(v1.3.0.9026) eucast expert rules 3.2

2026-10-01 04:13:33 +02:00 · 2020-09-24 00:30:11 +02:00
1 parent a1411ddafc
commit c19095a3d5
@@ -81,7 +81,7 @@
      </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="Latest development version">1.3.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -81,7 +81,7 @@
      </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="Latest development version">1.3.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -20,7 +20,7 @@
 <script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
 <script src="../extra.js"></script><meta property="og:title" content="Data sets for download / own use">
 <meta property="og:description" content="AMR">
-<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -39,7 +39,7 @@
      </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="Latest development version">1.3.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -211,7 +211,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <p>A data set with 67,151 rows and 16 columns, containing the following column names:<br><em>‘mo’, ‘fullname’, ‘kingdom’, ‘phylum’, ‘class’, ‘order’, ‘family’, ‘genus’, ‘species’, ‘subspecies’, ‘rank’, ‘ref’, ‘species_id’, ‘source’, ‘prevalence’, ‘snomed’</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
 <p>It was last updated on 3 September 2020 20:59:45 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
-<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds" target="_blank"><img src="download_rds.png" width="50px" title="2.7 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="6.1 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt" target="_blank"><img src="download_txt.png" width="50px" title="13.3 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sas" target="_blank"><img src="download_sas.png" width="50px" title="26.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav" target="_blank"><img src="download_sav.png" width="50px" title="28.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta" target="_blank"><img src="download_dta.png" width="50px" title="25.2 MB"></a></p>
+<p><strong>Direct download links:</strong></p>
+<ul>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file</a> (2.7 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx">Excel file</a> (6.1 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt">plain text file</a> (13.3 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sas">SAS file</a> (26.2 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">SPSS file</a> (28.2 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta">Stata file</a> (25.2 MB)</li>
+</ul>
 <div id="source" class="section level3">
 <h3 class="hasAnchor">
 <a href="#source" class="anchor"></a>Source</h3>
@@ -417,7 +430,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
 <p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
 <p>It was last updated on 28 May 2020 11:17:56 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
-<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds" target="_blank"><img src="download_rds.png" width="50px" title="0.3 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="0.4 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt" target="_blank"><img src="download_txt.png" width="50px" title="0.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sas" target="_blank"><img src="download_sas.png" width="50px" title="1.9 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav" target="_blank"><img src="download_sav.png" width="50px" title="1.9 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta" target="_blank"><img src="download_dta.png" width="50px" title="1.8 MB"></a></p>
+<p><strong>Direct download links:</strong></p>
+<ul>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file</a> (0.3 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.xlsx">Excel file</a> (0.4 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt">plain text file</a> (0.8 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sas">SAS file</a> (1.9 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav">SPSS file</a> (1.9 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta">Stata file</a> (1.8 MB)</li>
+</ul>
 <div id="source-1" class="section level3">
 <h3 class="hasAnchor">
 <a href="#source-1" class="anchor"></a>Source</h3>
@@ -466,10 +492,23 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div id="antibiotic-agents" class="section level2">
 <h2 class="hasAnchor">
 <a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
-<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>‘ab’, ‘atc’, ‘cid’, ‘name’, ‘group’, ‘atc_group1’, ‘atc_group2’, ‘abbreviations’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’, ‘loinc’</em>.</p>
+<p>A data set with 455 rows and 14 columns, containing the following column names:<br><em>‘ab’, ‘atc’, ‘cid’, ‘name’, ‘group’, ‘atc_group1’, ‘atc_group2’, ‘abbreviations’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’, ‘loinc’</em>.</p>
 <p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 31 July 2020 12:12:13 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
-<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds" target="_blank"><img src="download_rds.png" width="50px" title="37 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="65 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt" target="_blank"><img src="download_txt.png" width="50px" title="0.1 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sas" target="_blank"><img src="download_sas.png" width="50px" title="1.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav" target="_blank"><img src="download_sav.png" width="50px" title="1.3 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta" target="_blank"><img src="download_dta.png" width="50px" title="0.3 MB"></a></p>
+<p>It was last updated on 20 September 2020 11:45:13 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p><strong>Direct download links:</strong></p>
+<ul>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file</a> (31 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx">Excel file</a> (65 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt">plain text file</a> (0.1 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sas">SAS file</a> (1.8 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">SPSS file</a> (1.3 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta">Stata file</a> (0.3 MB)</li>
+</ul>
 <div id="source-2" class="section level3">
 <h3 class="hasAnchor">
 <a href="#source-2" class="anchor"></a>Source</h3>
@@ -544,9 +583,9 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <td align="center">Penicillins with extended spectrum</td>
 <td align="center">ac, amox, amx</td>
 <td align="center">actimoxi, amoclen, amolin, …</td>
-<td align="center">1.0</td>
+<td align="center">1.5</td>
 <td align="center">g</td>
-<td align="center">1.0</td>
+<td align="center">3.0</td>
 <td align="center">g</td>
 <td align="center">16365-9, 25274-2, 3344-9, …</td>
 </tr>
@@ -560,7 +599,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td>
 <td align="center">a/c, amcl, aml, …</td>
 <td align="center">amocla, amoclan, amoclav, …</td>
-<td align="center">1.0</td>
+<td align="center">1.5</td>
 <td align="center">g</td>
 <td align="center">3.0</td>
 <td align="center">g</td>
@@ -578,7 +617,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <td align="center">acillin, adobacillin, amblosin, …</td>
 <td align="center">2.0</td>
 <td align="center">g</td>
-<td align="center">2.0</td>
+<td align="center">6.0</td>
 <td align="center">g</td>
 <td align="center">21066-6, 3355-5, 33562-0, …</td>
 </tr>
@@ -624,7 +663,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>‘atc’, ‘cid’, ‘name’, ‘atc_group’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’</em>.</p>
 <p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
 <p>It was last updated on 29 August 2020 21:53:07 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antivirals.html">here</a>.</p>
-<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds" target="_blank"><img src="download_rds.png" width="50px" title="5 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="14 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt" target="_blank"><img src="download_txt.png" width="50px" title="16 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sas" target="_blank"><img src="download_sas.png" width="50px" title="80 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav" target="_blank"><img src="download_sav.png" width="50px" title="68 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta" target="_blank"><img src="download_dta.png" width="50px" title="67 kB"></a></p>
