>antivirals</code>, after you
 load the <code>AMR</code> package.</p>
 <p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R
 file</a> (5 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel file</a> (14 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel
 file</a> (14 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain text file</a> (16 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain
 text file</a> (16 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS file</a> (80 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS
 file</a> (80 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS file</a> (68 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS
 file</a> (68 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata file</a> (67 kB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata
 file</a> (67 kB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
 </h3>
-<p>This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
+<p>This data set contains all ATC codes gathered from WHO and all
 compound IDs from PubChem. It also contains all brand names (synonyms)
 as found on PubChem and Defined Daily Doses (DDDs) for oral and
 parenteral administration.</p>
 <ul>
 <li>
-<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
+<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO
-<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
+Collaborating Centre for Drug Statistics Methodology</a> (note: this may
 not be used for commercial purposes, but is freely available from the
 WHO CC website for personal use)</li>
 <li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US
 National Library of Medicine</a></li>
 </ul>
 </div>
 <div class="section level3">
@ -719,7 +810,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <td align="center">J05AF06</td>
 <td align="center">441300</td>
 <td align="center">Abacavir</td>
-<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
+<td align="center">Nucleoside and nucleotide reverse transcriptase
 inhibitors</td>
 <td align="center">Abacavir, Abacavir sulfate, Ziagen</td>
 <td align="center">0.6</td>
 <td align="center">g</td>
@ -730,7 +822,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <td align="center">J05AB01</td>
 <td align="center">135398513</td>
 <td align="center">Aciclovir</td>
-<td align="center">Nucleosides and nucleotides excl. reverse transcriptase inhibitors</td>
+<td align="center">Nucleosides and nucleotides excl. reverse
 transcriptase inhibitors</td>
 <td align="center">Acicloftal, Aciclovier, Aciclovir, …</td>
 <td align="center">4.0</td>
 <td align="center">g</td>
@ -741,8 +834,10 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <td align="center">J05AF08</td>
 <td align="center">60871</td>
 <td align="center">Adefovir dipivoxil</td>
-<td align="center">Nucleoside and nucleotide reverse transcriptase inhibitors</td>
+<td align="center">Nucleoside and nucleotide reverse transcriptase
-<td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, …</td>
+inhibitors</td>
 <td align="center">Adefovir di ester, Adefovir dipivoxil, Adefovir
 Dipivoxil, …</td>
 <td align="center">10.0</td>
 <td align="center">mg</td>
 <td align="center"></td>
@ -788,27 +883,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="intrinsic-bacterial-resistance">Intrinsic bacterial resistance<a class="anchor" aria-label="anchor" href="#intrinsic-bacterial-resistance"></a>
 </h2>
-<p>A data set with 134,956 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
+<p>A data set with 134,956 rows and 2 columns, containing the following
-<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>mo</em> and <em>ab</em>.</p>
-<p>It was last updated on 1 February 2022 22:08:19 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
+<p>This data set is in R available as <code>intrinsic_resistant</code>,
 after you load the <code>AMR</code> package.</p>
 <p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (78 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R
 file</a> (78 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (0.9 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel
 file</a> (0.9 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (5.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain
 text file</a> (5.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (10.4 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS
 file</a> (10.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (7.4 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS
 file</a> (7.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (10.2 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata
 file</a> (10.2 MB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
 </h3>
-<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3</a> (2021).</p>
+<p>This data set contains all defined intrinsic resistance by EUCAST of
 all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST
 Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’
 v3.3</a> (2021).</p>
 </div>
 <div class="section level3">
 <h3 id="example-content-4">Example content<a class="anchor" aria-label="anchor" href="#example-content-4"></a>
@ -1055,27 +1162,40 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
 </h2>
-<p>A data set with 20,318 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
+<p>A data set with 20,318 rows and 11 columns, containing the following
-<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
-<p>It was last updated on 1 February 2022 22:08:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
+<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
 <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
 <p>This data set is in R available as <code>rsi_translation</code>,
 after you load the <code>AMR</code> package.</p>
 <p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (39 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
 file</a> (39 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel file</a> (0.7 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel
 file</a> (0.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.7 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain
 text file</a> (1.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (3.6 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS
 file</a> (3.6 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.2 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS
 file</a> (2.2 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.4 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata
 file</a> (3.4 MB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
 </h3>
-<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST (2011-2021).</p>
+<p>This data set contains interpretation rules for MIC values and disk
 diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST
 (2011-2021).</p>
 </div>
 <div class="section level3">
 <h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
@ -1193,33 +1313,57 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div class="section level2">
 <h2 id="dosage-guidelines-from-eucast">Dosage guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-guidelines-from-eucast"></a>
 </h2>
-<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
+<p>A data set with 169 rows and 9 columns, containing the following
-<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
+column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
-<p>It was last updated on 23 July 2021 20:35:47 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
+<em>dose_times</em>, <em>administration</em>, <em>notes</em>,
 <em>original_txt</em> and <em>eucast_version</em>.</p>
 <p>This data set is in R available as <code>dosage</code>, after you
 load the <code>AMR</code> package.</p>
 <p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R
 file</a> (3 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel file</a> (14 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel
 file</a> (14 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain text file</a> (15 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain
 text file</a> (15 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS file</a> (52 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS
 file</a> (52 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS file</a> (45 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS
 file</a> (45 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata file</a> (44 kB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata
 file</a> (44 kB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
 </h3>
-<p>EUCAST breakpoints used in this package are based on the dosages in this data set.</p>
+<p>EUCAST breakpoints used in this package are based on the dosages in
-<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
+this data set.</p>
 <p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
 Breakpoint Tables’ v11.0</a> (2021).</p>
 </div>
 <div class="section level3">
 <h3 id="example-content-6">Example content<a class="anchor" aria-label="anchor" href="#example-content-6"></a>
 </h3>
 <table class="table">
 <colgroup>
 <col width="4%">
 <col width="10%">
 <col width="15%">
 <col width="10%">
 <col width="9%">
 <col width="13%">
 <col width="5%">
 <col width="16%">
 <col width="13%">
 </colgroup>
 <thead><tr class="header">
 <th align="center">ab</th>
 <th align="center">name</th>
@ -1316,12 +1460,14 @@ If you are reading this page from within R, please <a href="https://msberends.gi
      <footer><div class="copyright">
  <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
 Erwin E. A. Hassing.</p>
 </div>
 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
 2.0.2.</p>
 </div>
      </footer>
--- a/docs/authors.html
+++ b/docs/authors.html
@ -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">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9001</span>
      </span>
    </div>
@ -30,7 +30,7 @@
  </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    <span class="fa fa-question-circle"></span>
    How to
@ -269,11 +269,13 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
      <footer><div class="copyright">
-  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+  <p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
 Erwin E. A. Hassing.</p>
 </div>
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
 2.0.2.</p>
 </div>
      </footer></div>
--- a/docs/index.html
+++ b/docs/index.html
@ -47,7 +47,7 @@
      </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">1.8.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9001</span>
      </span>
    </div>
@ -61,7 +61,7 @@
  </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    <span class="fa fa-question-circle"></span>
    How to
@ -195,22 +195,74 @@
 <code>AMR</code> (for R) <img src="./logo.svg" align="right"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a>
 </h1></div>
 <blockquote>
-<p>Update: The latest <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST guideline for intrinsic resistance</a> (v3.3, October 2021) is now supported, the CLSI 2021 interpretation guideline is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021).</p>
+<p>Update March 2022: All functions in this package are considered to be
 stable. Updates to the AMR interpretation rules (such as by EUCAST and
 CLSI), the microbial taxonomy, and the antibiotic dosages will all be
 updated every 6 to 12 months.</p>
 </blockquote>
 <div class="section level3">
 <h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a>
 </h3>
-<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
+<p><code>AMR</code> is a free, open-source and independent <a href="https://www.r-project.org" class="external-link">R package</a> (see <a href="#copyright">Copyright</a>) to simplify the analysis and prediction
-<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
+of Antimicrobial Resistance (AMR) and to work with microbial and
-<p>The <code>AMR</code> package is available in <img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;"> Dutch, <img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;"> English, <img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;"> German, <img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;"> Italian, <img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;"> Portuguese, <img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;"> Spanish and <img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;"> Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
+antimicrobial data and properties, by using evidence-based methods.
