(v1.7.1.9048) unit tests

.github/workflows/check.yaml

@@ -77,37 +77,40 @@ jobs:
           - {os: windows-latest, r: '3.4',     allowfail: false}
           - {os: windows-latest, r: '3.3',     allowfail: false}
           - {os: windows-latest, r: '3.2',     allowfail: false}
-
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: false
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       R_REPOSITORIES: "https://cran.rstudio.com"
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    
-      R_KEEP_PKG_SOURCE: yes
-      R_CHECK_CRAN_INCOMING_: false
-      R_CHECK_FORCE_SUGGESTS_: false
-      R_CHECK_DEPENDS_ONLY_: true
-      R_CHECK_LENGTH_1_CONDITION_: verbose
-      R_CHECK_LENGTH_1_LOGIC2_: verbose
-      # during 'R CMD check', R_LIBS_USER will be overwritten, so:
-      R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
-      R_RUN_TINYTEST: true
-
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
       - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
-          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
+        # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
+        # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
+        run: |
+          sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
+      - name: Restore cached R packages
+        # this step will add the step 'Post Restore cached R packages' on a succesful run
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
         with:
-          extra-packages: rcmdcheck
+          path: ${{ env.R_LIBS_USER }}
-          
+          key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
+
+      - name: Unpack AMR and install R dependencies
+        if: always()
+        run: |
+          tar -xf data-raw/AMR_latest.tar.gz
+          Rscript -e "source('data-raw/_install_deps.R')"
+        shell: bash
+        
       - name: Show session info
         if: always()
         run: |
@@ -115,17 +118,41 @@ jobs:
           utils::sessionInfo()
           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
-
+        
-      - uses: r-lib/actions/check-r-package@v1
+      - name: Remove vignettes on R without knitr support
+        if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
+        # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
+        run: |
+          rm -rf AMR/vignettes
+          Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')"
+          rm AMR/DESCRIPTION
+          mv AMR/DESCRIPTION2 AMR/DESCRIPTION
+        shell: bash
+        
+      - name: Run R CMD check
+        if: always()
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+          _R_CHECK_DEPENDS_ONLY_: true
+          _R_CHECK_LENGTH_1_CONDITION_: verbose
+          _R_CHECK_LENGTH_1_LOGIC2_: verbose
+          # during 'R CMD check', R_LIBS_USER will be overwritten, so:
+          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
+          R_RUN_TINYTEST: true
+        run: |
+          R CMD check --no-manual --run-donttest --run-dontrun AMR
+        shell: bash
 
       - name: Show unit tests output
         if: always()
-        run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true
+        run: |
+          find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash
 
-      - name: Upload check results
+      - name: Upload artifacts
         if: always()
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@v2
         with:
-          name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
+          name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
-          path: check
+          path: AMR.Rcheck

.github/workflows/codecovr.yaml

@@ -26,11 +26,11 @@
 on:
   push:
     branches:
-      - premaster
+      - development
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 name: code-coverage
 

.github/workflows/lintr.yaml

@@ -26,11 +26,11 @@
 on:
   push:
     branches:
-      - premaster
+      - development
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 name: lintr
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.1.9041
+Version: 1.7.1.9048
-Date: 2021-09-29
+Date: 2021-10-04
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,5 +1,5 @@
-# `AMR` 1.7.1.9041
+# `AMR` 1.7.1.9048
-## <small>Last updated: 29 September 2021</small>
+## <small>Last updated:  4 October 2021</small>
 
 ### Breaking changes
 * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version

docs/articles/AMR.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">1.7.1.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9048</span>
       </span>
     </div>
 
@@ -191,7 +191,7 @@
       <h1 data-toc-skip>How to conduct AMR data analysis</h1>
                         <h4 data-toc-skip class="author">Matthijs S. Berends</h4>
             
-            <h4 data-toc-skip class="date">29 September 2021</h4>
+            <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>
       <div class="hidden name"><code>AMR.Rmd</code></div>
@@ -200,7 +200,7 @@
 
     
     
