(v1.7.1.9051) updated taxonomy, updated git branch name

2025-09-03 16:39:37 +02:00 · 2021-10-06 13:23:57 +02:00
parent 8f5e5a3fc2
commit 37e6e35ec4
139 changed files with 2694 additions and 1862 deletions
--- a/docs/articles/AMR.html
+++ b/docs/articles/AMR.html
@@ -193,7 +193,7 @@
            
            <h4 data-toc-skip class="date">04 October 2021</h4>
      
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
      <div class="hidden name"><code>AMR.Rmd</code></div>

    </div>
--- a/docs/articles/EUCAST.html
+++ b/docs/articles/EUCAST.html
@@ -191,7 +191,7 @@
      <h1 data-toc-skip>How to apply EUCAST rules</h1>
            
      
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
      <div class="hidden name"><code>EUCAST.Rmd</code></div>

    </div>
--- a/docs/articles/MDR.html
+++ b/docs/articles/MDR.html
@@ -191,7 +191,7 @@
      <h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
            
      
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
      <div class="hidden name"><code>MDR.Rmd</code></div>

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--- a/docs/articles/PCA.html
+++ b/docs/articles/PCA.html
@@ -191,7 +191,7 @@
      <h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
            
      
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
      <div class="hidden name"><code>PCA.Rmd</code></div>

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--- a/docs/articles/SPSS.html
+++ b/docs/articles/SPSS.html
@@ -193,7 +193,7 @@
            
            <h4 data-toc-skip class="date">29 August 2021</h4>
      
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
      <div class="hidden name"><code>SPSS.Rmd</code></div>

    </div>
@@ -287,10 +287,10 @@
 <a href="#rstudio" class="anchor" aria-hidden="true"></a>RStudio</h3>
 <p>To work with R, probably the best option is to use <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio</a>. It is an open-source and free desktop environment which not only allows you to run R code, but also supports project management, version management, package management and convenient import menus to work with other data sources. You can also install <a href="https://www.rstudio.com/products/rstudio/" class="external-link">RStudio Server</a> on a private or corporate server, which brings nothing less than the complete RStudio software to you as a website (at home or at work).</p>
 <p>To import a data file, just click <em>Import Dataset</em> in the Environment tab:</p>
-<p><img src="https://github.com/msberends/AMR/raw/master/docs/import1.png"></p>
+<p><img src="https://github.com/msberends/AMR/raw/main/docs/import1.png"></p>
 <p>If additional packages are needed, RStudio will ask you if they should be installed on beforehand.</p>
 <p>In the the window that opens, you can define all options (parameters) that should be used for import and you’re ready to go:</p>
-<p><img src="https://github.com/msberends/AMR/raw/master/docs/import2.png"></p>
+<p><img src="https://github.com/msberends/AMR/raw/main/docs/import2.png"></p>
 <p>If you want named variables to be imported as factors so it resembles SPSS more, use <code><a href="https://haven.tidyverse.org/reference/as_factor.html" class="external-link">as_factor()</a></code>.</p>
 <p>The difference is this:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
--- a/docs/articles/WHONET.html
+++ b/docs/articles/WHONET.html
@@ -191,7 +191,7 @@
      <h1 data-toc-skip>How to work with WHONET data</h1>
            
      
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd" class="external-link"><code>vignettes/WHONET.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/WHONET.Rmd" class="external-link"><code>vignettes/WHONET.Rmd</code></a></small>
      <div class="hidden name"><code>WHONET.Rmd</code></div>

    </div>
--- a/docs/articles/benchmarks.html
+++ b/docs/articles/benchmarks.html
@@ -191,7 +191,7 @@
      <h1 data-toc-skip>Benchmarks</h1>
            
      
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd" class="external-link"><code>vignettes/benchmarks.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/benchmarks.Rmd" class="external-link"><code>vignettes/benchmarks.Rmd</code></a></small>
      <div class="hidden name"><code>benchmarks.Rmd</code></div>

    </div>
--- a/docs/articles/datasets.html
+++ b/docs/articles/datasets.html
@@ -44,7 +44,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9050</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span>
      </span>
    </div>

@@ -190,7 +190,7 @@
    <div class="page-header toc-ignore">
      <h1 data-toc-skip>Data sets for download / own use</h1>
            