+<p><strong>Direct download links:</strong></p>
+<ul>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file</a> (5 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx">Excel file</a> (14 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt">plain text file</a> (16 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sas">SAS file</a> (80 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav">SPSS file</a> (68 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta">Stata file</a> (67 kB)</li>
+</ul>
 <div id="source-3" class="section level3">
 <h3 class="hasAnchor">
 <a href="#source-3" class="anchor"></a>Source</h3>
@@ -735,14 +787,27 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div id="intrinsic-bacterial-resistance" class="section level2">
 <h2 class="hasAnchor">
 <a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
-<p>A data set with 49,462 rows and 2 columns, containing the following column names:<br><em>‘microorganism’, ‘antibiotic’</em>.</p>
+<p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>‘microorganism’, ‘antibiotic’</em>.</p>
 <p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 14 August 2020 14:18:20 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
-<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds" target="_blank"><img src="download_rds.png" width="50px" title="97 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="0.5 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt" target="_blank"><img src="download_txt.png" width="50px" title="1.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sas" target="_blank"><img src="download_sas.png" width="50px" title="3.8 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav" target="_blank"><img src="download_sav.png" width="50px" title="4.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta" target="_blank"><img src="download_dta.png" width="50px" title="3.7 MB"></a></p>
+<p>It was last updated on 23 September 2020 23:42:04 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
+<p><strong>Direct download links:</strong></p>
+<ul>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file</a> (67 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx">Excel file</a> (0.9 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt">plain text file</a> (3.5 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sas">SAS file</a> (7.1 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav">SPSS file</a> (7.9 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta">Stata file</a> (7 MB)</li>
+</ul>
 <div id="source-4" class="section level3">
 <h3 class="hasAnchor">
 <a href="#source-4" class="anchor"></a>Source</h3>
-<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes’, version 3.1, 2016.</p>
+<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes’, v3.2 from 2020.</p>
 </div>
 <div id="example-content-4" class="section level3">
 <h3 class="hasAnchor">
@@ -768,23 +833,55 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
+<td align="center">Ampicillin/sulbactam</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Avoparcin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
 <td align="center">Azithromycin</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Cefazolin</td>
+<td align="center">Cefadroxil</td>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Cefoxitin</td>
+<td align="center">Cefazolin</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Clarithromycin</td>
+<td align="center">Cefoxitin</td>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Daptomycin</td>
+<td align="center">Cephalexin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Cephalothin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Clarithromycin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Clindamycin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Cycloserine</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Dalbavancin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Dirithromycin</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
@@ -792,8 +889,16 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
+<td align="center">Flurithromycin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
 <td align="center">Fusidic acid</td>
 </tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Josamycin</td>
+</tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Lincomycin</td>
@@ -804,7 +909,31 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Penicillin G</td>
+<td align="center">Midecamycin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Miocamycin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Norvancomycin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Oleandomycin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Oritavancin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Benzylpenicillin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Pirlimycin</td>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
@@ -816,18 +945,54 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
+<td align="center">Ramoplanin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
 <td align="center">Rifampicin</td>
 </tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Rokitamycin</td>
+</tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Roxithromycin</td>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
+<td align="center">Spiramycin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Tedizolid</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
 <td align="center">Teicoplanin</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
+<td align="center">Teicoplanin-macromethod</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Telavancin</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Telithromycin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Thiacetazone</td>
+</tr>
+<tr class="odd">
+<td align="center">Enterobacter cloacae</td>
+<td align="center">Troleandomycin</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
 <td align="center">Vancomycin</td>
 </tr>
 </tbody>
@@ -840,7 +1005,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <p>A data set with 18,650 rows and 10 columns, containing the following column names:<br><em>‘guideline’, ‘method’, ‘site’, ‘mo’, ‘ab’, ‘ref_tbl’, ‘disk_dose’, ‘breakpoint_S’, ‘breakpoint_R’, ‘uti’</em>.</p>
 <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
 <p>It was last updated on 29 July 2020 13:12:34 CEST. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
-<p><strong>Direct download links:</strong><br><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds" target="_blank"><img src="download_rds.png" width="50px" title="55 kB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx" target="_blank"><img src="download_xlsx.png" width="50px" title="0.6 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt" target="_blank"><img src="download_txt.png" width="50px" title="1.5 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas" target="_blank"><img src="download_sas.png" width="50px" title="3.2 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav" target="_blank"><img src="download_sav.png" width="50px" title="3.4 MB"></a><a class="dataset-download-button" href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta" target="_blank"><img src="download_dta.png" width="50px" title="3 MB"></a></p>
+<p><strong>Direct download links:</strong></p>
+<ul>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (32 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx">Excel file</a> (0.6 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt">plain text file</a> (1.5 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas">SAS file</a> (3.2 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav">SPSS file</a> (3.4 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta">Stata file</a> (3 MB)</li>
+</ul>
 <div id="source-5" class="section level3">
 <h3 class="hasAnchor">
 <a href="#source-5" class="anchor"></a>Source</h3>
@@ -81,7 +81,7 @@
      </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="Latest development version">1.3.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -81,7 +81,7 @@
      </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="Latest development version">1.3.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -43,7 +43,7 @@
      </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="Latest development version">1.3.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -81,7 +81,7 @@
      </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="Latest development version">1.3.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -236,19 +236,20 @@
      <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
    </div>