-<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>) but is <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
+<strong>Our aim is to provide a standard</strong> for clean and
 reproducible AMR data analysis, that can therefore empower
 epidemiological analyses to continuously enable surveillance and
 treatment evaluation in any setting.</p>
 <p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~71,000 distinct
 microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic
 and antiviral drugs</strong></a> by name and code (including ATC,
 WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about
 valid R/SI and MIC values. It supports any data format, including
 WHONET/EARS-Net data.</p>
 <p>The <code>AMR</code> package is available in
 <img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;">
 Danish,
 <img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;">
 Dutch,
 <img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;">
 English,
 <img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;">
 French,
 <img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;">
 German,
 <img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;">
 Italian,
 <img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;">
 Portuguese,
 <img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;">
 Russian,
 <img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;">
 Spanish and
 <img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;">
 Swedish. Antimicrobial drug (group) names and colloquial microorganism
 names are provided in these languages.</p>
 <p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">fully independent
 of any other R package</a> and works on Windows, macOS and Linux with
 all versions of R since R-3.0 (April 2013). <strong>It was designed to
 work in any setting, including those with very limited
 resources</strong>. It was created for both routine data analysis and
 academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration
 with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe
 Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>. This
 R package formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
 10.33612/diss.192486375</a>) but is <a href="./news">actively and
 durably maintained</a> by two public healthcare organisations in the
 Netherlands.</p>
 <div class="main-content" style="display: inline-block;">
 <p>
-<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 175 countries</strong><br> Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.
+<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
 <strong>Used in 175 countries</strong><br> Since its first public
 release in early 2018, this R package has been used in almost all
 countries in the world. Click the map to enlarge and to see the country
 names.
 </p>
 </div>
 <div class="section level5">
-<h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
+<h5 id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side">With <code>AMR</code> (for R), there’s always a knowledgeable
 microbiologist by your side!<a class="anchor" aria-label="anchor" href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side"></a>
 </h5>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
@ -224,7 +276,12 @@
  <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="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
+<p>With only having defined a row filter on Gram-negative bacteria with
 intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code>
 and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on
 two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and
 <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the
 <code>AMR</code> package make sure you get what you meant:</p>
 <table class="table">
 <thead><tr class="header">
 <th align="left">bacteria</th>
@ -338,9 +395,14 @@
 <div class="section level4">
 <h4 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>
 </h4>
-<p>The development of this package is part of, related to, or made possible by:</p>
+<p>The development of this package is part of, related to, or made
 possible by:</p>
 <div align="center">
-<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
+<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a>
 <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a>
 <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a>
 <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a>
 <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
 </div>
 </div>
 </div>
@ -349,21 +411,33 @@
 </h3>
 <p>This package can be used for:</p>
 <ul>
-<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
+<li>Reference for the taxonomy of microorganisms, since the package
-<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
+contains all microbial (sub)species from the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> and <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in
-<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
+Nomenclature</a> (<a href="./reference/mo_property.html">manual</a>)</li>
 <li>Interpreting raw MIC and disk diffusion values, based on the latest
 CLSI or EUCAST guidelines (<a href="./reference/as.rsi.html">manual</a>)</li>
 <li>Retrieving antimicrobial drug names, doses and forms of
 administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
 <li>Determining first isolates to be used for AMR data analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
 <li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
