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

.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: '3.2',     allowfail: false}
+          # - {os: macOS-latest,   r: '3.3',     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}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.1
-Date: 2022-03-17
+Version: 1.8.1.9001
+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

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')

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"))) {

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">1.8.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9001</span>
       </span>
     </div>
 
@@ -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

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">1.8.0.9010</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

docs/articles/AMR_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/EUCAST.html

@@ -185,7 +185,7 @@
 
       
 
-      </header><div class="row">
+      </header><script src="EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>How to apply EUCAST rules</h1>
@@ -201,39 +201,18 @@
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
-<p>What are EUCAST rules? The European Committee on Antimicrobial
-Susceptibility Testing (EUCAST) states <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">on
-their website</a>:</p>
+<p>What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Testing (EUCAST) states <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">on their website</a>:</p>
 <blockquote>
-<p><em>EUCAST expert rules are a tabulated collection of expert
-knowledge on intrinsic resistances, exceptional resistance phenotypes
-and interpretive rules that may be applied to antimicrobial
-susceptibility testing in order to reduce errors and make appropriate
-recommendations for reporting particular resistances.</em></p>
+<p><em>EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.</em></p>
 </blockquote>
-<p>In Europe, a lot of medical microbiological laboratories already
-apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008" class="external-link">Brown
-<em>et al.</em>, 2015</a>). Our package features their latest insights
-on intrinsic resistance and unusual phenotypes (v3.3, 2021).</p>
-<p>Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this
-purpose can also apply additional rules, like forcing
-<help title="ATC: J01CA01">ampicillin</help> = R in isolates when
-<help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
+<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008" class="external-link">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and unusual phenotypes (v3.3, 2021).</p>
+<p>Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
 </div>
 <div class="section level2">
 <h2 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a>
 </h2>
-<p>These rules can be used to discard impossible bug-drug combinations
-in your data. For example, <em>Klebsiella</em> produces beta-lactamase
-that prevents ampicillin (or amoxicillin) from working against it. In
-other words, practically every strain of <em>Klebsiella</em> is
-resistant to ampicillin.</p>
-<p>Sometimes, laboratory data can still contain such strains with
-ampicillin being susceptible to ampicillin. This could be because an
-antibiogram is available before an identification is available, and the
-antibiogram is then not re-interpreted based on the identification
-(namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can
-be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
+<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
+<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">oops</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <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="st">"Klebsiella"</span>, 
                           <span class="st">"Escherichia"</span><span class="op">)</span>,
@@ -247,10 +226,7 @@ be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</
 <span class="co">#            mo ampicillin</span>
 <span class="co"># 1  Klebsiella          R</span>
 <span class="co"># 2 Escherichia          S</span></code></pre></div>
-<p>A more convenient function is
-<code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline,
-but allows to check for one or more specific microorganisms or
-antibiotics:</p>
+<p>A more convenient function is <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline, but allows to check for one or more specific microorganisms or antibiotics:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><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="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,
                           <span class="st">"ampicillin"</span><span class="op">)</span>
@@ -259,11 +235,7 @@ antibiotics:</p>
 <span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"Klebsiella"</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="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span><span class="op">)</span>
 <span class="co"># [1]  TRUE FALSE</span></code></pre></div>
-<p>EUCAST rules can not only be used for correction, they can also be
-used for filling in known resistance and susceptibility based on results
-of other antimicrobials drugs. This process is called <em>interpretive
-reading</em>, is basically a form of imputation, and is part of the
-<code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
+<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em>, is basically a form of imputation, and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <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="st">"Staphylococcus aureus"</span>,
                           <span class="st">"Enterococcus faecalis"</span>,
@@ -425,14 +397,12 @@ reading</em>, is basically a form of imputation, and is part of the
 
       <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>

docs/articles/EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/MDR.html

@@ -185,11 +185,10 @@
 
       
 
-      </header><div class="row">
+      </header><script src="MDR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
-      <h1 data-toc-skip>How to determine multi-drug resistance
-(MDR)</h1>
+      <h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
             
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
@@ -199,87 +198,54 @@
 
     
     