-    <div id="amr-1309025" class="section level1">
-<h1 class="page-header" data-toc-text="1.3.0.9025">
-<a href="#amr-1309025" class="anchor"></a>AMR 1.3.0.9025<small> Unreleased </small>
+    <div id="amr-1309026" class="section level1">
+<h1 class="page-header" data-toc-text="1.3.0.9026">
+<a href="#amr-1309026" class="anchor"></a>AMR 1.3.0.9026<small> Unreleased </small>
 </h1>
-<div id="last-updated-19-september-2020" class="section level2">
+<div id="last-updated-24-september-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-19-september-2020" class="anchor"></a><small>Last updated: 19 September 2020</small>
+<a href="#last-updated-24-september-2020" class="anchor"></a><small>Last updated: 24 September 2020</small>
 </h2>
 <p>Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!</p>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
 <a href="#new" class="anchor"></a>New</h3>
 <ul>
+<li><p>Support for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can now correct for more than 180 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function consequently gained the parameters <code>version_breakpoints</code> (at the moment defaults to v10.0, 2020) and <code>version_expertrules</code> (at the moment defaults to v3.2, 2020). The <code>example_isolates</code> data set now also reflects the change from v3.1 to v3.2.</p></li>
 <li><p>A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: <a href="https://msberends.github.io/AMR/articles/datasets.html" class="uri">https://msberends.github.io/AMR/articles/datasets.html</a></p></li>
 <li>
 <p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
@@ -307,7 +308,7 @@
 </ul>
 </li>
 <li><p><code><a href="../reference/translate.html">get_locale()</a></code> now uses at default <code><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv("LANG")</a></code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html">Sys.getlocale()</a></code>. This can be overwritten by setting the option <code>AMR_locale</code>.</p></li>
-<li><p>Speed improvement for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code></p></li>
+<li><p>Big speed improvement for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code></p></li>
 <li><p>Overall speed improvement by tweaking joining functions</p></li>
 <li><p>Function <code><a href="../reference/mo_property.html">mo_shortname()</a></code> now returns the genus for input where the species is unknown</p></li>
 <li><p>BORSA is now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("BORSA")</a></code> will return “Staphylococcus”</p></li>
@@ -317,7 +318,16 @@
 <li><p>Small <code><a href="../reference/as.ab.html">as.ab()</a></code> algorithm improvements</p></li>
 <li><p>Fix for combining MIC values with raw numbers, i.e. <code><a href="https://rdrr.io/r/base/c.html">c(as.mic(2), 2)</a></code> previously failed but now returns a valid MIC class</p></li>
 <li><p><code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> and <code><a href="../reference/ggplot_rsi.html">geom_rsi()</a></code> gained parameters <code>minimum</code> and <code>language</code>, to influence the internal use of <code><a href="../reference/proportion.html">rsi_df()</a></code></p></li>
-<li><p>Added abbreviation “piptazo” to piperacillin/tazobactam (TZP)</p></li>
+<li>
+<p>Changes in the <code>antibiotics</code> data set:</p>
+<ul>
+<li>Updated oral and parental DDDs from the WHOCC</li>
+<li>Added abbreviation “piptazo” to ‘Piperacillin/tazobactam’ (TZP)</li>
+<li>‘Penicillin G’ (for intravenous use) is now named ‘Benzylpenicillin’ (code <code>PEN</code>)</li>
+<li>‘Penicillin V’ (for oral use, code <code>PNV</code>) was removed, since its actual entry ‘Phenoxymethylpenicillin’ (code <code>PHN</code>) already existed</li>
+<li>The group name (<code>antibiotics$group</code>) of ‘Linezolid’ (<code>LNZ</code>), ‘Cycloserine’ (<code>CYC</code>), ‘Tedizolid’ (<code>TZD</code>) and ‘Thiacetazone’ (<code>THA</code>) is now “Oxazolidinones” instead of “Other antibacterials”</li>
+</ul>
+</li>
 </ul>
 </div>
 <div id="other" class="section level3">
@@ -2,7 +2,7 @@ pandoc: 2.7.3
 pkgdown: 1.5.1.9000
 pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
 articles: []
-last_built: 2020-09-19T13:07Z
+last_built: 2020-09-23T22:29Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">