-<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 29 September 2021.</p>
+<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 04 October 2021.</p>
 <div id="introduction" class="section level1">
 <h1 class="hasAnchor">
 <a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
@@ -231,21 +231,21 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2021-09-29</td>
+<td align="center">2021-10-04</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
 <tr class="even">
-<td align="center">2021-09-29</td>
+<td align="center">2021-10-04</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 </tr>
 <tr class="odd">
-<td align="center">2021-09-29</td>
+<td align="center">2021-10-04</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -342,52 +342,52 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2017-08-27</td>
+<td align="center">2017-09-21</td>
-<td align="center">L5</td>
+<td align="center">T1</td>
-<td align="center">Hospital B</td>
-<td align="center">Escherichia coli</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="even">
-<td align="center">2017-02-15</td>
-<td align="center">L4</td>
-<td align="center">Hospital C</td>
-<td align="center">Escherichia coli</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="odd">
-<td align="center">2010-01-01</td>
-<td align="center">H4</td>
 <td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">M</td>
+<td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2014-12-09</td>
+<td align="center">2016-12-13</td>
-<td align="center">C5</td>
+<td align="center">P9</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">M</td>
+<td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2010-02-19</td>
+<td align="center">2013-09-17</td>
-<td align="center">W1</td>
+<td align="center">S3</td>
+<td align="center">Hospital A</td>
+<td align="center">Streptococcus pneumoniae</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">F</td>
+</tr>
+<tr class="even">
+<td align="center">2017-10-22</td>
+<td align="center">R4</td>
+<td align="center">Hospital C</td>
+<td align="center">Staphylococcus aureus</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+</tr>
+<tr class="odd">
+<td align="center">2012-01-06</td>
+<td align="center">P6</td>
 <td align="center">Hospital D</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
@@ -397,15 +397,15 @@
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2010-11-16</td>
+<td align="center">2014-06-30</td>
-<td align="center">X9</td>
+<td align="center">D3</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital C</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Staphylococcus aureus</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">S</td>
+<td align="center">M</td>
-<td align="center">S</td>
-<td align="center">F</td>
 </tr>
 </tbody>
 </table>
@@ -439,16 +439,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,412</td>
+<td align="right">10,351</td>
-<td align="right">52.06%</td>
+<td align="right">51.76%</td>
-<td align="right">10,412</td>
+<td align="right">10,351</td>
-<td align="right">52.06%</td>
+<td align="right">51.76%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,588</td>
+<td align="right">9,649</td>
-<td align="right">47.94%</td>
+<td align="right">48.25%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -501,9 +501,9 @@ Longest: 1</p>
 <span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
 <span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
 <span class="co"># 2</span>
-<span class="co"># =&gt; Found 10,617 'phenotype-based' first isolates (53.1% of total where a</span>
+<span class="co"># =&gt; Found 10,567 'phenotype-based' first isolates (52.8% of total where a</span>
 <span class="co">#    microbial ID was available)</span></code></pre></div>
-<p>So only 53.1% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
+<p>So only 52.8% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
@@ -511,10 +511,10 @@ Longest: 1</p>
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
-<p>So we end up with 10,617 isolates for analysis. Now our data looks like:</p>
+<p>So we end up with 10,567 isolates for analysis. Now our data looks like:</p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
-<table class="table">
+<table style="width:100%;" class="table">
 <colgroup>
 <col width="2%">
 <col width="9%">
@@ -528,7 +528,7 @@ Longest: 1</p>
 <col width="6%">
 <col width="11%">
 <col width="12%">
-<col width="7%">
+<col width="9%">
 <col width="5%">
 </colgroup>
 <thead><tr class="header">
@@ -549,94 +549,94 @@ Longest: 1</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
+<td align="left">2</td>
+<td align="center">2016-12-13</td>
+<td align="center">P9</td>
+<td align="center">Hospital D</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
 <td align="left">3</td>
-<td align="center">2010-01-01</td>
+<td align="center">2013-09-17</td>
-<td align="center">H4</td>
+<td align="center">S3</td>
 <td align="center">Hospital A</td>
-<td align="center">B_ESCHR_COLI</td>
+<td align="center">B_STRPT_PNMN</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
-<td align="center">S</td>
+<td align="center">F</td>
-<td align="center">S</td>
+<td align="center">Gram-positive</td>
-<td align="center">M</td>
+<td align="center">Streptococcus</td>
-<td align="center">Gram-negative</td>
+<td align="center">pneumoniae</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="left">4</td>
-<td align="center">2014-12-09</td>
+<td align="center">2017-10-22</td>
-<td align="center">C5</td>
+<td align="center">R4</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital C</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="odd">
-<td align="left">6</td>