-<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
+<li>Determining multi-drug resistance (MDR) / multi-drug resistant
-<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
+organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
-<li>Predicting future antimicrobial resistance using regression models (<a href="./articles/resistance_predict.html">tutorial</a>)</li>
+<li>Calculating (empirical) susceptibility of both mono therapy and
-<li>Getting properties for any microorganism (like Gram stain, species, genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
+combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
-<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
+<li>Predicting future antimicrobial resistance using regression models
 (<a href="./articles/resistance_predict.html">tutorial</a>)</li>
 <li>Getting properties for any microorganism (like Gram stain, species,
 genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
 <li>Getting properties for any antibiotic (like name, code of
 EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
 <li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
 <li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
-<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
+<li>Getting SNOMED codes of a microorganism, or getting properties of a
-<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
+microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
-<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
+<li>Getting LOINC codes of an antibiotic, or getting properties of an
 antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
 <li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to
 translate MIC values and disk diffusion diameters to R/SI (<a href="./articles/datasets.html">link</a>)</li>
 <li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
 </ul>
 </div>
@ -374,17 +448,24 @@
 <h4 id="latest-released-version">Latest released version<a class="anchor" aria-label="anchor" href="#latest-released-version"></a>
 </h4>
 <p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
-<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
+<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R
 network (CRAN)</a>. Install this package in R from CRAN by using the
 command:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></code></pre></div>
-<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
+<p>It will be downloaded and installed automatically. For RStudio, click
-<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
+on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type
 in “AMR” and press <kbd>Install</kbd>.</p>
 <p><strong>Note:</strong> Not all functions on this website may be
 available in this latest release. To use all functions and data sets
 mentioned on this website, install the latest development version.</p>
 </div>
 <div class="section level4">
 <h4 id="latest-development-version">Latest development version<a class="anchor" aria-label="anchor" href="#latest-development-version"></a>
 </h4>
 <p><a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p>
-<p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
+<p>The latest and unpublished development version can be installed from
 GitHub in two ways:</p>
 <ol style="list-style-type: decimal">
 <li>
 <p>Manually, using:</p>
@ -393,11 +474,16 @@
 <span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
 </li>
 <li>
-<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
+<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe
 platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our
 R-universe address</a> to your list of repositories (‘repos’):</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
                  msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em> &gt; <em>Check for Package Updates…</em>).</p>
+<p>After this, you can install and update this <code>AMR</code> package
 like any official release (e.g., using
 <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em>
 &gt; <em>Check for Package Updates…</em>).</p>
 </li>
 </ol>
 <p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz" class="external-link uri">https://github.com/msberends/AMR/raw/main/data-raw/AMR_latest.tar.gz</a></p>
@ -406,7 +492,8 @@
 <div class="section level3">
 <h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a>
 </h3>
-<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
+<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or
 click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
 </div>
 <div class="section level3">
 <h3 id="short-introduction">Short introduction<a class="anchor" aria-label="anchor" href="#short-introduction"></a>
@ -414,66 +501,181 @@
 <div class="section level4">
 <h4 id="microbial-taxonomic-reference-data">Microbial (taxonomic) reference data<a class="anchor" aria-label="anchor" href="#microbial-taxonomic-reference-data"></a>
 </h4>
-<p>This package contains the complete taxonomic tree of almost all ~71,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>), supplemented by data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished, which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
+<p>This package contains the complete taxonomic tree of almost all
 ~71,000 microorganisms from the authoritative and comprehensive
 Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">www.catalogueoflife.org</a>),
 supplemented by data from the List of Prokaryotic names with Standing in
 Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>).