-<title>Data sets with 558 antimicrobials — antibiotics • AMR (for R)</title>
+<title>Data sets with 557 antimicrobials — antibiotics • AMR (for R)</title>

 <!-- favicons -->
 <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
  <link href="../extra.css" rel="stylesheet">
  <script src="../extra.js"></script>

-<meta property="og:title" content="Data sets with 558 antimicrobials — antibiotics" />
+<meta property="og:title" content="Data sets with 557 antimicrobials — antibiotics" />
 <meta property="og:description" content="Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_property() functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -233,7 +233,7 @@
 <div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
-    <h1>Data sets with 558 antimicrobials</h1>
+    <h1>Data sets with 557 antimicrobials</h1>
    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
    <div class="hidden name"><code>antibiotics.Rd</code></div>
    </div>
@@ -250,7 +250,7 @@
    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>

    
-<h3>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
+<h3>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 455 observations and 14 variables:</h3>

 <ul>
 <li><p><code>ab</code><br /> Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -376,7 +376,7 @@
 <li><p>The <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> \(L\) is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \(L'\) based on the text length of the full name \(F\) is calculated as:</p></li>
 </ol>

-<p>$$L' = F - \frac{0.5L}{F}$$</p>
+<p>$$L' = 1 - \frac{0.5L}{F}$$</p>
 <p>The final matching score \(M\) is calculated as:
 $$M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}$$</p>
 <p>All matches are sorted descending on their matching score and for all user input values, the top match will be returned.</p>
@@ -50,7 +50,7 @@

 <meta property="og:title" content="Interpret MIC and disk, or clean raw R/SI data — as.rsi" />
 <meta property="og:description" content="Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Values that cannot be interpreted will be returned as NA with a warning." />
-<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
+<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />



@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9016</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -319,7 +319,8 @@
    </tr>
    <tr>
      <th>add_intrinsic_resistance</th>
-      <td><p><em>(only useful when using a EUCAST guideline)</em> a logical 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 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.</p></td>
+      <td><p><em>(only useful when using a EUCAST guideline)</em> a logical 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 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version list(version_txt = "v3.1", year = 2016, title = "EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes")
+list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes").</p></td>
    </tr>
    <tr>
      <th>col_mo</th>
@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -264,7 +264,7 @@
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>x</th>
-      <td><p>data with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td>
+      <td><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></td>
    </tr>
    <tr>
      <th>col_mo</th>
@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -49,8 +49,8 @@
  <script src="../extra.js"></script>

 <meta property="og:title" content="Apply EUCAST rules — eucast_rules" />
-<meta property="og:description" content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.
-To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details." />
+<meta property="og:description" content="Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, https://eucast.org), see Source.
+To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />


@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -240,16 +240,18 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
    </div>

    <div class="ref-description">
-    <p>Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href='http://eucast.org'>http://eucast.org</a>), see <em>Source</em>. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.</p>
-<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.</p>
+    <p>Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href='https://eucast.org'>https://eucast.org</a>), see <em>Source</em>.</p>
+<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details.</p>
    </div>

    <pre class="usage"><span class='fu'>eucast_rules</span>(
  <span class='kw'>x</span>,
  col_mo = <span class='kw'>NULL</span>,
  info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
-  rules = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR.eucast_rules"</span>, default = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>)),
+  rules = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR_eucastrules"</span>, default = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>)),
  verbose = <span class='fl'>FALSE</span>,
+  version_breakpoints = <span class='fl'>10</span>,
+  version_expertrules = <span class='fl'>3.2</span>,
  <span class='kw'>...</span>
 )</pre>

@@ -258,7 +260,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>x</th>
-      <td><p>data with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td>
+      <td><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></td>
    </tr>
    <tr>
      <th>col_mo</th>
@@ -270,11 +272,19 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
    </tr>
    <tr>
      <th>rules</th>
-      <td><p>a character vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"all"</code>, and defaults to <code><a href='https://rdrr.io/r/base/c.html'>c("breakpoints", "expert")</a></code>. The default value can be set to another value using e.g. <code><a href='https://rdrr.io/r/base/options.html'>options(AMR.eucast_rules = "all")</a></code>.</p></td>
+      <td><p>a character vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"all"</code>, and defaults to <code><a href='https://rdrr.io/r/base/c.html'>c("breakpoints", "expert")</a></code>. The default value can be set to another value, e.g. using <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_eucastrules = "all")</a></code>.</p></td>
    </tr>
    <tr>
      <th>verbose</th>
-      <td><p>a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.</p></td>
+      <td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.</p></td>
+    </tr>
+    <tr>
+      <th>version_breakpoints</th>
+      <td><p>the version number to use for the EUCAST Clinical Breakpoints guideline</p></td>
+    </tr>
+    <tr>
+      <th>version_expertrules</th>
+      <td><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline</p></td>
    </tr>
    <tr>
      <th>...</th>
@@ -290,9 +300,13 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
 Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60. <br />
 <a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>https://doi.org/10.1111/j.1469-0691.2011.03703.x</a></p></li>
 <li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016.  <br />
-<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p></li>
+<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p></li>
+<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020.  <br />
+<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'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf</a></p></li>
 <li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br />
-<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li>
+<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li>
+<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. <br />
+<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx'>https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx</a></p></li>
 </ul>

    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -302,104 +316,31 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test

    <p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br />
 <strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
-<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules. These rules are:</p><ol>
-<li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the drug <strong>without</strong> enzyme inhibitor is S</p></li>
-<li><p>A drug <strong>without</strong> enzyme inhibitor will be set to R if the drug <strong>with</strong> enzyme inhibitor is R</p></li>
+<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p><h3>'Other' rules</h3>
+
+
+<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol>
+<li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the same drug <strong>without</strong> enzyme inhibitor is S</p></li>
+<li><p>A drug <strong>without</strong> enzyme inhibitor will be set to R if the same drug <strong>with</strong> enzyme inhibitor is R</p></li>
 </ol>

-<p>These rules are not applied at default, since they are not approved by EUCAST. To use these rules, use <code>eucast_rules(..., rules = "all")</code>, or set the default behaviour of the <code>[eucast_rules()]</code> function with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR.eucast_rules = "all")</a></code> (or any other valid input value(s) to the <code>rules</code> parameter).</p>
-<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
+<p>Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.</p>
+<p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> parameter, or use <code>eucast_rules(..., rules = "all")</code>.</p>
+
    <h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>

    