-<td align="center">2010-11-16</td>
-<td align="center">X9</td>
-<td align="center">Hospital A</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="left">8</td>
-<td align="center">2011-07-04</td>
-<td align="center">T1</td>
-<td align="center">Hospital D</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="odd">
-<td align="left">10</td>
-<td align="center">2012-05-19</td>
-<td align="center">M7</td>
-<td align="center">Hospital D</td>
 <td align="center">B_STPHY_AURS</td>
-<td align="center">R</td>
-<td align="center">R</td>
-<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">M</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">14</td>
+<td align="left">9</td>
-<td align="center">2016-05-14</td>
+<td align="center">2014-05-28</td>
-<td align="center">C2</td>
+<td align="center">Y8</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
-<td align="center">I</td>
+<td align="center">S</td>
 <td align="center">R</td>
+<td align="center">S</td>
+<td align="center">F</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="odd">
+<td align="left">11</td>
+<td align="center">2010-02-13</td>
+<td align="center">Y5</td>
+<td align="center">Hospital A</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="left">12</td>
+<td align="center">2010-01-30</td>
+<td align="center">F3</td>
+<td align="center">Hospital C</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
@@ -665,8 +665,8 @@ Longest: 1</p>
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 10,617<br>
+Length: 10,567<br>
-Available: 10,617 (100.0%, NA: 0 = 0.0%)<br>
+Available: 10,567 (100.0%, NA: 0 = 0.0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@@ -683,33 +683,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,569</td>
+<td align="right">4,623</td>
-<td align="right">43.03%</td>
+<td align="right">43.75%</td>
-<td align="right">4,569</td>
+<td align="right">4,623</td>
-<td align="right">43.03%</td>
+<td align="right">43.75%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,718</td>
+<td align="right">2,765</td>
-<td align="right">25.60%</td>
+<td align="right">26.17%</td>
-<td align="right">7,287</td>
+<td align="right">7,388</td>
-<td align="right">68.64%</td>
+<td align="right">69.92%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,158</td>
+<td align="right">2,017</td>
-<td align="right">20.33%</td>
+<td align="right">19.09%</td>
-<td align="right">9,445</td>
+<td align="right">9,405</td>
-<td align="right">88.96%</td>
+<td align="right">89.00%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,172</td>
+<td align="right">1,162</td>
-<td align="right">11.04%</td>
+<td align="right">11.00%</td>
-<td align="right">10,617</td>
+<td align="right">10,567</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@@ -728,14 +728,14 @@ Longest: 24</p>
 <col width="9%">
 <col width="9%">
 <col width="9%">
-<col width="10%">
+<col width="11%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="6%">
 <col width="11%">
-<col width="12%">
+<col width="11%">
 <col width="9%">
 <col width="5%">
 </colgroup>
@@ -756,13 +756,28 @@ Longest: 24</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2016-05-14</td>
+<td align="center">2013-09-17</td>
-<td align="center">C2</td>
+<td align="center">S3</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital A</td>
+<td align="center">B_STRPT_PNMN</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">F</td>
+<td align="center">Gram-positive</td>
+<td align="center">Streptococcus</td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="center">2010-01-30</td>
+<td align="center">F3</td>
+<td align="center">Hospital C</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
-<td align="center">I</td>
 <td align="center">R</td>
+<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
@@ -770,28 +785,13 @@ Longest: 24</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
-<td align="center">2013-08-08</td>
-<td align="center">C10</td>
-<td align="center">Hospital C</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">M</td>
-<td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
 <tr class="odd">
-<td align="center">2017-08-12</td>
+<td align="center">2011-10-02</td>
-<td align="center">H8</td>
+<td align="center">B9</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital C</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
+<td align="center">I</td>
-<td align="center">S</td>
+<td align="center">I</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
@@ -801,42 +801,12 @@ Longest: 24</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2012-09-19</td>
+<td align="center">2017-09-14</td>
-<td align="center">S7</td>
+<td align="center">Y3</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital A</td>
-<td align="center">B_STPHY_AURS</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">F</td>
-<td align="center">Gram-positive</td>
-<td align="center">Staphylococcus</td>
-<td align="center">aureus</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="odd">
-<td align="center">2016-07-27</td>
-<td align="center">I10</td>
-<td align="center">Hospital C</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
-<td align="center">M</td>
-<td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="center">2013-11-25</td>
-<td align="center">P4</td>
-<td align="center">Hospital D</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
@@ -845,6 +815,36 @@ Longest: 24</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
+<tr class="odd">
+<td align="center">2013-01-07</td>
+<td align="center">L2</td>
+<td align="center">Hospital C</td>
+<td align="center">B_STRPT_PNMN</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">M</td>