-<p>With the function <code><a href="../reference/mdro.html">mdro()</a></code>, you can determine which
-micro-organisms are multi-drug resistant organisms (MDRO).</p>
+<p>With the function <code><a href="../reference/mdro.html">mdro()</a></code>, you can determine which micro-organisms are multi-drug resistant organisms (MDRO).</p>
 <div class="section level3">
 <h3 id="type-of-input">Type of input<a class="anchor" aria-label="anchor" href="#type-of-input"></a>
 </h3>
-<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function takes a data set as input, such as a
-regular <code>data.frame</code>. It tries to automatically determine the
-right columns for info about your isolates, such as the name of the
-species and all columns with results of antimicrobial agents. See the
-help page for more info about how to set the right settings for your
-data with the command <code><a href="../reference/mdro.html">?mdro</a></code>.</p>
-<p>For WHONET data (and most other data), all settings are automatically
-set correctly.</p>
+<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function takes a data set as input, such as a regular <code>data.frame</code>. It tries to automatically determine the right columns for info about your isolates, such as the name of the species and all columns with results of antimicrobial agents. See the help page for more info about how to set the right settings for your data with the command <code><a href="../reference/mdro.html">?mdro</a></code>.</p>
+<p>For WHONET data (and most other data), all settings are automatically set correctly.</p>
 </div>
 <div class="section level3">
 <h3 id="guidelines">Guidelines<a class="anchor" aria-label="anchor" href="#guidelines"></a>
 </h3>
-<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function support multiple guidelines. You can
-select a guideline with the <code>guideline</code> parameter. Currently
-supported guidelines are (case-insensitive):</p>
+<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function support multiple guidelines. You can select a guideline with the <code>guideline</code> parameter. Currently supported guidelines are (case-insensitive):</p>
 <ul>
 <li>
 <p><code>guideline = "CMI2012"</code> (default)</p>
-<p>Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant,
-extensively drug-resistant and pandrug-resistant bacteria: an
-international expert proposal for interim standard definitions for
-acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext" class="external-link">link</a>)</p>
+<p>Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext" class="external-link">link</a>)</p>
 </li>
 <li>
-<p><code>guideline = "EUCAST3.2"</code> (or simply
-<code>guideline = "EUCAST"</code>)</p>
-<p>The European international guideline - EUCAST Expert Rules Version
-3.2 “Intrinsic Resistance and Unusual Phenotypes” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf" class="external-link">link</a>)</p>
+<p><code>guideline = "EUCAST3.2"</code> (or simply <code>guideline = "EUCAST"</code>)</p>
+<p>The European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance and Unusual Phenotypes” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf" class="external-link">link</a>)</p>
 </li>
 <li>
 <p><code>guideline = "EUCAST3.1"</code></p>
-<p>The European international guideline - EUCAST Expert Rules Version
-3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf" class="external-link">link</a>)</p>
+<p>The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf" class="external-link">link</a>)</p>
 </li>
 <li>
 <p><code>guideline = "TB"</code></p>
-<p>The international guideline for multi-drug resistant tuberculosis -
-World Health Organization “Companion handbook to the WHO guidelines for
-the programmatic management of drug-resistant tuberculosis” (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/" class="external-link">link</a>)</p>
+<p>The international guideline for multi-drug resistant tuberculosis - World Health Organization “Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis” (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/" class="external-link">link</a>)</p>
 </li>
 <li>
 <p><code>guideline = "MRGN"</code></p>
-<p>The German national guideline - Mueller <em>et al.</em> (2015)
-Antimicrobial Resistance and Infection Control 4:7. DOI:
-10.1186/s13756-015-0047-6</p>
+<p>The German national guideline - Mueller <em>et al.</em> (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p>
 </li>
 <li>
 <p><code>guideline = "BRMO"</code></p>
-<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en
-Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen)
-(ZKH)” (<a href="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh" class="external-link">link</a>)</p>
+<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (<a href="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh" class="external-link">link</a>)</p>
 </li>
 </ul>
-<p>Please suggest your own (country-specific) guidelines by letting us
-know: <a href="https://github.com/msberends/AMR/issues/new" class="external-link uri">https://github.com/msberends/AMR/issues/new</a>.</p>
+<p>Please suggest your own (country-specific) guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="external-link uri">https://github.com/msberends/AMR/issues/new</a>.</p>
 <div class="section level4">
 <h4 id="custom-guidelines">Custom Guidelines<a class="anchor" aria-label="anchor" href="#custom-guidelines"></a>
 </h4>
-<p>You can also use your own custom guideline. Custom guidelines can be
-set with the <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function. This is of
-great importance if you have custom rules to determine MDROs in your
-hospital, e.g., rules that are dependent on ward, state of contact
-isolation or other variables in your data.</p>
-<p>If you are familiar with <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when()</a></code> of the
-<code>dplyr</code> package, you will recognise the input method to set
-your own rules. Rules must be set using what R considers to be the
-‘formula notation’:</p>
+<p>You can also use your own custom guideline. Custom guidelines can be set with the <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.</p>
+<p>If you are familiar with <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when()</a></code> of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what R considers to be the ‘formula notation’:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">custom</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">custom_mdro_guideline</a></span><span class="op">(</span><span class="va">CIP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type A"</span>,
                                 <span class="va">ERY</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type B"</span><span class="op">)</span></code></pre></div>
-<p>If a row/an isolate matches the first rule, the value after the first
-<code>~</code> (in this case <em>‘Elderly Type A’</em>) will be set as
-MDRO value. Otherwise, the second rule will be tried and so on. The
-maximum number of rules is unlimited.</p>
-<p>You can print the rules set in the console for an overview. Colours
-will help reading it if your console supports colours.</p>
+<p>If a row/an isolate matches the first rule, the value after the first <code>~</code> (in this case <em>‘Elderly Type A’</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The maximum number of rules is unlimited.</p>
+<p>You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">custom</span>
 <span class="co"># A set of custom MDRO rules:</span>
@@ -289,8 +255,7 @@ will help reading it if your console supports colours.</p>
 <span class="co"># </span>
 <span class="co"># Unmatched rows will return NA.</span>
 <span class="co"># Results will be of class &lt;factor&gt;, with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span></code></pre></div>
-<p>The outcome of the function can be used for the
-<code>guideline</code> argument in the <code><a href="../reference/mdro.html">mdro()</a></code> function:</p>
+<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code><a href="../reference/mdro.html">mdro()</a></code> function:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span>
 <span class="co"># Determining MDROs based on custom rules, resulting in factor levels:</span>
@@ -301,25 +266,14 @@ will help reading it if your console supports colours.</p>
 <span class="co"># x</span>
 <span class="co">#       Negative Elderly Type A Elderly Type B </span>
 <span class="co">#           1070            198            732</span></code></pre></div>
-<p>The rules set (the <code>custom</code> object in this case) could be
-exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> if you
-collaborate with multiple users. The custom rules set could then be
-imported using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>.</p>
+<p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>.</p>
 </div>
 </div>
 <div class="section level3">
 <h3 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a>
 </h3>
-<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered
-<code>factor</code> for predefined guidelines. For example, the output
-of the default guideline by Magiorakos <em>et al.</em> returns a
-<code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in
-that order.</p>
-<p>The next example uses the <code>example_isolates</code> data set.
-This is a data set included with this package and contains full
-antibiograms of 2,000 microbial isolates. It reflects reality and can be
-used to practise AMR data analysis. If we test the MDR/XDR/PDR guideline
-on this data set, we get:</p>
+<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code> for predefined guidelines. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
+<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains full antibiograms of 2,000 microbial isolates. It reflects reality and can be used to practise AMR data analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>   <span class="co"># to support pipes: %&gt;%</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
@@ -343,32 +297,16 @@ on this data set, we get:</p>
 <span class="co"># Table 5 - Acinetobacter spp.... OK.</span>
 <span class="co"># Warning: in `mdro()`: NA introduced for isolates where the available percentage of</span>
 <span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
-<p>Only results with ‘R’ are considered as resistance. Use
-<code>combine_SI = FALSE</code> to also consider ‘I’ as resistance.</p>
-<p>Determining multidrug-resistant organisms (MDRO), according to:
-Guideline: Multidrug-resistant, extensively drug-resistant and
-pandrug-resistant bacteria: an international expert proposal for interim
-standard definitions for acquired resistance. Author(s): Magiorakos AP,
-Srinivasan A, Carey RB, …, Vatopoulos A, Weber JT, Monnet DL Source:
-Clinical Microbiology and Infection 18:3, 2012; doi:
-10.1111/j.1469-0691.2011.03570.x</p>
+<p>Only results with ‘R’ are considered as resistance. Use <code>combine_SI = FALSE</code> to also consider ‘I’ as resistance.</p>
+<p>Determining multidrug-resistant organisms (MDRO), according to: Guideline: Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Author(s): Magiorakos AP, Srinivasan A, Carey RB, …, Vatopoulos A, Weber JT, Monnet DL Source: Clinical Microbiology and Infection 18:3, 2012; doi: 10.1111/j.1469-0691.2011.03570.x</p>
 <p>(16 isolates had no test results)</p>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered (numeric)<br>
 Length: 2,000<br>
-Levels: 4: Negative &lt; Multi-drug-resistant (MDR) &lt; Extensively
-drug-resistant …<br>
+Levels: 4: Negative &lt; Multi-drug-resistant (MDR) &lt; Extensively drug-resistant …<br>
 Available: 1,729 (86.45%, NA: 271 = 13.55%)<br>
 Unique: 2</p>
-<table style="width:100%;" class="table">
-<colgroup>
-<col width="4%">
-<col width="38%">
-<col width="9%">
-<col width="12%">
-<col width="16%">
-<col width="19%">
-</colgroup>
+<table class="table">
 <thead><tr class="header">
 <th align="left"></th>
 <th align="left">Item</th>
@@ -396,8 +334,7 @@ Unique: 2</p>
 </tr>
 </tbody>
 </table>
-<p>For another example, I will create a data set to determine multi-drug
-resistant TB:</p>
+<p>For another example, I will create a data set to determine multi-drug resistant TB:</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># random_rsi() is a helper function to generate</span>
 <span class="co"># a random vector with values S, I and R</span>
@@ -408,8 +345,7 @@ resistant TB:</p>
                          pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<p>Because all column names are automatically verified for valid drug
-names or codes, this would have worked exactly the same way:</p>
+<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same way:</p>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
@@ -422,21 +358,20 @@ names or codes, this would have worked exactly the same way:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
 <span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
-<span class="co"># 1          I         S            I          I            S            S</span>
-<span class="co"># 2          R         S            I          S            R            R</span>
-<span class="co"># 3          I         R            I          S            R            S</span>
-<span class="co"># 4          I         I            I          R            S            R</span>
-<span class="co"># 5          R         S            I          R            S            I</span>
-<span class="co"># 6          S         S            I          S            R            R</span>
+<span class="co"># 1          S         R            S          I            R            S</span>
+<span class="co"># 2          I         I            S          S            I            I</span>
+<span class="co"># 3          I         S            R          R            R            S</span>
+<span class="co"># 4          S         S            I          S            R            S</span>
+<span class="co"># 5          R         R            S          I            R            I</span>
+<span class="co"># 6          R         S            R          S            S            I</span>
 <span class="co">#   kanamycin</span>
-<span class="co"># 1         R</span>
-<span class="co"># 2         I</span>
+<span class="co"># 1         I</span>
+<span class="co"># 2         S</span>
 <span class="co"># 3         S</span>
-<span class="co"># 4         S</span>
-<span class="co"># 5         S</span>
-<span class="co"># 6         R</span></code></pre></div>
-<p>We can now add the interpretation of MDR-TB to our data set. You can
-use:</p>
+<span class="co"># 4         I</span>
+<span class="co"># 5         I</span>
+<span class="co"># 6         I</span></code></pre></div>
+<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
 <p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
@@ -455,26 +390,17 @@ use:</p>
 <span class="co">#            management of drug-resistant tuberculosis</span>
 <span class="co"># Author(s): WHO (World Health Organization)</span>
 <span class="co"># Version:   WHO/HTM/TB/2014.11, 2014</span>
-<span class="co"># Source:    https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></code></pre></div>
+<span class="co"># Source:    https://www.who.int/publications/i/item/9789241548809</span></code></pre></div>
 <p>Create a frequency table of the results:</p>
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered (numeric)<br>
 Length: 5,000<br>
-Levels: 5: Negative &lt; Mono-resistant &lt; Poly-resistant &lt;
-Multi-drug-resistant &lt;…<br>
+Levels: 5: Negative &lt; Mono-resistant &lt; Poly-resistant &lt; Multi-drug-resistant &lt;…<br>
 Available: 5,000 (100%, NA: 0 = 0%)<br>
 Unique: 5</p>
-<table style="width:100%;" class="table">
-<colgroup>
-<col width="4%">
-<col width="38%">
-<col width="9%">
-<col width="12%">
-<col width="16%">
-<col width="19%">
-</colgroup>
+<table class="table">
 <thead><tr class="header">
 <th align="left"></th>
 <th align="left">Item</th>
@@ -487,40 +413,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3261</td>
-<td align="right">65.22%</td>
-<td align="right">3261</td>
-<td align="right">65.22%</td>
+<td align="right">3244</td>
+<td align="right">64.88%</td>
+<td align="right">3244</td>
+<td align="right">64.88%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">987</td>
-<td align="right">19.74%</td>
-<td align="right">4248</td>
-<td align="right">84.96%</td>
+<td align="right">990</td>
+<td align="right">19.80%</td>
+<td align="right">4234</td>
+<td align="right">84.68%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">437</td>
-<td align="right">8.74%</td>
-<td align="right">4685</td>
-<td align="right">93.70%</td>
+<td align="right">417</td>
+<td align="right">8.34%</td>
+<td align="right">4651</td>
+<td align="right">93.02%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">218</td>
-<td align="right">4.36%</td>
-<td align="right">4903</td>
-<td align="right">98.06%</td>
+<td align="right">248</td>
+<td align="right">4.96%</td>
+<td align="right">4899</td>
+<td align="right">97.98%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">97</td>
-<td align="right">1.94%</td>
+<td align="right">101</td>
+<td align="right">2.02%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -539,14 +465,12 @@ Unique: 5</p>
 
       <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>

docs/articles/MDR_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/PCA.html

@@ -185,11 +185,10 @@
 
       
 
-      </header><div class="row">
+      </header><script src="PCA_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
-      <h1 data-toc-skip>How to conduct principal component analysis
-(PCA) for AMR</h1>
+      <h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
             
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
@@ -199,8 +198,7 @@
 
     
     
-<p><strong>NOTE: This page will be updated soon, as the pca() function
-is currently being developed.</strong></p>
+<p><strong>NOTE: This page will be updated soon, as the pca() function is currently being developed.</strong></p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -208,12 +206,11 @@ is currently being developed.</strong></p>
 <div class="section level2">
 <h2 id="transforming">Transforming<a class="anchor" aria-label="anchor" href="#transforming"></a>
 </h2>
-<p>For PCA, we need to transform our AMR data first. This is what the
-<code>example_isolates</code> data set in this package looks like:</p>
+<p>For PCA, we need to transform our AMR data first. This is what the <code>example_isolates</code> data set in this package looks like:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
-<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
+<span class="fu"><a href="https://dplyr.tidyverse.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
 <span class="co"># Rows: 2,000</span>
 <span class="co"># Columns: 49</span>
 <span class="co"># $ date            <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
@@ -265,8 +262,7 @@ is currently being developed.</strong></p>
 <span class="co"># $ COL             <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R…</span>
 <span class="co"># $ MUP             <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span>
 <span class="co"># $ RIF             <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R,…</span></code></pre></div>
-<p>Now to transform this to a data set with only resistance percentages
-per taxonomic order and genus:</p>
+<p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">resistance_data</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span>order <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>,       <span class="co"># group on anything, like order</span>
@@ -290,15 +286,12 @@ per taxonomic order and genus:</p>
 <div class="section level2">
 <h2 id="perform-principal-component-analysis">Perform principal component analysis<a class="anchor" aria-label="anchor" href="#perform-principal-component-analysis"></a>
 </h2>
-<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows
-that contain numeric values in all selected variables, so we now only
-need to do:</p>
+<p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">pca_result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
 <span class="co"># ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span>
 <span class="co">#   and "TOB". Total observations available: 7.</span></code></pre></div>
-<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>
-function:</p>
+<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> function:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span>
 <span class="co"># Groups (n=4, named as 'order'):</span>
@@ -310,11 +303,7 @@ function:</p>
 <span class="co"># Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></code></pre></div>
 <pre><code><span class="co"># Groups (n=4, named as 'order'):</span>
 <span class="co"># [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"</span></code></pre>
-<p>Good news. The first two components explain a total of 93.3% of the
-variance (see the PC1 and PC2 values of the <em>Proportion of
-Variance</em>. We can create a so-called biplot with the base R
-<code><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot()</a></code> function, to see which antimicrobial resistance
-per drug explain the difference per microorganism.</p>
+<p>Good news. The first two components explain a total of 93.3% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
 </div>
 <div class="section level2">
 <h2 id="plotting-the-results">Plotting the results<a class="anchor" aria-label="anchor" href="#plotting-the-results"></a>
@@ -322,9 +311,7 @@ per drug explain the difference per microorganism.</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></code></pre></div>
 <p><img src="PCA_files/figure-html/unnamed-chunk-5-1.png" width="750"></p>
-<p>But we can’t see the explanation of the points. Perhaps this works
-better with our new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function, that
-automatically adds the right labels and even groups:</p>
+<p>But we can’t see the explanation of the points. Perhaps this works better with our new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function, that automatically adds the right labels and even groups:</p>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></code></pre></div>
 <p><img src="PCA_files/figure-html/unnamed-chunk-6-1.png" width="750"></p>
@@ -348,14 +335,12 @@ automatically adds the right labels and even groups:</p>
 