 <p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
-<p>The following antibiotics are used for the functions <code>eucast_rules()</code> and <code><a href='mdro.html'>mdro()</a></code>. These are shown below in the format '<strong>antimicrobial ID</strong>: name (<a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted by name:</p>
-<p><strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
-<strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
-<strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
-<strong>AMP</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
-<strong>SAM</strong>: ampicillin/sulbactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01'>J01CR01</a>),
-<strong>AZM</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
-<strong>AZL</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
-<strong>ATM</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
-<strong>CAP</strong>: capreomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30'>J04AB30</a>),
-<strong>RID</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
-<strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
-<strong>FEP</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
-<strong>CTX</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
-<strong>CTT</strong>: cefotetan (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05'>J01DC05</a>),
-<strong>FOX</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
-<strong>CPT</strong>: ceftaroline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DI02'>J01DI02</a>),
-<strong>CAZ</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
-<strong>CRO</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
-<strong>CXM</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
-<strong>CED</strong>: cephradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
-<strong>CHL</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
-<strong>CIP</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
-<strong>CLR</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
-<strong>CLI</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
-<strong>COL</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
-<strong>DAP</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
-<strong>DOR</strong>: doripenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH04'>J01DH04</a>),
-<strong>DOX</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
-<strong>ETP</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
-<strong>ERY</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
-<strong>ETH</strong>: ethambutol (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK02'>J04AK02</a>),
-<strong>FLC</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
-<strong>FOS</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
-<strong>FUS</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
-<strong>GAT</strong>: gatifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA16'>J01MA16</a>),
-<strong>GEN</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
-<strong>GEH</strong>: gentamicin-high (no ATC code),
-<strong>IPM</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
-<strong>INH</strong>: isoniazid (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AC01'>J04AC01</a>),
-<strong>KAN</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
-<strong>LVX</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
-<strong>LIN</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
-<strong>LNZ</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
-<strong>MEM</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
-<strong>MTR</strong>: metronidazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XD01'>J01XD01</a>),
-<strong>MEZ</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
-<strong>MNO</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
-<strong>MFX</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
-<strong>NAL</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
-<strong>NEO</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
-<strong>NET</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
-<strong>NIT</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
-<strong>NOR</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
-<strong>NOV</strong>: novobiocin (<a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
-<strong>OFX</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
-<strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF04'>J01CF04</a>),
-<strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
-<strong>PIP</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
-<strong>TZP</strong>: piperacillin/tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
-<strong>PLB</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
-<strong>PRI</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
-<strong>PZA</strong>: pyrazinamide (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK01'>J04AK01</a>),
-<strong>QDA</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
-<strong>RIB</strong>: rifabutin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB04'>J04AB04</a>),
-<strong>RIF</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
-<strong>RFP</strong>: rifapentine (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB05'>J04AB05</a>),
-<strong>RXT</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
-<strong>SIS</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
-<strong>STH</strong>: streptomycin-high (no ATC code),
-<strong>TEC</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
-<strong>TLV</strong>: telavancin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA03'>J01XA03</a>),
-<strong>TCY</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
-<strong>TIC</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
-<strong>TCC</strong>: ticarcillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR03'>J01CR03</a>),
-<strong>TGC</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
-<strong>TOB</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
-<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
-<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
-<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
-    <h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
+<p>The following antibiotics are used for the functions <code>eucast_rules()</code> and <code><a href='mdro.html'>mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
+<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&amp;showdescription=no'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&amp;showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01CR01</a>), avoparcin (<code>AVO</code>, no ATC code), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&amp;showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&amp;showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), capreomycin (<code>CAP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30&amp;showdescription=no'>J04AB30</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&amp;showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&amp;showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&amp;showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&amp;showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&amp;showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&amp;showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>J01DB04</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&amp;showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&amp;showdescription=no'>J01DD16</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&amp;showdescription=no'>J01DD10</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&amp;showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&amp;showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&amp;showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&amp;showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&amp;showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&amp;showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&amp;showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&amp;showdescription=no'>J01DD01</a>), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&amp;showdescription=no'>J01DC05</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&amp;showdescription=no'>J01DC07</a>), cefoxitin (<code>FOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01&amp;showdescription=no'>J01DC01</a>), cefoxitin screening (<code>FOX1</code>, no ATC code), cefpiramide (<code>CPM</code>, <a href='https://www.whocc.no/atLine truncated
+    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>

    

-<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
-The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
+<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
    <h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>

    
@@ -423,7 +364,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
                COL = <span class='st'>"-"</span>,       <span class='co'># Colistin</span>
                CAZ = <span class='st'>"-"</span>,       <span class='co'># Ceftazidime</span>
                CXM = <span class='st'>"-"</span>,       <span class='co'># Cefuroxime</span>
-                PEN = <span class='st'>"S"</span>,       <span class='co'># Penicillin G</span>
+                PEN = <span class='st'>"S"</span>,       <span class='co'># Benzylpenicillin</span>
                FOX = <span class='st'>"S"</span>,       <span class='co'># Cefoxitin</span>
                stringsAsFactors = <span class='fl'>FALSE</span>)

@@ -436,7 +377,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
 <span class='co'># 5 Pseudomonas aeruginosa    -    -    -    -    -    S    S</span>


-<span class='co'># apply EUCAST rules: 18 results are forced as R or S</span>
+<span class='co'># apply EUCAST rules: some results wil be changed</span>
 <span class='kw'>b</span> <span class='op'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>)