+<td align="center">Gram-positive</td>
+<td align="center">Streptococcus</td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="center">2015-06-10</td>
+<td align="center">O6</td>
+<td align="center">Hospital D</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">F</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
 </tbody>
 </table>
 <p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@@ -866,50 +866,50 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2159</td>
+<td align="center">2182</td>
-<td align="center">142</td>
+<td align="center">119</td>
-<td align="center">2268</td>
+<td align="center">2322</td>
-<td align="center">4569</td>
+<td align="center">4623</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">3349</td>
+<td align="center">3388</td>
-<td align="center">169</td>
+<td align="center">143</td>
-<td align="center">1051</td>
+<td align="center">1092</td>
-<td align="center">4569</td>
+<td align="center">4623</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3375</td>
+<td align="center">3434</td>
 <td align="center">0</td>
-<td align="center">1194</td>
+<td align="center">1189</td>
-<td align="center">4569</td>
+<td align="center">4623</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">3985</td>
+<td align="center">4002</td>
 <td align="center">0</td>
-<td align="center">584</td>
+<td align="center">621</td>
-<td align="center">4569</td>
+<td align="center">4623</td>
 </tr>
 <tr class="odd">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMX</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1172</td>
+<td align="center">1162</td>
-<td align="center">1172</td>
+<td align="center">1162</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">930</td>
+<td align="center">928</td>
-<td align="center">35</td>
+<td align="center">43</td>
-<td align="center">207</td>
+<td align="center">191</td>
-<td align="center">1172</td>
+<td align="center">1162</td>
 </tr>
 </tbody>
 </table>
@@ -932,34 +932,34 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">3985</td>
+<td align="center">4002</td>
 <td align="center">0</td>
-<td align="center">584</td>
+<td align="center">621</td>
-<td align="center">4569</td>
+<td align="center">4623</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1073</td>
+<td align="center">1043</td>
 <td align="center">0</td>
-<td align="center">99</td>
+<td align="center">119</td>
-<td align="center">1172</td>
+<td align="center">1162</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2409</td>
+<td align="center">2461</td>
 <td align="center">0</td>
-<td align="center">309</td>
+<td align="center">304</td>
-<td align="center">2718</td>
+<td align="center">2765</td>
 </tr>
 <tr class="even">
 <td align="center">S. pneumoniae</td>
 <td align="center">GEN</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">2158</td>
+<td align="center">2017</td>
-<td align="center">2158</td>
+<td align="center">2017</td>
 </tr>
 </tbody>
 </table>
@@ -973,7 +973,7 @@ Longest: 24</p>
 <p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
 <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
-<span class="co"># [1] 0.5429029</span></code></pre></div>
+<span class="co"># [1] 0.5489732</span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> 
@@ -987,19 +987,19 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5478773</td>
+<td align="center">0.5483971</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5516767</td>
+<td align="center">0.5501101</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5306768</td>
+<td align="center">0.5632754</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5297098</td>
+<td align="center">0.5369668</td>
 </tr>
 </tbody>
 </table>
@@ -1018,23 +1018,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5478773</td>
+<td align="center">0.5483971</td>
-<td align="center">3227</td>
+<td align="center">3213</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5516767</td>
+<td align="center">0.5501101</td>
-<td align="center">3638</td>
+<td align="center">3632</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5306768</td>
+<td align="center">0.5632754</td>
-<td align="center">1581</td>
+<td align="center">1612</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5297098</td>
+<td align="center">0.5369668</td>
-<td align="center">2171</td>
+<td align="center">2110</td>
 </tr>
 </tbody>
 </table>
@@ -1055,27 +1055,27 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7699715</td>
+<td align="center">0.7637897</td>
-<td align="center">0.8721821</td>
+<td align="center">0.8656716</td>
-<td align="center">0.9748304</td>
+<td align="center">0.9781527</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8233788</td>
+<td align="center">0.8356282</td>
-<td align="center">0.9155290</td>
+<td align="center">0.8975904</td>
-<td align="center">0.9872014</td>
+<td align="center">0.9845095</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.7969095</td>
+<td align="center">0.7949367</td>
-<td align="center">0.8863135</td>
+<td align="center">0.8900542</td>
-<td align="center">0.9790287</td>
+<td align="center">0.9804702</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5338276</td>
+<td align="center">0.5389192</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5338276</td>
+<td align="center">0.5389192</td>
 </tr>
 </tbody>
 </table>
@@ -1090,33 +1090,33 @@ Longest: 24</p>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">penicillins</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">resistance</span>, as_percent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span> 
   <span class="co"># format the antibiotic column names, using so-called snake case,</span>
