(v1.7.1.9001) unit tests

.github/workflows/check.yaml

@@ -23,6 +23,8 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
+# This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0.
+
 on:
   push:
     branches:
@@ -96,12 +98,18 @@ jobs:
         run: |
           sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
 
+      - name: Query dependencies
+        # this will change once a week, so it will cache dependency updates
+        run: |
+          writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
+        shell: Rscript {0}
+        
       - name: Restore cached R packages
         # this step will add the step 'Post Restore cached R packages' on a succesful run
         uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
+          key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
 
       - name: Unpack AMR and install R dependencies
         if: always()

.github/workflows/codecovr.yaml

@@ -48,12 +48,18 @@ jobs:
           
       - uses: r-lib/actions/setup-pandoc@master
 
+      - name: Query dependencies
+        # this will change once a week, so it will cache dependency updates
+        run: |
+          writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
+        shell: Rscript {0}
+        
       - name: Restore cached R packages
         # this step will add the step 'Post Restore cached R packages' on a succesful run
         uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: macOS-latest-r-release-v5-codecovr
+          key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
 
       - name: Unpack AMR and install R dependencies
         run: |
@@ -73,6 +79,7 @@ jobs:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           R_RUN_TINYTEST: true
         run: |
+          install.packages("covr", repos = "https://cran.rstudio.com/")
           library(AMR)
           library(tinytest)
           x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.1.9000
+Version: 1.7.1.9001
-Date: 2021-06-04
+Date: 2021-06-05
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# `AMR` 1.7.1.9000
+# `AMR` 1.7.1.9001
-## <small>Last updated:  4 June 2021</small>
+## <small>Last updated:  5 June 2021</small>
 
 ### Changed
 * Added more antibiotic class selectors, such as `lincosamides()` and `lipoglycopeptides()`
@@ -8,7 +8,6 @@
 # `AMR` 1.7.1
 
 ### Breaking change
-* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
 * All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:
   ```r
   # select columns with results for carbapenems
@@ -28,6 +27,7 @@
   ```
 
 ### New
+* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
 * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
 * Function `italicise_taxonomy()` to make taxonomic names within a string italic, with support for markdown and ANSI
 * Support for all four methods to determine first isolates as summarised by Hindler *et al.* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.

R/amr.R

@@ -61,7 +61,7 @@
 #' Matthijs S. Berends \cr
 #' m.s.berends \[at\] umcg \[dot\] nl \cr
 #' University of Groningen
-#' Department of Medical Microbiology and Infection Prevention
+#' Department of Medical Microbiology and Infection Prevention \cr
 #' University Medical Center Groningen \cr
 #' Post Office Box 30001 \cr
 #' 9700 RB Groningen \cr

data-raw/_install_deps.R

@@ -26,7 +26,6 @@
 # some old R instances have trouble installing tinytest, so we ship it too
 install.packages("data-raw/tinytest_1.2.4.10.tar.gz")
 install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
-install.packages("covr", repos = "https://cran.rstudio.com/")
 
 pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?")))
 cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")

docs/404.html

@@ -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">1.7.1.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -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">1.7.1.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 

docs/articles/datasets.html

@@ -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">1.7.1.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 
@@ -192,7 +192,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 class="date">04 June 2021</h4>
+            <h4 class="date">05 June 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>

docs/articles/index.html

@@ -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">1.7.1.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 

docs/authors.html

@@ -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">1.7.1.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </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">1.7.1.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 

docs/news/index.html

@@ -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">1.7.1.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 
@@ -236,12 +236,12 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1719000" class="section level1">
+    <div id="amr-1719001" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.1.9000">
+<h1 class="page-header" data-toc-text="1.7.1.9001">
-<a href="#amr-1719000" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9000</h1>
+<a href="#amr-1719001" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9001</h1>
-<div id="last-updated-4-june-2021" class="section level2">
+<div id="last-updated-5-june-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-4-june-2021" class="anchor"></a><small>Last updated: 4 June 2021</small>
+<a href="#last-updated-5-june-2021" class="anchor"></a><small>Last updated: 5 June 2021</small>
 </h2>
 <div id="changed" class="section level3">
 <h3 class="hasAnchor">
@@ -260,7 +260,6 @@
 <h3 class="hasAnchor">
 <a href="#breaking-change" class="anchor"></a>Breaking change</h3>
 <ul>
-<li><p>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</p></li>
 <li>
 <p>All antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code><a href="../reference/AMR-deprecated.html">filter_carbapenems()</a></code>, <code><a href="../reference/AMR-deprecated.html">filter_aminoglycosides()</a></code>). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
@@ -286,6 +285,7 @@
 <h3 class="hasAnchor">
 <a href="#new" class="anchor"></a>New</h3>
 <ul>
+<li>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</li>
 <li>Function <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> that brings support for custom AMR rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
 </li>
 <li>Function <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to make taxonomic names within a string italic, with support for markdown and ANSI</li>

docs/pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-06-04T19:07Z
+last_built: 2021-06-05T13:10Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/AMR.html

@@ -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">1.7.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 
@@ -286,7 +286,7 @@
 <p>Matthijs S. Berends <br />
 m.s.berends [at] umcg [dot] nl <br />
 University of Groningen
-Department of Medical Microbiology and Infection Prevention
+Department of Medical Microbiology and Infection Prevention <br />
 University Medical Center Groningen <br />
 Post Office Box 30001 <br />
 9700 RB Groningen <br />

docs/reference/antibiotic_class_selectors.html

@@ -83,7 +83,7 @@
       </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">1.7.1.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 

docs/reference/custom_eucast_rules.html

@@ -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">1.7.1.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 

docs/reference/index.html

@@ -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">1.7.1.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 

docs/survey.html

@@ -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">1.7.1.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
       </span>
     </div>
 

man/AMR.Rd

@@ -50,7 +50,7 @@ For suggestions, comments or questions, please contact us at:
 Matthijs S. Berends \cr
 m.s.berends [at] umcg [dot] nl \cr
 University of Groningen
-Department of Medical Microbiology and Infection Prevention
+Department of Medical Microbiology and Infection Prevention \cr
 University Medical Center Groningen \cr
 Post Office Box 30001 \cr
 9700 RB Groningen \cr