 <span class='kw'>b</span>
@@ -449,7 +390,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<


 <span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
-<span class='co'># with 18 rows, containing all details about the transformations:</span>
+<span class='co'># containing all details about the transformations:</span>
 <span class='kw'>c</span> <span class='op'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>, verbose = <span class='fl'>TRUE</span>)
 <span class='co'># }</span>
 </pre>
@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -81,7 +81,7 @@
      </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="Latest development version">1.3.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -296,7 +296,7 @@
        <td>
          <p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
        </td>
-        <td><p>Data sets with 558 antimicrobials</p></td>
+        <td><p>Data sets with 557 antimicrobials</p></td>
      </tr><tr>
        
        <td>
@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -247,7 +247,7 @@

    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>

-    <p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 49,462 observations and 2 variables:</p><ul>
+    <p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 93,892 observations and 2 variables:</p><ul>
 <li><p><code>microorganism</code><br /> Name of the microorganism</p></li>
 <li><p><code>antibiotic</code><br /> Name of the antibiotic drug</p></li>
 </ul>
@@ -255,7 +255,7 @@
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    <p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt'>https://github.com/msberends/AMR/blob/master/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 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version 3.1, 2016.</p>
+<p>This data set is based on 'EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes', v3.2 from 2020.</p>
    <h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>

    
@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -268,7 +268,7 @@
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>x</th>
-      <td><p>data with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td>
+      <td><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></td>
    </tr>
    <tr>
      <th>guideline</th>
@@ -346,86 +346,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
    

 <p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
-<p>The following antibiotics are used for the functions <code><a href='eucast_rules.html'>eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format '<strong>antimicrobial ID</strong>: name (<a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted by name:</p>
-<p><strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
-<strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
-<strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
-<strong>AMP</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
-<strong>SAM</strong>: ampicillin/sulbactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01'>J01CR01</a>),
-<strong>AZM</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
-<strong>AZL</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
-<strong>ATM</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
-<strong>CAP</strong>: capreomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30'>J04AB30</a>),
-<strong>RID</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
-<strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
-<strong>FEP</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
-<strong>CTX</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
-<strong>CTT</strong>: cefotetan (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05'>J01DC05</a>),
-<strong>FOX</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
-<strong>CPT</strong>: ceftaroline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DI02'>J01DI02</a>),
-<strong>CAZ</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
-<strong>CRO</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
-<strong>CXM</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
-<strong>CED</strong>: cephradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
-<strong>CHL</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
-<strong>CIP</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
-<strong>CLR</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
-<strong>CLI</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
-<strong>COL</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
-<strong>DAP</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
-<strong>DOR</strong>: doripenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH04'>J01DH04</a>),
-<strong>DOX</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
-<strong>ETP</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
-<strong>ERY</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
-<strong>ETH</strong>: ethambutol (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK02'>J04AK02</a>),
-<strong>FLC</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
-<strong>FOS</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
-<strong>FUS</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
-<strong>GAT</strong>: gatifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA16'>J01MA16</a>),
-<strong>GEN</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
-<strong>GEH</strong>: gentamicin-high (no ATC code),
-<strong>IPM</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
-<strong>INH</strong>: isoniazid (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AC01'>J04AC01</a>),
-<strong>KAN</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
-<strong>LVX</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
-<strong>LIN</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
-<strong>LNZ</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
-<strong>MEM</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
-<strong>MTR</strong>: metronidazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XD01'>J01XD01</a>),
-<strong>MEZ</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
-<strong>MNO</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
-<strong>MFX</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
-<strong>NAL</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
-<strong>NEO</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
-<strong>NET</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
-<strong>NIT</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
-<strong>NOR</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
-<strong>NOV</strong>: novobiocin (<a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
-<strong>OFX</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
-<strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF04'>J01CF04</a>),
-<strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
-<strong>PIP</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
-<strong>TZP</strong>: piperacillin/tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
-<strong>PLB</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
-<strong>PRI</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
-<strong>PZA</strong>: pyrazinamide (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK01'>J04AK01</a>),
-<strong>QDA</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
-<strong>RIB</strong>: rifabutin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB04'>J04AB04</a>),
-<strong>RIF</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
-<strong>RFP</strong>: rifapentine (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB05'>J04AB05</a>),
-<strong>RXT</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
-<strong>SIS</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
-<strong>STH</strong>: streptomycin-high (no ATC code),
-<strong>TEC</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
-<strong>TLV</strong>: telavancin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA03'>J01XA03</a>),
-<strong>TCY</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
-<strong>TIC</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
-<strong>TCC</strong>: ticarcillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR03'>J01CR03</a>),
-<strong>TGC</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
-<strong>TOB</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
-<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
-<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
-<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
+<p>The following antibiotics are used for the functions <code><a href='eucast_rules.html'>eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
+<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&amp;showdescription=no'>J01GB06</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>J01CR02</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&amp;showdescription=no'>J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01CR01</a>), avoparcin (<code>AVO</code>, no ATC code), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&amp;showdescription=no'>J01FA10</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01CA09</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>J01DF01</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>J01CA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&amp;showdescription=no'>J01CE01</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), capreomycin (<code>CAP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30&amp;showdescription=no'>J04AB30</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01CA03</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>J01CA05</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&amp;showdescription=no'>J01DB10</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&amp;showdescription=no'>J01DC04</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>J01DB05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&amp;showdescription=no'>J01DB02</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&amp;showdescription=no'>J01DC03</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&amp;showdescription=no'>J01DB07</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&amp;showdescription=no'>J01DB06</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>J01DB04</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&amp;showdescription=no'>J01DD15</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&amp;showdescription=no'>J01DD16</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>J01DE01</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&amp;showdescription=no'>J01DD10</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&amp;showdescription=no'>J01DD08</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&amp;showdescription=no'>J01DD05</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&amp;showdescription=no'>J01DC09</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01DD09</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&amp;showdescription=no'>J01DC06</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&amp;showdescription=no'>J01DD12</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&amp;showdescription=no'>J01DD62</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&amp;showdescription=no'>J01DC11</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&amp;showdescription=no'>J01DD01</a>), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&amp;showdescription=no'>J01DC05</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&amp;showdescription=no'>J01DC07</a>), cefoxitin (<code>FOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01&amp;showdescription=no'>J01DC01</a>), cefoxitin screening (<code>FOX1</code>, no ATC code), cefpiramide (<code>CPM</code>, <a href='https://www.whocc.no/atLine truncated
    <h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>