 This supplementation is needed until the <a href="https://github.com/Sp2000/colplus" class="external-link">CoL+ project</a> is finished,
 which we await. With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be
 checked which version of the CoL is included in this package.</p>
 <p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
 </div>
 <div class="section level4">
 <h4 id="antimicrobial-reference-data">Antimicrobial reference data<a class="anchor" aria-label="anchor" href="#antimicrobial-reference-data"></a>
 </h4>
-<p>This package contains <strong>all ~570 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals Community Register of the European Commission</a>.</p>
+<p>This package contains <strong>all ~570 antibiotic, antimycotic and
-<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
+antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC)
 codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the
 World Health Organization Collaborating Centre for Drug Statistics
 Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link uri">https://www.whocc.no</a>) and the <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">Pharmaceuticals
 Community Register of the European Commission</a>.</p>
 <p><strong>NOTE: The WHOCC copyright does not allow use for commercial
 purposes, unlike any other info from this package. See <a href="https://www.whocc.no/copyright_disclaimer/" class="external-link uri">https://www.whocc.no/copyright_disclaimer/</a>.</strong></p>
 <p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
 </div>
 <div class="section level4">
 <h4 id="whonet--ears-net">WHONET / EARS-Net<a class="anchor" aria-label="anchor" href="#whonet--ears-net"></a>
 </h4>
-<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure as a WHONET export file. Furthermore, this package also contains a <a href="./reference/antibiotics.html">data set antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
+<p>We support WHONET and EARS-Net data. Exported files from WHONET can
-<p>Read our tutorial about <a href="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
+be imported into R and can be analysed easily using this package. For
 education purposes, we created an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a>
 with the exact same structure as a WHONET export file. Furthermore, this
 package also contains a <a href="./reference/antibiotics.html">data set
 antibiotics</a> with all EARS-Net antibiotic abbreviations, and knows
 almost all WHONET abbreviations for microorganisms. When using WHONET
 data as input for analysis, all input parameters will be set
 automatically.</p>
 <p>Read our tutorial about <a href="./articles/WHONET.html">how to work
 with WHONET data here</a>.</p>
 </div>
 <div class="section level4">
 <h4 id="overview-of-functions">Overview of functions<a class="anchor" aria-label="anchor" href="#overview-of-functions"></a>
 </h4>
-<p>The <code>AMR</code> package basically does four important things:</p>
+<p>The <code>AMR</code> package basically does four important
 things:</p>
 <ol style="list-style-type: decimal">
 <li>
-<p>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use intelligent rules to guess results that you would expect:</p>
+<p>It <strong>cleanses existing data</strong> by providing new
 <em>classes</em> for microoganisms, antibiotics and antimicrobial
 results (both S/I/R and MIC). By installing this package, you teach R
 everything about microbiology that is needed for analysis. These
 functions all use intelligent rules to guess results that you would
 expect:</p>
 <ul>
-<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AURS”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
+<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human
-<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial IDs, these IDs are also human readable based on those used by EARS-Net. For example, the ID of amoxicillin is <code>AMX</code> and the ID of gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also uses intelligent rules to find results like accepting misspelling, trade names and abbrevations used in many laboratory systems. For instance, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine. To accomplish this, the package contains a database with most LIS codes, official names, trade names, ATC codes, defined daily doses (DDD) and drug categories of antibiotics.</li>
+readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em>
-<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on raw MIC values (in mg/L) or disk diffusion values (in mm), or transform existing values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
+is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S.
-<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result in “&lt;=0.002”.</li>
+aureus</em> is “B_STPHY_AURS”. The function takes almost any text as
 input that looks like the name or code of a microorganism like “E.
 coli”, “esco” or “esccol” and tries to find expected results using
 intelligent rules combined with the included Catalogue of Life data set.
 It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group
 <em>Staphylococci</em> into coagulase negative and positive (CoNS and
 CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can
 categorise <em>Streptococci</em> into Lancefield groups (like
 beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
 <li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial
 IDs, these IDs are also human readable based on those used by EARS-Net.
 For example, the ID of amoxicillin is <code>AMX</code> and the ID of
 gentamicin is <code>GEN</code>. The <code><a href="reference/as.ab.html">as.ab()</a></code> function also
 uses intelligent rules to find results like accepting misspelling, trade
 names and abbrevations used in many laboratory systems. For instance,
 the values “Furabid”, “Furadantin”, “nitro” all return the ID of
 Nitrofurantoine. To accomplish this, the package contains a database
 with most LIS codes, official names, trade names, ATC codes, defined
 daily doses (DDD) and drug categories of antibiotics.</li>
 <li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on
 raw MIC values (in mg/L) or disk diffusion values (in mm), or transform
 existing values to valid antimicrobial results. It produces just S, I or
 R based on your input and warns about invalid values. Even values like
 “&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
 <li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a
 so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values
 as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result
 in “&lt;=0.002”.</li>
 </ul>
 </li>
 <li>
-<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
+<p>It <strong>enhances existing data</strong> and <strong>adds new
 data</strong> from data sets included in this package.</p>
 <ul>
-<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST expert rules to isolates</a> (not the translation from MIC to R/SI values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
+<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
-<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
+expert rules to isolates</a> (not the translation from MIC to R/SI
 values, use <code><a href="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
 <li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of
 every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">using
 guidelines from the CLSI</a> (Clinical and Laboratory Standards
 Institute).