       <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>

docs/articles/PCA_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
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+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/SPSS.html

@@ -185,14 +185,13 @@
 
       
 
-      </header><div class="row">
+      </header><script src="SPSS_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
-                        <h4 data-toc-skip class="author">Dr. Matthijs
-Berends</h4>
+                        <h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
             
-            <h4 data-toc-skip class="date">14 March 2022</h4>
+            <h4 data-toc-skip class="date">27 March 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
       <div class="hidden name"><code>SPSS.Rmd</code></div>
@@ -204,135 +203,45 @@ Berends</h4>
 <div class="section level2">
 <h2 id="spss-sas-stata">SPSS / SAS / Stata<a class="anchor" aria-label="anchor" href="#spss-sas-stata"></a>
 </h2>
-<p>SPSS (Statistical Package for the Social Sciences) is probably the
-most well-known software package for statistical analysis. SPSS is
-easier to learn than R, because in SPSS you only have to click a menu to
-run parts of your analysis. Because of its user-friendliness, it is
-taught at universities and particularly useful for students who are new
-to statistics. From my experience, I would guess that pretty much all
-(bio)medical students know it at the time they graduate. SAS and Stata
-are comparable statistical packages popular in big industries.</p>
+<p>SPSS (Statistical Package for the Social Sciences) is probably the most well-known software package for statistical analysis. SPSS is easier to learn than R, because in SPSS you only have to click a menu to run parts of your analysis. Because of its user-friendliness, it is taught at universities and particularly useful for students who are new to statistics. From my experience, I would guess that pretty much all (bio)medical students know it at the time they graduate. SAS and Stata are comparable statistical packages popular in big industries.</p>
 </div>
 <div class="section level2">
 <h2 id="compared-to-r">Compared to R<a class="anchor" aria-label="anchor" href="#compared-to-r"></a>
 </h2>
-<p>As said, SPSS is easier to learn than R. But SPSS, SAS and Stata come
-with major downsides when comparing it with R:</p>
+<p>As said, SPSS is easier to learn than R. But SPSS, SAS and Stata come with major downsides when comparing it with R:</p>
 <ul>
 <li>
 <p><strong>R is highly modular.</strong></p>
-<p>The <a href="https://cran.r-project.org/" class="external-link">official R network
-(CRAN)</a> features more than 16,000 packages at the time of writing,
-our <code>AMR</code> package being one of them. All these packages were
-peer-reviewed before publication. Aside from this official channel,
-there are also developers who choose not to submit to CRAN, but rather
-keep it on their own public repository, like GitHub. So there may even
-be a lot more than 14,000 packages out there.</p>
-<p>Bottom line is, you can really extend it yourself or ask somebody to
-do this for you. Take for example our <code>AMR</code> package. Among
-other things, it adds reliable reference data to R to help you with the
-data cleaning and analysis. SPSS, SAS and Stata will never know what a
-valid MIC value is or what the Gram stain of <em>E. coli</em> is. Or
-that all species of <em>Klebiella</em> are resistant to amoxicillin and
-that Floxapen<sup>®</sup> is a trade name of flucloxacillin. These facts
-and properties are often needed to clean existing data, which would be
-very inconvenient in a software package without reliable reference data.
-See below for a demonstration.</p>
+<p>The <a href="https://cran.r-project.org/" class="external-link">official R network (CRAN)</a> features more than 16,000 packages at the time of writing, our <code>AMR</code> package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitHub. So there may even be a lot more than 14,000 packages out there.</p>
+<p>Bottom line is, you can really extend it yourself or ask somebody to do this for you. Take for example our <code>AMR</code> package. Among other things, it adds reliable reference data to R to help you with the data cleaning and analysis. SPSS, SAS and Stata will never know what a valid MIC value is or what the Gram stain of <em>E. coli</em> is. Or that all species of <em>Klebiella</em> are resistant to amoxicillin and that Floxapen<sup>®</sup> is a trade name of flucloxacillin. These facts and properties are often needed to clean existing data, which would be very inconvenient in a software package without reliable reference data. See below for a demonstration.</p>
 </li>
 <li>
 <p><strong>R is extremely flexible.</strong></p>
-<p>Because you write the syntax yourself, you can do anything you want.
-The flexibility in transforming, arranging, grouping and summarising
-data, or drawing plots, is endless - with SPSS, SAS or Stata you are
-bound to their algorithms and format styles. They may be a bit flexible,
-but you can probably never create that very specific publication-ready
-plot without using other (paid) software. If you sometimes write
-syntaxes in SPSS to run a complete analysis or to ‘automate’ some of
-your work, you could do this a lot less time in R. You will notice that
-writing syntaxes in R is a lot more nifty and clever than in SPSS.
-Still, as working with any statistical package, you will have to have
-knowledge about what you are doing (statistically) and what you are
-willing to accomplish.</p>
+<p>Because you write the syntax yourself, you can do anything you want. The flexibility in transforming, arranging, grouping and summarising data, or drawing plots, is endless - with SPSS, SAS or Stata you are bound to their algorithms and format styles. They may be a bit flexible, but you can probably never create that very specific publication-ready plot without using other (paid) software. If you sometimes write syntaxes in SPSS to run a complete analysis or to ‘automate’ some of your work, you could do this a lot less time in R. You will notice that writing syntaxes in R is a lot more nifty and clever than in SPSS. Still, as working with any statistical package, you will have to have knowledge about what you are doing (statistically) and what you are willing to accomplish.</p>
 </li>
 <li>
 <p><strong>R can be easily automated.</strong></p>
-<p>Over the last years, <a href="https://rmarkdown.rstudio.com/" class="external-link">R
-Markdown</a> has really made an interesting development. With R
-Markdown, you can very easily produce reports, whether the format has to
-be Word, PowerPoint, a website, a PDF document or just the raw data to
-Excel. It even allows the use of a reference file containing the layout
-style (e.g. fonts and colours) of your organisation. I use this a lot to
-generate weekly and monthly reports automatically. Just write the code
-once and enjoy the automatically updated reports at any interval you
-like.</p>
-<p>For an even more professional environment, you could create <a href="https://shiny.rstudio.com/" class="external-link">Shiny apps</a>: live manipulation of
-data using a custom made website. The webdesign knowledge needed
-(JavaScript, CSS, HTML) is almost <em>zero</em>.</p>
+<p>Over the last years, <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a> has really made an interesting development. With R Markdown, you can very easily produce reports, whether the format has to be Word, PowerPoint, a website, a PDF document or just the raw data to Excel. It even allows the use of a reference file containing the layout style (e.g. fonts and colours) of your organisation. I use this a lot to generate weekly and monthly reports automatically. Just write the code once and enjoy the automatically updated reports at any interval you like.</p>
+<p>For an even more professional environment, you could create <a href="https://shiny.rstudio.com/" class="external-link">Shiny apps</a>: live manipulation of data using a custom made website. The webdesign knowledge needed (JavaScript, CSS, HTML) is almost <em>zero</em>.</p>
 </li>
 <li>
 <p><strong>R has a huge community.</strong></p>
-<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
-online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">439,954
-R-related questions</a> have already been asked on this platform (that
-covers questions and answers for any programming language). In my own
-experience, most questions are answered within a couple of
-minutes.</p>
+<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">440,893 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
 </li>
 <li>
-<p><strong>R understands any data type, including
-SPSS/SAS/Stata.</strong></p>
-<p>And that’s not vice versa I’m afraid. You can import data from any
-source into R. For example from SPSS, SAS and Stata (<a href="https://haven.tidyverse.org/" class="external-link">link</a>), from Minitab, Epi Info
-and EpiData (<a href="https://cran.r-project.org/package=foreign" class="external-link">link</a>), from Excel
-(<a href="https://readxl.tidyverse.org/" class="external-link">link</a>), from flat files like
-CSV, TXT or TSV (<a href="https://readr.tidyverse.org/" class="external-link">link</a>), or
-directly from databases and datawarehouses from anywhere on the world
-(<a href="https://dbplyr.tidyverse.org/" class="external-link">link</a>). You can even scrape
-websites to download tables that are live on the internet (<a href="https://github.com/hadley/rvest" class="external-link">link</a>) or get the results of
-an API call and transform it into data in only one command (<a href="https://github.com/Rdatatable/data.table/wiki/Convenience-features-of-fread" class="external-link">link</a>).</p>
-<p>And the best part - you can export from R to most data formats as
-well. So you can import an SPSS file, do your analysis neatly in R and
-export the resulting tables to Excel files for sharing.</p>
+<p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>
+<p>And that’s not vice versa I’m afraid. You can import data from any source into R. For example from SPSS, SAS and Stata (<a href="https://haven.tidyverse.org/" class="external-link">link</a>), from Minitab, Epi Info and EpiData (<a href="https://cran.r-project.org/package=foreign" class="external-link">link</a>), from Excel (<a href="https://readxl.tidyverse.org/" class="external-link">link</a>), from flat files like CSV, TXT or TSV (<a href="https://readr.tidyverse.org/" class="external-link">link</a>), or directly from databases and datawarehouses from anywhere on the world (<a href="https://dbplyr.tidyverse.org/" class="external-link">link</a>). You can even scrape websites to download tables that are live on the internet (<a href="https://github.com/hadley/rvest" class="external-link">link</a>) or get the results of an API call and transform it into data in only one command (<a href="https://github.com/Rdatatable/data.table/wiki/Convenience-features-of-fread" class="external-link">link</a>).</p>
+<p>And the best part - you can export from R to most data formats as well. So you can import an SPSS file, do your analysis neatly in R and export the resulting tables to Excel files for sharing.</p>
 </li>
 <li>
 <p><strong>R is completely free and open-source.</strong></p>
-<p>No strings attached. It was created and is being maintained by
-volunteers who believe that (data) science should be open and publicly
-available to everybody. SPSS, SAS and Stata are quite expensive. IBM
-SPSS Staticstics only comes with subscriptions nowadays, varying <a href="https://www.ibm.com/products/spss-statistics/pricing" class="external-link">between USD
-1,300 and USD 8,500</a> per user <em>per year</em>. SAS Analytics Pro
-costs <a href="https://www.sas.com/store/products-solutions/sas-analytics-pro/prodPERSANL.html" class="external-link">around
-USD 10,000</a> per computer. Stata also has a business model with
-subscription fees, varying <a href="https://www.stata.com/order/new/bus/single-user-licenses/dl/" class="external-link">between
-USD 600 and USD 2,800</a> per computer per year, but lower prices come
-with a limitation of the number of variables you can work with. And
-still they do not offer the above benefits of R.</p>
-<p>If you are working at a midsized or small company, you can save it
-tens of thousands of dollars by using R instead of e.g. SPSS - gaining
-even more functions and flexibility. And all R enthousiasts can do as
-much PR as they want (like I do here), because nobody is officially
-associated with or affiliated by R. It is really free.</p>
+<p>No strings attached. It was created and is being maintained by volunteers who believe that (data) science should be open and publicly available to everybody. SPSS, SAS and Stata are quite expensive. IBM SPSS Staticstics only comes with subscriptions nowadays, varying <a href="https://www.ibm.com/products/spss-statistics/pricing" class="external-link">between USD 1,300 and USD 8,500</a> per user <em>per year</em>. SAS Analytics Pro costs <a href="https://www.sas.com/store/products-solutions/sas-analytics-pro/prodPERSANL.html" class="external-link">around USD 10,000</a> per computer. Stata also has a business model with subscription fees, varying <a href="https://www.stata.com/order/new/bus/single-user-licenses/dl/" class="external-link">between USD 600 and USD 2,800</a> per computer per year, but lower prices come with a limitation of the number of variables you can work with. And still they do not offer the above benefits of R.</p>
+<p>If you are working at a midsized or small company, you can save it tens of thousands of dollars by using R instead of e.g. SPSS - gaining even more functions and flexibility. And all R enthousiasts can do as much PR as they want (like I do here), because nobody is officially associated with or affiliated by R. It is really free.</p>
 </li>
 <li>
-<p><strong>R is (nowadays) the preferred analysis software in
-academic papers.</strong></p>
-<p>At present, R is among the world most powerful statistical languages,
-and it is generally very popular in science (Bollmann <em>et al.</em>,
-2017). For all the above reasons, the number of references to R as an
-analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/" class="external-link">is
-rising continuously</a> and has even surpassed SPSS for academic use
-(Muenchen, 2014).</p>
-<p>I believe that the thing with SPSS is, that it has always had a great
-user interface which is very easy to learn and use. Back when they
-developed it, they had very little competition, let alone from R. R
-didn’t even had a professional user interface until the last decade
-(called RStudio, see below). How people used R between the nineties and
-2010 is almost completely incomparable to how R is being used now. The
-language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been
-restyled completely</a> by volunteers who are dedicated professionals in
-the field of data science. SPSS was great when there was nothing else
-that could compete. But now in 2022, I don’t see any reason why SPSS
-would be of any better use than R.</p>
+<p><strong>R is (nowadays) the preferred analysis software in academic papers.</strong></p>
+<p>At present, R is among the world most powerful statistical languages, and it is generally very popular in science (Bollmann <em>et al.</em>, 2017). For all the above reasons, the number of references to R as an analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/" class="external-link">is rising continuously</a> and has even surpassed SPSS for academic use (Muenchen, 2014).</p>
+<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2022, I don’t see any reason why SPSS would be of any better use than R.</p>
 </li>
 </ul>
 <p>To demonstrate the first point:</p>
@@ -376,23 +285,13 @@ would be of any better use than R.</p>
 <div class="section level3">
 <h3 id="rstudio">RStudio<a class="anchor" aria-label="anchor" href="#rstudio"></a>
 </h3>
-<p>To work with R, probably the best option is to use <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio</a>. It is an
-open-source and free desktop environment which not only allows you to
-run R code, but also supports project management, version management,
-package management and convenient import menus to work with other data
-sources. You can also install <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio Server</a> on a
-private or corporate server, which brings nothing less than the complete
-RStudio software to you as a website (at home or at work).</p>
-<p>To import a data file, just click <em>Import Dataset</em> in the
-Environment tab:</p>
+<p>To work with R, probably the best option is to use <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio</a>. It is an open-source and free desktop environment which not only allows you to run R code, but also supports project management, version management, package management and convenient import menus to work with other data sources. You can also install <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio Server</a> on a private or corporate server, which brings nothing less than the complete RStudio software to you as a website (at home or at work).</p>
+<p>To import a data file, just click <em>Import Dataset</em> in the Environment tab:</p>
 <p><img src="https://github.com/msberends/AMR/raw/main/docs/import1.png"></p>
-<p>If additional packages are needed, RStudio will ask you if they
-should be installed on beforehand.</p>
-<p>In the the window that opens, you can define all options (parameters)
-that should be used for import and you’re ready to go:</p>
+<p>If additional packages are needed, RStudio will ask you if they should be installed on beforehand.</p>
+<p>In the the window that opens, you can define all options (parameters) that should be used for import and you’re ready to go:</p>
 <p><img src="https://github.com/msberends/AMR/raw/main/docs/import2.png"></p>
-<p>If you want named variables to be imported as factors so it resembles
-SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html" class="external-link">as_factor()</a></code>.</p>
+<p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html" class="external-link">as_factor()</a></code>.</p>
 <p>The difference is this:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">SPSS_data</span>
@@ -430,8 +329,7 @@ SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.ht
 <div class="section level3">
 <h3 id="base-r">Base R<a class="anchor" aria-label="anchor" href="#base-r"></a>
 </h3>
-<p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/" class="external-link">great <code>haven</code> package</a>
-yourself:</p>
+<p>To import data from SPSS, SAS or Stata, you can use the <a href="https://haven.tidyverse.org/" class="external-link">great <code>haven</code> package</a> yourself:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># download and install the latest version:</span>
 <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">"haven"</span><span class="op">)</span>
@@ -511,14 +409,12 @@ yourself:</p>
 