-            <h4 data-toc-skip class="date">05 October 2021</h4>
+            <h4 data-toc-skip class="date">06 October 2021</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="hidden name"><code>datasets.Rmd</code></div>
@@ -207,22 +207,22 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div id="microorganisms-currently-accepted-names" class="section level2">
 <h2 class="hasAnchor">
 <a href="#microorganisms-currently-accepted-names" class="anchor" aria-hidden="true"></a>Microorganisms (currently accepted names)</h2>
-<p>A data set with 70,026 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
+<p>A data set with 70,760 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
 <p>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 11 March 2021 20:59:32 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+<p>It was last updated on 6 October 2021 09:31:11 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (2.2 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">R file</a> (2.2 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel file</a> (6.4 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel file</a> (6.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt" class="external-link">plain text file</a> (14.8 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain text file</a> (14.9 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS file</a> (27.4 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS file</a> (30.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS file</a> (27.8 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS file</a> (18 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata file</a> (25.1 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata file</a> (29.2 MB)</li>
 </ul>
 <p><strong>NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
 <div id="source" class="section level3">
@@ -233,7 +233,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <li>
 <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
 <li>
-<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: March 2021)</li>
+<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
 <li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
 </ul>
 </div>
@@ -261,7 +261,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 </tr>
 <tr class="even">
 <td align="center">Bacteria</td>
-<td align="center">22,118</td>
+<td align="center">22,852</td>
 </tr>
 <tr class="odd">
 <td align="center">Chromista</td>
@@ -427,23 +427,23 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <div id="microorganisms-previously-accepted-names" class="section level2">
 <h2 class="hasAnchor">
 <a href="#microorganisms-previously-accepted-names" class="anchor" aria-hidden="true"></a>Microorganisms (previously accepted names)</h2>
-<p>A data set with 14,100 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
+<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
 <p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
 <p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
+<p>It was last updated on 5 October 2021 13:12:28 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel file</a> (0.5 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel file</a> (0.5 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain text file</a> (0.9 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain text file</a> (1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS file</a> (2.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS file</a> (2.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS file</a> (2.2 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS file</a> (1.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata file</a> (2 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata file</a> (2 MB)</li>
 </ul>
 <div id="source-1" class="section level3">
 <h3 class="hasAnchor">
@@ -453,7 +453,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <li>
 <a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
 <li>
-<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: March 2021)</li>
+<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
 </ul>
 </div>
 <div id="example-content-1" class="section level3">
@@ -498,17 +498,17 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <p>It was last updated on 2 September 2021 11:50:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (32 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (32 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel file</a> (65 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel file</a> (65 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt" class="external-link">plain text file</a> (0.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain text file</a> (0.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS file</a> (1.8 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS file</a> (1.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS file</a> (0.3 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS file</a> (0.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata file</a> (0.3 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata file</a> (0.3 MB)</li>
 </ul>
 <div id="source-2" class="section level3">
 <h3 class="hasAnchor">
@@ -666,17 +666,17 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel file</a> (14 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel file</a> (14 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.txt" class="external-link">plain text file</a> (16 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain text file</a> (16 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sas" class="external-link">SAS file</a> (80 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS file</a> (80 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS file</a> (68 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS file</a> (68 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.dta" class="external-link">Stata file</a> (67 kB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata file</a> (67 kB)</li>
 </ul>
 <div id="source-3" class="section level3">
 <h3 class="hasAnchor">
@@ -790,20 +790,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#intrinsic-bacterial-resistance" class="anchor" aria-hidden="true"></a>Intrinsic bacterial resistance</h2>
 <p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>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 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
+<p>It was last updated on 6 October 2021 08:29:50 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (69 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">R file</a> (69 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (0.9 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (0.9 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (3.5 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (3.5 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (7.1 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (7.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (7.9 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (5.1 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (7 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (7 MB)</li>
 </ul>
 <div id="source-4" class="section level3">
 <h3 class="hasAnchor">
@@ -1005,20 +1005,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor" aria-hidden="true"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
 <p>A data set with 22,000 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
 <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 12 July 2021 10:54:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
+<p>It was last updated on 5 October 2021 13:13:41 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (37 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (37 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel file</a> (0.7 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel file</a> (0.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.8 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (3.8 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (3.8 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.4 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.5 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.5 MB)</li>
 </ul>
 <div id="source-5" class="section level3">
 <h3 class="hasAnchor">
@@ -1138,17 +1138,17 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">R file</a> (3 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel file</a> (14 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel file</a> (14 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.txt" class="external-link">plain text file</a> (15 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain text file</a> (15 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.sas" class="external-link">SAS file</a> (52 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS file</a> (52 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.sav" class="external-link">SPSS file</a> (45 kB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS file</a> (45 kB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.dta" class="external-link">Stata file</a> (44 kB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata file</a> (44 kB)</li>
 </ul>
 <div id="source-6" class="section level3">
 <h3 class="hasAnchor">
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -92,7 +92,7 @@
      </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">1.7.1.9048</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9051</span>
      </span>
    </div>

--- a/docs/articles/resistance_predict.html
+++ b/docs/articles/resistance_predict.html
@@ -191,7 +191,7 @@
      <h1 data-toc-skip>How to predict antimicrobial resistance</h1>
            
      
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/resistance_predict.Rmd" class="external-link"><code>vignettes/resistance_predict.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/resistance_predict.Rmd" class="external-link"><code>vignettes/resistance_predict.Rmd</code></a></small>
      <div class="hidden name"><code>resistance_predict.Rmd</code></div>

    </div>
--- a/docs/articles/welcome_to_AMR.html
+++ b/docs/articles/welcome_to_AMR.html
@@ -191,7 +191,7 @@
      <h1 data-toc-skip>Welcome to the <code>AMR</code> package</h1>
            
      
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/welcome_to_AMR.Rmd" class="external-link"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/welcome_to_AMR.Rmd" class="external-link"><code>vignettes/welcome_to_AMR.Rmd</code></a></small>
      <div class="hidden name"><code>welcome_to_AMR.Rmd</code></div>

    </div>