 <ul>
-<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
+<li>You can also identify first <em>weighted</em> isolates of every
 patient, an adjusted version of the CLSI guideline. This takes into
 account key antibiotics of every strain and compares them.</li>
 </ul>
 </li>
-<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are multi-drug resistant organisms (MDRO). It supports a variety of international guidelines, such as the MDR-paper by Magiorakos <em>et al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID 21793988</a>), the exceptional phenotype definitions of EUCAST and the WHO guideline on multi-drug resistant TB. It also supports the national guidelines of the Netherlands and Germany.</li>
+<li>Use <code><a href="reference/mdro.html">mdro()</a></code> to determine which micro-organisms are
-<li>The <a href="./reference/microorganisms.html">data set microorganisms</a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any SNOMED CT code associated with a microorganism. As all these function use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code>mo_genus("MRSA")</code> and <code>mo_genus("S. aureus")</code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Danish, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
+multi-drug resistant organisms (MDRO). It supports a variety of
-<li>The <a href="./reference/antibiotics.html">data set antibiotics</a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, LOINC code, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>, <code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code>ab_name("Fluclox")</code>, <code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
+international guidelines, such as the MDR-paper by Magiorakos <em>et
 al.</em> (2012, <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=21793988" class="external-link">PMID
 21793988</a>), the exceptional phenotype definitions of EUCAST and the
 WHO guideline on multi-drug resistant TB. It also supports the national
 guidelines of the Netherlands and Germany.</li>
 <li>The <a href="./reference/microorganisms.html">data set
 microorganisms</a> contains the complete taxonomic tree of ~70,000
 microorganisms. Furthermore, some colloquial names and all Gram stains
 are available, which enables resistance analysis of e.g. different
 antibiotics per Gram stain. The package also contains functions to look
 up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>,
 <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even
 <code><a href="reference/mo_property.html">mo_phylum()</a></code>. Use <code><a href="reference/mo_property.html">mo_snomed()</a></code> to look up any
 SNOMED CT code associated with a microorganism. As all these function
 use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent
 rules for determination. For example, <code>mo_genus("MRSA")</code> and
 <code>mo_genus("S. aureus")</code> will both return
 <code>"Staphylococcus"</code>. They also come with support for German,
 Danish, Dutch, Spanish, Italian, French and Portuguese. These functions
 can be used to add new variables to your data.</li>
 <li>The <a href="./reference/antibiotics.html">data set antibiotics</a>
 contains ~450 antimicrobial drugs with their EARS-Net code, ATC code,
 PubChem compound ID, LOINC code, official name, common LIS codes and
 DDDs of both oral and parenteral administration. It also contains all
 (thousands of) trade names found in PubChem. Use functions like
 <code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code>, <code><a href="reference/ab_property.html">ab_atc()</a></code>,
 <code><a href="reference/ab_property.html">ab_loinc()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up
 values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code>
 internally so they support the same intelligent rules to guess the most
 probable result. For example, <code>ab_name("Fluclox")</code>,
 <code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code>
 will all return <code>"Flucloxacillin"</code>. These functions can again
 be used to add new variables to your data.</li>
 </ul>
 </li>
 <li>
-<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
+<p>It <strong>analyses the data</strong> with convenient functions
 that use well-known methods.</p>
 <ul>
-<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
+<li>Calculate the microbial susceptibility or resistance (and even
-<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
+co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and
-<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
+<code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the
 <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>,
 <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and
 <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of
 isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>,
 <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions.