       <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>

docs/articles/SPSS_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/WHONET.html

@@ -185,7 +185,7 @@
 
       
 
-      </header><div class="row">
+      </header><script src="WHONET_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>How to work with WHONET data</h1>
@@ -201,43 +201,26 @@
 <div class="section level3">
 <h3 id="import-of-data">Import of data<a class="anchor" aria-label="anchor" href="#import-of-data"></a>
 </h3>
-<p>This tutorial assumes you already imported the WHONET data with
-e.g. the <a href="https://readxl.tidyverse.org/" class="external-link"><code>readxl</code>
-package</a>. In RStudio, this can be done using the menu button ‘Import
-Dataset’ in the tab ‘Environment’. Choose the option ‘From Excel’ and
-select your exported file. Make sure date fields are imported
-correctly.</p>
+<p>This tutorial assumes you already imported the WHONET data with e.g. the <a href="https://readxl.tidyverse.org/" class="external-link"><code>readxl</code> package</a>. In RStudio, this can be done using the menu button ‘Import Dataset’ in the tab ‘Environment’. Choose the option ‘From Excel’ and select your exported file. Make sure date fields are imported correctly.</p>
 <p>An example syntax could look like this:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://readxl.tidyverse.org" class="external-link">readxl</a></span><span class="op">)</span>
 <span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html" class="external-link">read_excel</a></span><span class="op">(</span>path <span class="op">=</span> <span class="st">"path/to/your/file.xlsx"</span><span class="op">)</span></code></pre></div>
-<p>This package comes with an <a href="https://msberends.github.io/AMR/reference/WHONET.html">example
-data set <code>WHONET</code></a>. We will use it for this analysis.</p>
+<p>This package comes with an <a href="https://msberends.github.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
 </div>
 <div class="section level3">
 <h3 id="preparation">Preparation<a class="anchor" aria-label="anchor" href="#preparation"></a>
 </h3>
-<p>First, load the relevant packages if you did not yet did this. I use
-the tidyverse for all of my analyses. All of them. If you don’t know it
-yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="external-link uri">https://www.tidyverse.org/</a>.</p>
+<p>First, load the relevant packages if you did not yet did this. I use the tidyverse for all of my analyses. All of them. If you don’t know it yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="external-link uri">https://www.tidyverse.org/</a>.</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>   <span class="co"># part of tidyverse</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span> <span class="co"># part of tidyverse</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>     <span class="co"># this package</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
-<p>We will have to transform some variables to simplify and automate the
-analysis:</p>
+<p>We will have to transform some variables to simplify and automate the analysis:</p>
 <ul>
-<li>Microorganisms should be transformed to our own microorganism codes
-(called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our
-Catalogue of Life reference data set</a>, which contains all ~70,000
-microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa.
-We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also
-recognises almost all WHONET abbreviations of microorganisms.</li>
-<li>Antimicrobial results or interpretations have to be clean and valid.
-In other words, they should only contain values <code>"S"</code>,
-<code>"I"</code> or <code>"R"</code>. That is exactly where the
-<code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
+<li>Microorganisms should be transformed to our own microorganism codes (called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
+<li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
 </ul>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># transform variables</span>
@@ -247,9 +230,7 @@ In other words, they should only contain values <code>"S"</code>,
   <span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP_ND10</span><span class="op">:</span><span class="va">CIP_EE</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></code></pre></div>
 <p>No errors or warnings, so all values are transformed succesfully.</p>
-<p>We also created a package dedicated to data cleaning and checking,
-called the <code>cleaner</code> package. Its <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>
-function can be used to create frequency tables.</p>
+<p>We also created a package dedicated to data cleaning and checking, called the <code>cleaner</code> package. Its <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> function can be used to create frequency tables.</p>
 <p>So let’s check our data, with a couple of frequency tables:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># our newly created `mo` variable, put in the mo_name() function</span>
@@ -262,14 +243,6 @@ Unique: 37</p>
 <p>Shortest: 11<br>
 Longest: 40</p>
 <table class="table">
-<colgroup>
-<col width="4%">
-<col width="47%">
-<col width="7%">
-<col width="10%">
-<col width="13%">
-<col width="15%">
-</colgroup>
 <thead><tr class="header">
 <th align="left"></th>
 <th align="left">Item</th>
@@ -415,8 +388,7 @@ Drug group: Beta-lactams/penicillins<br>
 <div class="section level3">
 <h3 id="a-first-glimpse-at-results">A first glimpse at results<a class="anchor" aria-label="anchor" href="#a-first-glimpse-at-results"></a>
 </h3>
-<p>An easy <code>ggplot</code> will already give a lot of information,
-using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function:</p>
+<p>An easy <code>ggplot</code> will already give a lot of information, using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function:</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">Country</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@@ -436,14 +408,12 @@ using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a>
 