   <span class="co"># so 'Amoxicillin/clavulanic acid' becomes 'amoxicillin_clavulanic_acid'</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html" class="external-link">rename_with</a></span><span class="op">(</span>.fn <span class="op">=</span> <span class="va">ab_name</span>, .cols <span class="op">=</span> <span class="fu"><a href="../reference/antibiotic_class_selectors.html">penicillins</a></span><span class="op">(</span><span class="op">)</span>, snake_case <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
+  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html" class="external-link">rename_with</a></span><span class="op">(</span><span class="va">set_ab_names</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">penicillins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
 <th align="left">hospital</th>
-<th align="right">Amoxicillin</th>
+<th align="right">amoxicillin</th>
-<th align="right">Amoxicillin/clavulanic acid</th>
+<th align="right">amoxicillin_clavulanic_acid</th>
 </tr></thead>
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
 <td align="right">54.8%</td>
-<td align="right">26.7%</td>
+<td align="right">27.0%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
-<td align="right">55.2%</td>
+<td align="right">55.0%</td>
-<td align="right">26.9%</td>
+<td align="right">26.1%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">53.1%</td>
+<td align="right">56.3%</td>
 <td align="right">26.9%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital D</td>
-<td align="right">53.0%</td>
+<td align="right">53.7%</td>
-<td align="right">25.4%</td>
+<td align="right">25.3%</td>
 </tr>
 </tbody>
 </table>
@@ -1200,18 +1200,18 @@ Longest: 24</p>
 <code class="sourceCode R"><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
 <span class="va">mic_values</span>
 <span class="co"># Class &lt;mic&gt;</span>
-<span class="co">#   [1] 0.005   0.125   32      0.0625  0.5     0.125   16      0.25    0.025  </span>
+<span class="co">#   [1] 0.5     0.125   0.002   2       0.0625  128     64      0.002   0.002  </span>
-<span class="co">#  [10] &lt;=0.001 &lt;=0.001 0.0625  0.01    1       2       32      0.01    8      </span>
+<span class="co">#  [10] 8       0.025   256     0.0625  0.25    128     256     0.0625  4      </span>
-<span class="co">#  [19] 0.005   32      0.005   32      128     0.125   0.125   2       &lt;=0.001</span>
+<span class="co">#  [19] 0.025   256     64      256     4       &lt;=0.001 128     0.0625  0.025  </span>
-<span class="co">#  [28] 4       8       0.005   0.002   0.5     0.002   0.5     64      0.125  </span>
+<span class="co">#  [28] 256     0.25    0.25    0.01    0.002   0.125   16      0.002   2      </span>
-<span class="co">#  [37] 0.01    0.002   0.0625  128     0.5     1       0.125   0.0625  0.002  </span>
+<span class="co">#  [37] 0.01    2       8       8       0.125   64      4       128     32     </span>
-<span class="co">#  [46] 32      0.025   0.005   8       0.002   &lt;=0.001 8       1       16     </span>
+<span class="co">#  [46] 0.25    32      1       1       256     128     128     64      4      </span>
-<span class="co">#  [55] &lt;=0.001 0.25    0.125   0.025   4       8       0.0625  16      4      </span>
+<span class="co">#  [55] 128     128     128     0.025   1       4       16      0.01    0.005  </span>
-<span class="co">#  [64] 64      &lt;=0.001 128     0.125   0.5     4       32      &lt;=0.001 128    </span>
+<span class="co">#  [64] 0.025   2       0.002   0.25    0.0625  0.005   0.005   16      8      </span>
-<span class="co">#  [73] 16      64      16      0.125   4       2       0.002   0.025   8      </span>
+<span class="co">#  [73] 32      0.002   0.01    256     256     1       8       32      8      </span>
-<span class="co">#  [82] 4       2       0.01    4       0.125   &lt;=0.001 0.002   0.01    0.5    </span>
+<span class="co">#  [82] 0.125   0.002   0.005   32      16      8       256     32      0.5    </span>
-<span class="co">#  [91] 32      128     0.01    1       0.125   4       0.002   0.25    0.25   </span>
+<span class="co">#  [91] 4       0.25    1       0.25    2       2       0.125   0.25    16     </span>
-<span class="co"># [100] 16</span></code></pre></div>
+<span class="co"># [100] 4</span></code></pre></div>
 <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># base R:</span>
 <span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
@@ -1240,10 +1240,10 @@ Longest: 24</p>
 <span class="co">#   to review it.</span>
 <span class="va">disk_values</span>
 <span class="co"># Class &lt;disk&gt;</span>
-<span class="co">#   [1] 26 27 19 22 20 17 23 26 26 17 21 21 22 18 19 25 18 20 17 20 20 22 17 31 24</span>
+<span class="co">#   [1] 20 29 17 26 24 21 24 26 23 31 21 20 29 20 23 20 20 31 21 22 24 19 28 29 24</span>
-<span class="co">#  [26] 28 22 20 31 18 19 26 25 19 22 19 26 26 24 18 18 19 31 25 31 21 28 23 22 21</span>
+<span class="co">#  [26] 31 31 25 30 24 30 30 30 25 22 30 25 22 27 28 19 18 19 31 20 18 18 23 25 23</span>
-<span class="co">#  [51] 22 18 22 18 29 25 29 29 29 24 22 19 23 23 23 22 17 24 17 26 23 25 30 26 17</span>
+<span class="co">#  [51] 27 21 24 25 25 21 22 23 25 29 22 21 22 28 30 27 25 21 18 27 30 21 29 25 31</span>
-<span class="co">#  [76] 17 20 31 17 30 25 18 18 22 29 25 24 29 27 26 30 29 18 21 18 24 25 26 31 25</span></code></pre></div>
+<span class="co">#  [76] 18 19 17 18 23 24 26 30 29 24 24 20 29 28 27 18 31 23 26 30 23 17 23 28 31</span></code></pre></div>
 <div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># base R:</span>
 <span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>