 All these functions can be used with the <code>dplyr</code> package
 (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>)</li>
 <li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for
 the <code>ggplot2</code> package</li>
 <li>Predict antimicrobial resistance for the nextcoming years using
 logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code>
 function</li>
 </ul>
 </li>
 <li>
-<p>It <strong>teaches the user</strong> how to use all the above actions.</p>
+<p>It <strong>teaches the user</strong> how to use all the above
 actions.</p>
 <ul>
-<li>Aside from this website with many tutorials, the package itself contains extensive help pages with many examples for all functions.</li>
+<li>Aside from this website with many tutorials, the package itself
 contains extensive help pages with many examples for all functions.</li>
 <li>The package also contains example data sets:
 <ul>
-<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code> data set</a>. This data set contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis.</li>
+<li>The <a href="./reference/example_isolates.html"><code>example_isolates</code>
-<li>The <a href="./reference/WHONET.html"><code>WHONET</code> data set</a>. This data set only contains fake data, but with the exact same structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
+data set</a>. This data set contains 2,000 microbial isolates with their
 full antibiograms. It reflects reality and can be used to practice AMR
 data analysis.</li>
 <li>The <a href="./reference/WHONET.html"><code>WHONET</code> data
 set</a>. This data set only contains fake data, but with the exact same
 structure as files exported by WHONET. Read more about WHONET <a href="./articles/WHONET.html">on its tutorial page</a>.</li>
 </ul>
 </li>
 </ul>
@ -484,7 +686,9 @@
 <div class="section level3">
 <h3 id="copyright">Copyright<a class="anchor" aria-label="anchor" href="#copyright"></a>
 </h3>
-<p>This R package is free, open-source software and licensed under the <a href="./LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. In a nutshell, this means that this package:</p>
+<p>This R package is free, open-source software and licensed under the
 <a href="./LICENSE-text.html">GNU General Public License v2.0
 (GPL-2)</a>. In a nutshell, this means that this package:</p>
 <ul>
 <li><p>May be used for commercial purposes</p></li>
 <li><p>May be used for private purposes</p></li>
@ -492,15 +696,18 @@
 <li>
 <p>May be modified, although:</p>
 <ul>
-<li>Modifications <strong>must</strong> be released under the same license when distributing the package</li>
+<li>Modifications <strong>must</strong> be released under the same
 license when distributing the package</li>
 <li>Changes made to the code <strong>must</strong> be documented</li>
 </ul>
 </li>
 <li>
 <p>May be distributed, although:</p>
 <ul>
-<li>Source code <strong>must</strong> be made available when the package is distributed</li>
+<li>Source code <strong>must</strong> be made available when the package
-<li>A copy of the license and copyright notice <strong>must</strong> be included with the package.</li>
+is distributed</li>
 <li>A copy of the license and copyright notice <strong>must</strong> be
 included with the package.</li>
 </ul>
 </li>
 <li><p>Comes with a LIMITATION of liability</p></li>
@ -556,12 +763,14 @@
      <footer><div class="copyright">
  <p></p>
-<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
+<p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
 Erwin E. A. Hassing.</p>
 </div>
 <div class="pkgdown">
  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
 2.0.2.</p>
 </div>
      </footer>
--- a/docs/news/index.html
+++ b/docs/news/index.html
--- a/docs/survey.html
+++ b/docs/survey.html
@ -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">1.8.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9001</span>
      </span>
    </div>
@ -30,7 +30,7 @@
  </a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    <span class="fa fa-question-circle"></span>
    How to
--- a/index.md
+++ b/index.md
@ -1,6 +1,6 @@
 # `AMR` (for R) <img src="./logo.svg" align="right"/>
-> Update: The latest [EUCAST guideline for intrinsic resistance](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) (v3.3, October 2021) is now supported, the CLSI 2021 interpretation guideline is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021).
+> Update March 2022: All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
 ### What is `AMR` (for R)?