       <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>

docs/articles/WHONET_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/benchmarks.html

@@ -185,7 +185,7 @@
 
       
 
-      </header><div class="row">
+      </header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Benchmarks</h1>
@@ -198,30 +198,14 @@
 
     
     
-<p>One of the most important features of this package is the complete
-microbial taxonomic database, supplied by the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (CoL) and
-the <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with
-Standing in Nomenclature</a> (LPSN). We created a function
-<code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid
-microbial ID by using intelligent rules combined with the microbial
-taxonomy.</p>
-<p>Using the <code>microbenchmark</code> package, we can review the
-calculation performance of this function. Its function
-<code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark()</a></code> runs different input expressions
-independently of each other and measures their time-to-result.</p>
+<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (CoL) and the <a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN). We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the microbial taxonomy.</p>
+<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/joshuaulrich/microbenchmark/" class="external-link">microbenchmark</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></code></pre></div>
-<p>In the next test, we try to ‘coerce’ different input values into the
-microbial code of <em>Staphylococcus aureus</em>. Coercion is a
-computational process of forcing output based on an input. For
-microorganism names, coercing user input to taxonomically valid
-microorganism names is crucial to ensure correct interpretation and to
-enable grouping based on taxonomic properties.</p>
-<p>The actual result is the same every time: it returns its
-microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for
-<em>Bacteria</em>, its taxonomic kingdom).</p>
+<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
+<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, its taxonomic kingdom).</p>
 <p>But the calculation time differs a lot:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">S.aureus</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>
@@ -238,42 +222,29 @@ microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for
   <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
   <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
   times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
-<span class="co">#                                   expr   min    lq  mean median  uq max neval</span>
-<span class="co">#                           as.mo("sau")  12.0  13.0  17.0   14.0  15  53    25</span>
-<span class="co">#                          as.mo("stau")  51.0  59.0  74.0   71.0  90  97    25</span>
-<span class="co">#                          as.mo("STAU")  53.0  60.0  77.0   87.0  91  96    25</span>
-<span class="co">#                        as.mo("staaur")  11.0  13.0  16.0   14.0  15  48    25</span>
-<span class="co">#                        as.mo("STAAUR")  13.0  14.0  19.0   15.0  16  48    25</span>
-<span class="co">#                     as.mo("S. aureus")  28.0  31.0  48.0   59.0  63  70    25</span>
-<span class="co">#                      as.mo("S aureus")  28.0  29.0  42.0   33.0  58  83    25</span>
-<span class="co">#         as.mo("Staphylococcus aureus")   3.9   4.1   6.1    4.4   5  43    25</span>
-<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 270.0  270.0 270 390    25</span>
-<span class="co">#       as.mo("Sthafilokkockus aaureuz") 160.0 190.0 200.0  200.0 220 240    25</span>
-<span class="co">#                          as.mo("MRSA")  13.0  13.0  19.0   14.0  15  50    25</span>
-<span class="co">#                          as.mo("VISA")  21.0  22.0  29.0   24.0  27  61    25</span></code></pre></div>
+<span class="co">#                                   expr   min    lq  mean median    uq max neval</span>
+<span class="co">#                           as.mo("sau")  19.0  20.0  25.0   20.0  26.0  55    25</span>
+<span class="co">#                          as.mo("stau")  94.0  95.0 110.0  100.0 130.0 140    25</span>
+<span class="co">#                          as.mo("STAU")  92.0  97.0 110.0  110.0 120.0 140    25</span>
+<span class="co">#                        as.mo("staaur")  19.0  19.0  24.0   20.0  21.0  56    25</span>
+<span class="co">#                        as.mo("STAAUR")  19.0  20.0  21.0   20.0  20.0  49    25</span>
+<span class="co">#                     as.mo("S. aureus")  54.0  57.0  72.0   64.0  86.0  96    25</span>
+<span class="co">#                      as.mo("S aureus")  55.0  55.0  72.0   57.0  90.0 100    25</span>
+<span class="co">#         as.mo("Staphylococcus aureus")   5.6   5.7   8.5    5.8   6.2  40    25</span>
+<span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 360.0 370.0 400.0  400.0 420.0 550    25</span>
+<span class="co">#       as.mo("Sthafilokkockus aaureuz") 280.0 290.0 300.0  300.0 320.0 350    25</span>
+<span class="co">#                          as.mo("MRSA")  19.0  20.0  24.0   20.0  21.0  51    25</span>
+<span class="co">#                          as.mo("VISA")  34.0  34.0  48.0   36.0  65.0  73    25</span></code></pre></div>
 <p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
-<p>In the table above, all measurements are shown in milliseconds
-(thousands of seconds). A value of 5 milliseconds means it can determine
-200 input values per second. It case of 200 milliseconds, this is only 5
-input values per second. It is clear that accepted taxonomic names are
-extremely fast, but some variations are up to 61 times slower to
-determine.</p>
-<p>To improve performance, we implemented two important algorithms to
-save unnecessary calculations: <strong>repetitive results</strong> and
-<strong>already precalculated results</strong>.</p>
+<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 69 times slower to determine.</p>
+<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
 <div class="section level3">
 <h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
 </h3>
-<p>Repetitive results are values that are present more than once in a
-vector. Unique values will only be calculated once by
-<code><a href="../reference/as.mo.html">as.mo()</a></code>. So running
-<code>as.mo(c("E. coli", "E. coli"))</code> will check the value
-<code>"E. coli"</code> only once.</p>
-<p>To prove this, we will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for testing - a
-helper function that returns the full microbial name (genus, species and
-possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
+<p>Repetitive results are values that are present more than once in a vector. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. So running <code>as.mo(c("E. coli", "E. coli"))</code> will check the value <code>"E. coli"</code> only once.</p>
+<p>To prove this, we will use <code><a href="../reference/mo_property.html">mo_name()</a></code> for testing - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># start with the example_isolates data set</span>
 <span class="va">x</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> 
@@ -287,8 +258,8 @@ possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()<
 <span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
 <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
 <span class="co"># Class &lt;mo&gt;</span>
-<span class="co"># [1] B_ACNTB      B_ESCHR_COLI B_STRPT_GRPC B_STPHY_HMNS B_STPHY_CONS</span>
-<span class="co"># [6] B_ESCHR_COLI</span>
+<span class="co"># [1] B_ENTRBC_CLOC B_ESCHR_COLI  B_STRPT_PYGN  B_STPHY_AURS  B_ESCHR_COLI </span>
+<span class="co"># [6] B_STRPT_PNMN</span>
   