    
@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -270,7 +270,7 @@
 <li><p>The <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> \(L\) is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \(L'\) based on the text length of the full name \(F\) is calculated as:</p></li>
 </ol>

-<p>$$L' = F - \frac{0.5L}{F}$$</p>
+<p>$$L' = 1 - \frac{0.5L}{F}$$</p>
 <p>The final matching score \(M\) is calculated as:
 $$M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}$$</p>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -262,7 +262,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
    <p>The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you will need to have the <code>readxl</code> package installed.</p>
 <p><code>set_mo_source()</code> will check the file for validity: it must be a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href='microorganisms.html'>microorganisms$mo</a></code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source()</code> will read the file into R and export it to <code>"~/.mo_source.rds"</code> after the user <strong>specifically confirms and allows</strong> that this file will be created. For this reason, this function only works in interactive sessions.</p>
 <p>The created compressed data file <code>"~/.mo_source.rds"</code> will be used at default for MO determination (function <code><a href='as.mo.html'>as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus()</a></code> and <code><a href='mo_property.html'>mo_gramstain()</a></code>). The location of the original file will be saved as an R option with <code><a href='https://rdrr.io/r/base/options.html'>options(mo_source = path)</a></code>. Its timestamp will be saved with <code><a href='https://rdrr.io/r/base/options.html'>options(mo_source_datetime = ...)</a></code>.</p>
-<p>The function <code>get_mo_source()</code> will return the data set by reading <code>"~/.mo_source.rds"</code> with <code><a href='https://rdrr.io/r/base/readRDS.html'>readRDS()</a></code>. If the original file has changed (by checking the aforementioned options <code>mo_source</code> and <code>mo_source_datetime</code>), it will call <code>set_mo_source()</code> to update the data file automatically.</p>
+<p>The function <code>get_mo_source()</code> will return the data set by reading <code>"~/.mo_source.rds"</code> with <code><a href='https://rdrr.io/r/base/readRDS.html'>readRDS()</a></code>. If the original file has changed (by checking the aforementioned options <code>mo_source</code> and <code>mo_source_datetime</code>), it will call <code>set_mo_source()</code> to update the data file automatically if used in an interactive session.</p>
 <p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file created with <code>set_mo_source()</code> will then have a size of 0.1 kB and can be read by <code>get_mo_source()</code> in only a couple of microseconds (millionths of a second).</p>
    <h2 class="hasAnchor" id="how-to-setup"><a class="anchor" href="#how-to-setup"></a>How to setup</h2>

@@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -82,7 +82,7 @@
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
      </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="Latest development version">1.3.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>

@@ -81,7 +81,7 @@
      </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="Latest development version">1.3.0.9025</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span>
      </span>
    </div>