(v1.7.1.9039) reinitiate all units tests

.github/workflows/check.yaml

@@ -128,18 +128,6 @@ jobs:
           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
         
-      # - name: Only keep vignettes on release version
-      - name: Remove vignettes
-        # if: matrix.config.r != 'release'
-        if: always()
-        # 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:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.1.9038
-Date: 2021-09-01
+Version: 1.7.1.9039
+Date: 2021-09-03
 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` 1.7.1.9038
-## <small>Last updated:  1 September 2021</small>
+# `AMR` 1.7.1.9039
+## <small>Last updated:  3 September 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/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">1.7.1.9038</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9039</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">01 September 2021</h4>
+            <h4 data-toc-skip class="date">03 September 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>
@@ -495,7 +495,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#antibiotic-agents" class="anchor" aria-hidden="true"></a>Antibiotic agents</h2>
 <p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
 <p>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 19 August 2021 21:21:57 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>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>

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">1.7.1.9038</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9039</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-1719038" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.1.9038">
-<a href="#amr-1719038" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9038</h1>
-<div id="last-updated-1-september-2021" class="section level2">
+    <div id="amr-1719039" class="section level1">
+<h1 class="page-header" data-toc-text="1.7.1.9039">
+<a href="#amr-1719039" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9039</h1>
+<div id="last-updated-3-september-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-1-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 1 September 2021</small>
+<a href="#last-updated-3-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 3 September 2021</small>
 </h2>
 <div id="breaking-changes" class="section level3">
 <h3 class="hasAnchor">

inst/tinytest/test-ab_class_selectors.R

@@ -56,6 +56,7 @@ expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance
 
 expect_equal(ncol(example_isolates[, c(administrable_per_os() & penicillins())]), 5, tolerance = 0.5)
 expect_equal(ncol(example_isolates[, c(administrable_iv() & penicillins())]), 7, tolerance = 0.5)
+expect_equal(ncol(example_isolates[, c(administrable_iv() | penicillins())]), 37, tolerance = 0.5)
 
 # filter using any() or all()
 expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)

tests/tinytest.R

@@ -34,13 +34,11 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
                                          "inst/tinytest",
                                          "tinytest"),
                         verbose = 99,
-                        pattern = "first.*\\.[rR]$",
                         color = FALSE)
     cat("SUMMARY:\n")
     print(summary(out))
     cat("WARNINGS:\n")
     print(warnings())
     cat(attributes(out)$duration, "\n")
-    
   }
 }