 <span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
 <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@@ -301,38 +272,28 @@ possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()<
 <span class="co"># now let's see:</span>
 <span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
                          times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#        expr min  lq mean median  uq max neval</span>
-<span class="co">#  mo_name(x) 200 204  265    225 320 392    10</span></code></pre></div>
-<p>So getting official taxonomic names of 2,000,000 (!!) items
-consisting of 90 unique values only takes 0.225 seconds. That is 112
-nanoseconds on average. You only lose time on your unique input
-values.</p>
+<span class="co">#  mo_name(x) 259 264  357    299 451 509    10</span></code></pre></div>
+<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.299 seconds. That is 149 nanoseconds on average. You only lose time on your unique input values.</p>
 </div>
 <div class="section level3">
 <h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
 </h3>
-<p>What about precalculated results? If the input is an already
-precalculated result of a helper function such as
-<code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all. In other
-words, if you run <code><a href="../reference/mo_property.html">mo_name()</a></code> on a valid taxonomic name, it
-will return the results immediately (see ‘C’ below):</p>
+<p>What about precalculated results? If the input is an already precalculated result of a helper function such as <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all. In other words, if you run <code><a href="../reference/mo_property.html">mo_name()</a></code> on a valid taxonomic name, it will return the results immediately (see ‘C’ below):</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"STAAUR"</span><span class="op">)</span>,
                          B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
                          C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
                          times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
-<span class="co">#  expr   min    lq  mean median    uq   max neval</span>
-<span class="co">#     A  8.35  8.84  9.10   9.01  9.32 10.20    10</span>
-<span class="co">#     B 23.00 24.70 30.30  25.00 26.90 72.70    10</span>
-<span class="co">#     C  2.05  2.07  2.44   2.41  2.83  3.05    10</span></code></pre></div>
-<p>So going from <code>mo_name("Staphylococcus aureus")</code> to
-<code>"Staphylococcus aureus"</code> takes 0.0024 seconds - it doesn’t
-even start calculating <em>if the result would be the same as the
-expected resulting value</em>. That goes for all helper functions:</p>
+<span class="co">#  expr   min    lq mean median    uq   max neval</span>
+<span class="co">#     A 11.90 12.10 13.0  13.50 13.70 13.80    10</span>
+<span class="co">#     B 60.90 61.20 67.7  66.20 66.90 99.70    10</span>
+<span class="co">#     C  2.91  2.94  3.2   3.32  3.38  3.46    10</span></code></pre></div>
+<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0033 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
                          B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@@ -343,31 +304,23 @@ expected resulting value</em>. That goes for all helper functions:</p>
                          G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
                          H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
                          times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#  expr  min   lq mean median   uq  max neval</span>
-<span class="co">#     A 1.89 1.93 2.09   2.05 2.17 2.40    10</span>
-<span class="co">#     B 1.89 1.93 2.08   2.00 2.19 2.63    10</span>
-<span class="co">#     C 1.91 1.92 2.10   1.97 2.30 2.43    10</span>
-<span class="co">#     D 1.90 1.94 2.21   2.02 2.53 2.88    10</span>
-<span class="co">#     E 1.87 1.95 2.09   2.04 2.22 2.33    10</span>
-<span class="co">#     F 1.84 1.91 1.97   1.92 2.04 2.14    10</span>
-<span class="co">#     G 1.87 1.92 2.10   1.96 2.12 2.96    10</span>
-<span class="co">#     H 1.90 1.96 2.12   2.06 2.21 2.47    10</span></code></pre></div>
-<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the
-function has zero knowledge about the actual microorganism, namely
-<em>S. aureus</em>. But since the result would be
-<code>"Firmicutes"</code> anyway, there is no point in calculating the
-result. And because this package contains all phyla of all known
-bacteria, it can just return the initial value immediately.</p>
+<span class="co">#     A 2.92 2.93 3.02   2.94 3.02 3.40    10</span>
+<span class="co">#     B 2.87 2.90 3.14   3.09 3.32 3.71    10</span>
+<span class="co">#     C 2.91 2.94 3.15   3.12 3.33 3.46    10</span>
+<span class="co">#     D 2.86 2.90 3.05   2.96 3.27 3.30    10</span>
+<span class="co">#     E 2.87 2.88 3.03   2.96 3.16 3.29    10</span>
+<span class="co">#     F 2.92 2.95 3.08   2.98 3.29 3.35    10</span>
+<span class="co">#     G 2.89 2.96 3.04   2.99 3.11 3.29    10</span>
+<span class="co">#     H 2.85 2.95 3.11   3.08 3.31 3.38    10</span></code></pre></div>
+<p>Of course, when running <code>mo_phylum("Firmicutes")</code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
 </div>
 <div class="section level3">
 <h3 id="results-in-other-languages">Results in other languages<a class="anchor" aria-label="anchor" href="#results-in-other-languages"></a>
 </h3>
-<p>When the system language is non-English and supported by this
-<code>AMR</code> package, some functions will have a translated result.
-This almost does’t take extra time (compare “en” from the table below
-with the other languages):</p>
+<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time (compare “en” from the table below with the other languages):</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">CoNS</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"CoNS"</span><span class="op">)</span>
 <span class="va">CoNS</span>
@@ -394,21 +347,20 @@ with the other languages):</p>
                          ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
                          sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>,
                          times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
-<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
 <span class="co"># Unit: milliseconds</span>
 <span class="co">#  expr   min    lq  mean median    uq    max neval</span>
-<span class="co">#    da 2.133 2.304 3.442  2.494 2.816 46.020   100</span>
-<span class="co">#    de 2.128 2.312 3.068  2.520 2.699 53.220   100</span>
-<span class="co">#    en 1.014 1.115 1.262  1.227 1.362  2.424   100</span>
-<span class="co">#    es 2.133 2.338 2.981  2.570 2.737 43.770   100</span>
-<span class="co">#    fr 1.986 2.149 3.139  2.377 2.567 41.610   100</span>
-<span class="co">#    it 2.072 2.268 2.911  2.468 2.656 44.560   100</span>
-<span class="co">#    nl 2.115 2.286 2.962  2.521 2.723 43.240   100</span>
-<span class="co">#    pt 2.055 2.205 2.912  2.520 2.687 39.520   100</span>
-<span class="co">#    ru 1.998 2.210 2.866  2.474 2.631 39.820   100</span>
-<span class="co">#    sv 2.022 2.187 2.759  2.357 2.536 38.560   100</span></code></pre></div>
-<p>Currently supported languages are Danish, Dutch, English, French,
-German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
+<span class="co">#    da 3.546 3.643 4.072  3.704 3.832 35.930   100</span>
+<span class="co">#    de 3.597 3.659 4.422  3.734 3.839 36.400   100</span>
+<span class="co">#    en 1.672 1.726 1.804  1.767 1.794  2.259   100</span>
+<span class="co">#    es 3.609 3.685 4.496  3.760 3.843 36.540   100</span>
+<span class="co">#    fr 3.484 3.567 3.725  3.654 3.713  6.281   100</span>
+<span class="co">#    it 3.523 3.615 4.419  3.720 3.787 36.720   100</span>
+<span class="co">#    nl 3.614 3.676 3.805  3.732 3.838  4.703   100</span>
+<span class="co">#    pt 3.512 3.595 4.077  3.659 3.789 37.310   100</span>
+<span class="co">#    ru 3.556 3.647 4.057  3.680 3.812 35.230   100</span>
+<span class="co">#    sv 3.540 3.642 4.093  3.732 3.803 36.340   100</span></code></pre></div>
+<p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
 </div>
   </div>
 
@@ -422,14 +374,12 @@ German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
 
       <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>

docs/articles/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

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">1.8.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9001</span>
       </span>
     </div>
 
@@ -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
@@ -190,7 +190,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">15 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>

docs/articles/datasets_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/index.html

@@ -185,13 +185,11 @@
 
 
       <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>

docs/articles/resistance_predict.html

@@ -185,7 +185,7 @@
 
       
 
-      </header><div class="row">
+      </header><script src="resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>How to predict antimicrobial resistance</h1>
@@ -201,13 +201,8 @@
 <div class="section level2">
 <h2 id="needed-r-packages">Needed R packages<a class="anchor" aria-label="anchor" href="#needed-r-packages"></a>
 </h2>
-<p>As with many uses in R, we need some additional packages for AMR data
-analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a> by Dr
-Hadley Wickham. The tidyverse tremendously improves the way we conduct
-data science - it allows for a very natural way of writing syntaxes and
-creating beautiful plots in R.</p>
-<p>Our <code>AMR</code> package depends on these packages and even
-extends their use and functions.</p>
+<p>As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a> by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.</p>
+<p>Our <code>AMR</code> package depends on these packages and even extends their use and functions.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
 <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span>
@@ -219,34 +214,24 @@ extends their use and functions.</p>
 <div class="section level2">
 <h2 id="prediction-analysis">Prediction analysis<a class="anchor" aria-label="anchor" href="#prediction-analysis"></a>
 </h2>
-<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>,
-which takes the same input as functions for <a href="./AMR.html">other
-AMR data analysis</a>. Based on a date column, it calculates cases per
-year and uses a regression model to predict antimicrobial
-resistance.</p>
+<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR data analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
 <p>It is basically as easy as:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">resistance_predict</span>(<span class="at">tbl =</span> example_isolates, <span class="at">col_date =</span> <span class="st">"date"</span>, <span class="at">col_ab =</span> <span class="st">"TZP"</span>, <span class="at">model =</span> <span class="st">"binomial"</span>)</span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="co"># or:</span></span>
-<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>example_isolates <span class="sc">%&gt;%</span> </span>
-<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a>  <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
-<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>                     model  <span class="st">"binomial"</span>)</span>
-<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
-<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>predict_TZP <span class="ot">&lt;-</span> example_isolates <span class="sc">%&gt;%</span> </span>
-<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a>  <span class="fu">resistance_predict</span>(<span class="at">col_ab =</span> <span class="st">"TZP"</span>,</span>
-<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a>                     <span class="at">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
-<p>The function will look for a date column itself if
-<code>col_date</code> is not set.</p>
-<p>When running any of these commands, a summary of the regression model
-will be printed unless using
-<code>resistance_predict(..., info = FALSE)</code>.</p>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true"></a><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></span>
+<span id="cb2-2"><a href="#cb2-2" aria-hidden="true"></a><span class="kw">resistance_predict</span>(<span class="dt">tbl =</span> example_isolates, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>, <span class="dt">model =</span> <span class="st">"binomial"</span>)</span>
+<span id="cb2-3"><a href="#cb2-3" aria-hidden="true"></a></span>
+<span id="cb2-4"><a href="#cb2-4" aria-hidden="true"></a><span class="co"># or:</span></span>
+<span id="cb2-5"><a href="#cb2-5" aria-hidden="true"></a>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
+<span id="cb2-6"><a href="#cb2-6" aria-hidden="true"></a><span class="st">  </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
+<span id="cb2-7"><a href="#cb2-7" aria-hidden="true"></a>                     model  <span class="st">"binomial"</span>)</span>
+<span id="cb2-8"><a href="#cb2-8" aria-hidden="true"></a></span>
+<span id="cb2-9"><a href="#cb2-9" aria-hidden="true"></a><span class="co"># to bind it to object 'predict_TZP' for example:</span></span>
+<span id="cb2-10"><a href="#cb2-10" aria-hidden="true"></a>predict_TZP &lt;-<span class="st"> </span>example_isolates <span class="op">%&gt;%</span><span class="st"> </span></span>
+<span id="cb2-11"><a href="#cb2-11" aria-hidden="true"></a><span class="st">  </span><span class="kw">resistance_predict</span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>,</span>
+<span id="cb2-12"><a href="#cb2-12" aria-hidden="true"></a>                     <span class="dt">model =</span> <span class="st">"binomial"</span>)</span></code></pre></div>
+<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
+<p>When running any of these commands, a summary of the regression model will be printed unless using <code>resistance_predict(..., info = FALSE)</code>.</p>
 <pre><code><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre>
-<p>This text is only a printed summary - the actual result (output) of
-the function is a <code>data.frame</code> containing for each year: the
-number of observations, the actual observed resistance, the estimated
-resistance and the standard error below and above the estimation:</p>
+<p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">predict_TZP</span>
 <span class="co">#    year      value    se_min    se_max observations   observed  estimated</span>
@@ -281,18 +266,12 @@ resistance and the standard error below and above the estimation:</p>
 <span class="co"># 29 2030 0.48639359 0.3782932 0.5944939           NA         NA 0.48639359</span>
 <span class="co"># 30 2031 0.51109592 0.3973697 0.6248221           NA         NA 0.51109592</span>
 <span class="co"># 31 2032 0.53574417 0.4169574 0.6545309           NA         NA 0.53574417</span></code></pre></div>
-<p>The function <code>plot</code> is available in base R, and can be
-extended by other packages to depend the output based on the type of
-input. We extended its function to cope with resistance predictions:</p>
+<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
-<p>This is the fastest way to plot the result. It automatically adds the
-right axes, error bars, titles, number of available observations and
-type of model.</p>
-<p>We also support the <code>ggplot2</code> package with our custom
-function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing
-plots:</p>
+<p>This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.</p>
+<p>We also support the <code>ggplot2</code> package with our custom function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing plots:</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
@@ -304,9 +283,7 @@ plots:</p>
 <div class="section level3">
 <h3 id="choosing-the-right-model">Choosing the right model<a class="anchor" aria-label="anchor" href="#choosing-the-right-model"></a>
 </h3>
-<p>Resistance is not easily predicted; if we look at vancomycin
-resistance in Gram-positive bacteria, the spread (i.e. standard error)
-is enormous:</p>
+<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram-positive bacteria, the spread (i.e. standard error) is enormous:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@@ -314,13 +291,8 @@ is enormous:</p>
   <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
 <span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
-<p>Vancomycin resistance could be 100% in ten years, but might also stay
-around 0%.</p>
-<p>You can define the model with the <code>model</code> parameter. The
-model chosen above is a generalised linear regression model using a
-binomial distribution, assuming that a period of zero resistance was
-followed by a period of increasing resistance leading slowly to more and
-more resistance.</p>
+<p>Vancomycin resistance could be 100% in ten years, but might also stay around 0%.</p>
+<p>You can define the model with the <code>model</code> parameter. The model chosen above is a generalised linear regression model using a binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance.</p>
 <p>Valid values are:</p>
 <table class="table">
 <colgroup>
@@ -336,8 +308,7 @@ more resistance.</p>
 <tbody>
 <tr class="odd">
 <td>
-<code>"binomial"</code> or <code>"binom"</code> or
-<code>"logit"</code>
+<code>"binomial"</code> or <code>"binom"</code> or <code>"logit"</code>
 </td>
 <td><code>glm(..., family = binomial)</code></td>
 <td>Generalised linear model with binomial distribution</td>
@@ -358,9 +329,7 @@ more resistance.</p>
 </tr>
 </tbody>
 </table>
-<p>For the vancomycin resistance in Gram-positive bacteria, a linear
-model might be more appropriate since no binomial distribution is to be
-expected based on the observed years:</p>
+<p>For the vancomycin resistance in Gram-positive bacteria, a linear model might be more appropriate since no binomial distribution is to be expected based on the observed years:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@@ -369,8 +338,7 @@ expected based on the observed years:</p>
 <span class="co"># ℹ Using column 'date' as input for `col_date`.</span></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
 <p>This seems more likely, doesn’t it?</p>
-<p>The model itself is also available from the object, as an
-<code>attribute</code>:</p>
+<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
 <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attributes.html" class="external-link">attributes</a></span><span class="op">(</span><span class="va">predict_TZP</span><span class="op">)</span><span class="op">$</span><span class="va">model</span>
 