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">1.7.1.9041</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9048</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">29 September 2021</h4>
+            <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/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>

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">1.7.1.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9048</span>
       </span>
     </div>
 

docs/articles/welcome_to_AMR.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">1.7.1.9040</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9048</span>
       </span>
     </div>
 

docs/news/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">1.7.1.9041</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9048</span>
       </span>
     </div>
 
@@ -240,12 +240,12 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1719041" class="section level1">
+    <div id="amr-1719048" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.1.9041">
+<h1 class="page-header" data-toc-text="1.7.1.9048">
-<a href="#amr-1719041" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9041</h1>
+<a href="#amr-1719048" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9048</h1>
-<div id="last-updated-29-september-2021" class="section level2">
+<div id="last-updated-4-october-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-29-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 29 September 2021</small>
+<a href="#last-updated-4-october-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 4 October 2021</small>
 </h2>
 <div id="breaking-changes" class="section level3">
 <h3 class="hasAnchor">

git_development.sh

@@ -127,7 +127,7 @@ echo "••••••••••••••••••••"
 echo "• Building package •"
 echo "••••••••••••••••••••"
 echo "• Building 'data-raw/AMR_latest.tar.gz'..."
-Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = TRUE, binary = FALSE, quiet = TRUE)"
+Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = FALSE, binary = FALSE, quiet = TRUE)"
 rm data-raw/AMR_latest.tar.gz
 mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz
 

inst/tinytest/test-ab_property.R

@@ -69,7 +69,7 @@ expect_identical(colnames(set_ab_names(example_isolates[, 20:25], language = "nl
                  c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine"))
 expect_identical(colnames(set_ab_names(example_isolates[, 20:25], "atc")),
                  c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01"))
-if (AMR:::pkg_is_available("dplyr")) {
+if (AMR:::pkg_is_available("dplyr") && packageVersion("dplyr") >= "1.0.0") {
   expect_identical(example_isolates %>% set_ab_names(),
                    example_isolates %>% rename_with(set_ab_names))
 }

vignettes/AMR.Rmd

@@ -385,13 +385,13 @@ data_1st %>%
   summarise(across(penicillins(), resistance, as_percent = TRUE)) %>% 
   # format the antibiotic column names, using so-called snake case,
   # so 'Amoxicillin/clavulanic acid' becomes 'amoxicillin_clavulanic_acid'
-  rename_with(.fn = ab_name, .cols = penicillins(), snake_case = TRUE)
+  rename_with(set_ab_names, penicillins())
 ```
 ```{r, echo = FALSE, message = FALSE}
 data_1st %>% 
   group_by(hospital) %>% 
   summarise(across(penicillins(), resistance, as_percent = TRUE)) %>% 
-  rename_with(.fn = ab_name, .cols = penicillins(), snake_case = TRUE) %>% 
+  rename_with(set_ab_names, penicillins()) %>% 
   knitr::kable(align = "lrr")
 ```