@@ -399,14 +367,12 @@ expected based on the observed years:</p>
 
       <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>

docs/articles/resistance_predict_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/welcome_to_AMR.html

@@ -185,7 +185,7 @@
 
       
 
-      </header><div class="row">
+      </header><script src="welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Welcome to the <code>AMR</code> package</h1>
@@ -198,83 +198,33 @@
 
     
     
-<p>Note: to keep the package size as small as possible, we only included
-this vignette on CRAN. You can read more vignettes on our website about
-how to conduct AMR data analysis, determine MDRO’s, find explanation of
-EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
+<p>Note: to keep the package size as small as possible, we only included this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDRO’s, find explanation of EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
 <hr>
-<p><code>AMR</code> is a free, open-source and independent R package
-(see <a href="https://msberends.github.io/AMR/#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 antimicrobial resistance
-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 ~71,000 distinct microbial
-species and all ~570 antibiotic, antimycotic and antiviral drugs by name
-and code (including ATC, 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 Danish, Dutch, English,
-French, German, Italian, Portuguese, Russian, Spanish and Swedish.
-Antimicrobial drug (group) names and colloquial microorganism names are
-provided in these languages.</p>
-<p>This package is fully independent of any other R package 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>. Since its first public release in
-early 2018, this package has been downloaded from more than 175
-countries.</p>
+<p><code>AMR</code> is a free, open-source and independent R package (see <a href="https://msberends.github.io/AMR/#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 antimicrobial resistance 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 ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, 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 Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
+<p>This package is fully independent of any other R package 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>. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.</p>
 <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 Catalogue of Life and List
-of Prokaryotic names with Standing in Nomenclature</li>
-<li>Interpreting raw MIC and disk diffusion values, based on the latest
-CLSI or EUCAST guidelines</li>
-<li>Retrieving antimicrobial drug names, doses and forms of
-administration from clinical health care records</li>
+<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</li>
+<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</li>
+<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records</li>
 <li>Determining first isolates to be used for AMR data analysis</li>
 <li>Calculating antimicrobial resistance</li>
-<li>Determining multi-drug resistance (MDR) / multi-drug resistant
-organisms (MDRO)</li>
-<li>Calculating (empirical) susceptibility of both mono therapy and
-combination therapies</li>
-<li>Predicting future antimicrobial resistance using regression
-models</li>
-<li>Getting properties for any microorganism (like Gram stain, species,
-genus or family)</li>
-<li>Getting properties for any antibiotic (like name, code of
-EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)</li>
+<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)</li>
+<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies</li>
+<li>Predicting future antimicrobial resistance using regression models</li>
+<li>Getting properties for any microorganism (like Gram stain, species, genus or family)</li>
+<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)</li>
 <li>Plotting antimicrobial resistance</li>
 <li>Applying EUCAST expert rules</li>
-<li>Getting SNOMED codes of a microorganism, or getting properties of a
-microorganism based on a SNOMED code</li>
-<li>Getting LOINC codes of an antibiotic, or getting properties of an
-antibiotic based on a LOINC code</li>
-<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to
-translate MIC values and disk diffusion diameters to R/SI</li>
+<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code</li>
+<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code</li>
+<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI</li>
 <li>Principal component analysis for AMR</li>
 </ul>
-<p>All reference data sets (about microorganisms, antibiotics, R/SI
-interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are
-publicly and freely available. We continually export our data sets to
-formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat
-files that are machine-readable and suitable for input in any software
-program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all
-download links on our website</a>, which is automatically updated with
-every code change.</p>
-<p>This R package 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 actively and durably maintained (see
-<a href="https://msberends.github.io/AMR/news/index.html">changelog)</a>)
-by two public healthcare organisations in the Netherlands.</p>
+<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
+<p>This R package 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 actively and durably maintained (see <a href="https://msberends.github.io/AMR/news/index.html">changelog)</a>) by two public healthcare organisations in the Netherlands.</p>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@@ -287,14 +237,12 @@ by two public healthcare organisations in the Netherlands.</p>
 
       <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>

docs/articles/welcome_to_AMR_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

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">1.8.0.9010</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

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">1.8.0.9010</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9001</span>
       </span>
     </div>
 
@@ -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
@@ -195,11 +195,10 @@
 <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>

docs/news/index.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
@@ -157,16 +157,22 @@
     </div>
 
     <div class="section level2">
-<h2 class="page-header" data-toc-text="1.8.0.9010" id="amr-1809010">
-<code>AMR</code> 1.8.0.9010<a class="anchor" aria-label="anchor" href="#amr-1809010"></a></h2>
+<h2 class="page-header" data-toc-text="1.8.1.9001" id="amr-1819001">
+<code>AMR</code> 1.8.1.9001<a class="anchor" aria-label="anchor" href="#amr-1819001"></a></h2>
 <div class="section level3">
-<h3 id="last-updated-march-1-8-0-9010"><small>Last updated: 15 March 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-march-1-8-0-9010"></a></h3>
-<p>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>
+<h3 id="last-updated-april-1-8-1-9001"><small>Last updated: 8 April 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-april-1-8-1-9001"></a></h3>
 <div class="section level4">
-<h4 id="changed-1-8-0-9010">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9010"></a></h4>
+<h4 id="changed-1-8-1-9001">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9001"></a></h4>
+<ul><li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>
+</li>
+</ul></div>
+</div>
+</div>
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="1.8.1" id="amr-181">
+<code>AMR</code> 1.8.1<small>2022-03-24</small><a class="anchor" aria-label="anchor" href="#amr-181"></a></h2>
+<div class="section level4">
+<h4 id="changed-1-8-1">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1"></a></h4>
 <ul><li><p>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on values containing capped
 values (such as <code>&gt;=</code>), sometimes leading to
 <code>NA</code></p></li>
@@ -187,11 +193,10 @@ ignoring non-taxonomic text, such as:</p>
 <li><p>Increased speed for loading the package</p></li>
 </ul></div>
 <div class="section level4">
-<h4 id="other-1-8-0-9010">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9010"></a></h4>
+<h4 id="other-1-8-1">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1"></a></h4>
 <ul><li>Fix for unit testing on R 3.3</li>
 <li>Fix for size of some image elements, as requested by CRAN</li>
 </ul></div>
-</div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.8.0" id="amr-180">
@@ -814,8 +819,8 @@ vector is the start of a new episode. They also support
 code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for
 species outside the taxonomic kingdom of Bacteria.</p></li>
 <li><p>Function <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for
-intrinsic resistance, based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
-Intrinsic Resistance and Unusual Phenotypes v3.2</a> from 2020.</p></li>
+intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual
+Phenotypes v3.2 from 2020.</p></li>
 <li><p>Functions <code><a href="../reference/random.html">random_mic()</a></code>, <code><a href="../reference/random.html">random_disk()</a></code>
 and <code><a href="../reference/random.html">random_rsi()</a></code> for random value generation. The functions
 <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code> take
@@ -3071,10 +3076,8 @@ abbreviations</li>
 tables</strong>, with additional info in a header</li>
 <li>Function <code>MDRO</code> to <strong>determine Multi Drug Resistant
 Organisms (MDRO)</strong> with support for country-specific guidelines.
-<ul><li>
-<a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">Exceptional
-resistances defined by EUCAST</a> are also supported instead of
-countries alone</li>
+<ul><li>Exceptional resistances defined by EUCAST are also supported instead
+of countries alone</li>
 <li>Functions <code>BRMO</code> and <code>MRGN</code> are wrappers for
 Dutch and German guidelines, respectively</li>
 </ul></li>

docs/pkgdown.yml

@@ -1,4 +1,4 @@
-pandoc: 2.17.1.1
+pandoc: 2.9.2.1
 pkgdown: 2.0.2
 pkgdown_sha: ~
 articles:
@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2022-03-14T15:38Z
+last_built: 2022-03-27T07:33Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

docs/reference/AMR-deprecated.html

@@ -184,13 +184,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>retired</
 
 
       <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>

docs/reference/AMR.html

@@ -221,13 +221,11 @@ The Netherlands
 
 
       <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>

docs/reference/WHOCC.html

@@ -195,13 +195,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
 
       <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>

docs/reference/WHONET.html

@@ -215,13 +215,11 @@
 
 
       <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>

docs/reference/ab_from_text.html

@@ -275,13 +275,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/ab_property.html

@@ -344,13 +344,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/age.html

@@ -226,13 +226,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/age_groups.html

@@ -250,13 +250,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/antibiotic_class_selectors.html

@@ -256,7 +256,7 @@
 <p>The <code>ab_class()</code> function can be used to filter/select on a manually defined antibiotic class. It searches for results in the <a href="antibiotics.html">antibiotics</a> data set within the columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code>.</p>
 <p>The <code>ab_selector()</code> function can be used to internally filter the <a href="antibiotics.html">antibiotics</a> data set on any results, see <em>Examples</em>. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.</p>
 <p>The <code>administrable_per_os()</code> and <code>administrable_iv()</code> functions also rely on the <a href="antibiotics.html">antibiotics</a> data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the <a href="antibiotics.html">antibiotics</a> data set.</p>
-<p>The <code>not_intrinsic_resistant()</code> function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies <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) to determine intrinsic resistance, using the <code><a href="eucast_rules.html">eucast_rules()</a></code> function internally. Because of this determination, this function is quite slow in terms of performance.</p>
+<p>The <code>not_intrinsic_resistant()</code> function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of <em>E. coli</em> and <em>K. pneumoniae</em> and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies <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) to determine intrinsic resistance, using the <code><a href="eucast_rules.html">eucast_rules()</a></code> function internally. Because of this determination, this function is quite slow in terms of performance.</p>
     </div>
     <div id="full-list-of-supported-antibiotic-classes">
     <h2>Full list of supported (antibiotic) classes</h2>
@@ -430,13 +430,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/antibiotics.html

@@ -259,13 +259,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
 
       <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>

docs/reference/as.ab.html

@@ -280,13 +280,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 
 
       <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>

docs/reference/as.disk.html

@@ -239,13 +239,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/as.mic.html

@@ -273,13 +273,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/as.mo.html

@@ -377,13 +377,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 
       <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>

docs/reference/as.rsi.html

@@ -231,7 +231,7 @@
 <dt>conserve_capped_values</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that MIC values starting with <code>"&gt;"</code> (but not <code>"&gt;="</code>) must always return "R" , and that MIC values starting with <code>"&lt;"</code> (but not <code>"&lt;="</code>) must always return "S"</p></dd>
 <dt>add_intrinsic_resistance</dt>
-<dd><p><em>(only useful when using a EUCAST guideline)</em> a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, that itself 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></dd>
+<dd><p><em>(only useful when using a EUCAST guideline)</em> a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, that itself 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></dd>
 <dt>reference_data</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for interpretation, which defaults to the <a href="rsi_translation.html">rsi_translation</a> data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the <a href="rsi_translation.html">rsi_translation</a> data set (same column names and column types). Please note that the <code>guideline</code> argument will be ignored when <code>reference_data</code> is manually set.</p></dd>
 <dt>col_mo</dt>
@@ -334,7 +334,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 <span class="co"># \donttest{</span>
 <span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://docs.ropensci.org/skimr/" class="external-link">"skimr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
   <span class="co"># class &lt;rsi&gt; supported in skim() too:</span>
-  <span class="fu"><a href="https://docs.ropensci.org/skimr/reference/skim.html" class="external-link">skim</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
+  <span class="fu">skim</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
 <span class="op">}</span>
 <span class="co"># }</span>
 <span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span>
@@ -423,13 +423,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/atc_online.html

@@ -257,13 +257,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/availability.html

@@ -216,13 +216,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/bug_drug_combinations.html

@@ -265,13 +265,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/catalogue_of_life.html

@@ -235,13 +235,11 @@ Function <code><a href="as.mo.html">as.mo()</a></code> to use the data for intel
 
 
       <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>

docs/reference/catalogue_of_life_version.html

@@ -200,13 +200,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 
       <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>

docs/reference/count.html

@@ -358,13 +358,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
 
       <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>

docs/reference/custom_eucast_rules.html

@@ -301,13 +301,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/dosage.html

@@ -202,13 +202,11 @@
 
 
       <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>

docs/reference/eucast_rules.html

@@ -334,13 +334,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/example_isolates.html

@@ -199,13 +199,11 @@
 
 
       <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>

docs/reference/example_isolates_unclean.html

@@ -194,13 +194,11 @@
 
 
       <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>

docs/reference/first_isolate.html

@@ -371,13 +371,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/g.test.html

@@ -323,13 +323,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>questioni
 
 
       <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>

docs/reference/get_episode.html

@@ -278,13 +278,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/ggplot_pca.html

@@ -304,13 +304,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/ggplot_rsi.html

@@ -395,13 +395,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/guess_ab_col.html

@@ -243,13 +243,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/index.html

@@ -157,10 +157,7 @@
 
     <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2">
           <h2 id="preparing-data-microorganisms">Preparing data: microorganisms <a href="#preparing-data-microorganisms" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>These functions are meant to get taxonomically valid properties of
-microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach
-this package how to translate your own codes to valid microorganism
-codes.</p>
+          <p class="section-desc"></p><p>These functions are meant to get taxonomically valid properties of microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach this package how to translate your own codes to valid microorganism codes.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
@@ -176,9 +173,7 @@ codes.</p>
         <td><p>User-Defined Reference Data Set for Microorganisms</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="preparing-data-antibiotics">Preparing data: antibiotics <a href="#preparing-data-antibiotics" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>Use these functions to get valid properties of antibiotics from any
-input or to clean your input. You can even retrieve drug names and doses
-from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p>
+          <p class="section-desc"></p><p>Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p>
@@ -198,13 +193,7 @@ from clinical text records, using <code><a href="../reference/ab_from_text.html"
         <td><p>Get ATC Properties from WHOCC Website</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="preparing-data-antimicrobial-resistance">Preparing data: antimicrobial resistance <a href="#preparing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can
-transform your raw input to valid MIC or disk diffusion values. Use
-<code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”,
-“I” and “S”, or to interpret MIC or disk diffusion values as R/SI based
-on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend
-antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
-rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p>
+          <p class="section-desc"></p><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">NA_rsi_</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> </p>
@@ -228,14 +217,7 @@ rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a>
         <td><p>Define Custom EUCAST Rules</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="analysing-data-antimicrobial-resistance">Analysing data: antimicrobial resistance <a href="#analysing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>Use these function for the analysis part. You can use
-<code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any
-antibiotic column. Be sure to first select the isolates that are
-appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or
-<code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain
-resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>,
-<code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant
-microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
+          <p class="section-desc"></p><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
@@ -287,9 +269,7 @@ microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).
         <td><p>Guess Antibiotic Column</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="background-information-on-included-data">Background information on included data <a href="#background-information-on-included-data" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>Some pages about our package and its external sources. Be sure to
-read our <a href="./../articles/index.html">How To’s</a> for more
-information about how to work with functions in this package.</p>
+          <p class="section-desc"></p><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="AMR.html">AMR</a></code> </p>
@@ -353,9 +333,7 @@ information about how to work with functions in this package.</p>
         <td><p>Data Set with 500 Isolates - WHONET Example</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="other-miscellaneous-functions">Other: miscellaneous functions <a href="#other-miscellaneous-functions" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>These functions are mostly for internal use, but some of them may
-also be suitable for your analysis. Especially the ‘like’ function can
-be useful: <code>if (x %like% y) {...}</code>.</p>
+          <p class="section-desc"></p><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="age_groups.html">age_groups()</a></code> </p>
@@ -403,8 +381,7 @@ be useful: <code>if (x %like% y) {...}</code>.</p>
         <td><p>Random MIC Values/Disk Zones/RSI Generation</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="other-statistical-tests">Other: statistical tests <a href="#other-statistical-tests" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were
-added to this package for convenience.</p>
+          <p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="g.test.html">g.test()</a></code> </p>
@@ -420,9 +397,7 @@ added to this package for convenience.</p>
         <td><p>Skewness of the Sample</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="other-deprecated-functions">Other: deprecated functions <a href="#other-deprecated-functions" class="anchor" aria-hidden="true"></a></h2>
-          <p class="section-desc"></p><p>These functions are deprecated, meaning that they will still work but
-show a warning with every use and will be removed in a future
-version.</p>
+          <p class="section-desc"></p><p>These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.</p>
         </th>
       </tr></tbody><tbody><tr><td>
           <p><code><a href="AMR-deprecated.html">AMR-deprecated</a></code> </p>
@@ -437,13 +412,11 @@ version.</p>
 
 
       <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>

docs/reference/intrinsic_resistant.html

@@ -173,7 +173,7 @@
     <div id="details">
     <h2>Details</h2>
     <p>The repository of this <code>AMR</code> package contains a file comprising this data set with full taxonomic and antibiotic names: <a href="https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt</a>. This file <strong>allows for machine reading EUCAST guidelines about intrinsic resistance</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.</p>
-<p>This data set 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>
+<p>This data set 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>
     </div>
     <div id="reference-data-publicly-available">
     <h2>Reference Data Publicly Available</h2>
@@ -210,13 +210,11 @@
 
 
       <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>

docs/reference/italicise_taxonomy.html

@@ -221,13 +221,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/join.html

@@ -242,13 +242,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/key_antimicrobials.html

@@ -308,13 +308,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/kurtosis.html

@@ -210,13 +210,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/lifecycle.html

@@ -211,13 +211,11 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
 
 
       <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>

docs/reference/like.html

@@ -260,13 +260,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/mdro.html

@@ -245,7 +245,7 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
 <li><p><code>guideline = "EUCAST3.1"</code></p>
 <p>The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf" class="external-link">link</a>)</p></li>
 <li><p><code>guideline = "TB"</code></p>
-<p>The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/" class="external-link">link</a>)</p></li>
+<p>The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href="https://www.who.int/publications/i/item/9789241548809" class="external-link">link</a>)</p></li>
 <li><p><code>guideline = "MRGN"</code></p>
 <p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; doi: <a href="https://doi.org/10.1186/s13756-015-0047-6" class="external-link">10.1186/s13756-015-0047-6</a></p></li>
 <li><p><code>guideline = "BRMO"</code></p>
@@ -352,13 +352,11 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 
 
       <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>

docs/reference/microorganisms.codes.html

@@ -203,13 +203,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 
       <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>

docs/reference/microorganisms.html

@@ -254,13 +254,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 
       <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>

docs/reference/microorganisms.old.html

@@ -210,13 +210,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 
       <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>

docs/reference/mo_matching_score.html

@@ -231,13 +231,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/mo_property.html

@@ -253,7 +253,7 @@
 <p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p>
 <p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318" class="external-link">PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
 <p>Determination of yeasts - <code>mo_is_yeast()</code> - will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). <em>True yeasts</em> are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
-<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which 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). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
+<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which 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). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
 <p>All output <a href="translate.html">will be translated</a> where possible.</p>
 <p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
 <p>SNOMED codes - <code>mo_snomed()</code> - are from the US Edition of SNOMED CT from 1 September 2020. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
@@ -433,13 +433,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
 
       <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>

docs/reference/mo_source.html

@@ -267,13 +267,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>

docs/reference/pca.html

@@ -266,13 +266,11 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
 
 
       <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>
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