.github/prehooks/pre-commit

@@ -5,7 +5,7 @@ echo "Running pre-commit hook..."
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 echo ">>  Updating R documentation..."
 if command -v Rscript > /dev/null; then
-  if "$(Rscript -e 'cat(all(c('"'roxygen2'"', '"'pkgload'"') %in% rownames(installed.packages())))')" == "TRUE"; then
+  if [ "$(Rscript -e 'cat(all(c('"'roxygen2'"', '"'pkgload'"') %in% rownames(installed.packages())))')" == "TRUE" ]; then
     Rscript -e "suppressMessages(roxygen2::roxygenise())"
     currentpkg=`Rscript -e "cat(pkgload::pkg_name())"`
     git add man/*
@@ -53,7 +53,7 @@ sed -i -- "s/^Version: .*/Version: ${currentversion}/" DESCRIPTION
 sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
 echo ">>  - updated DESCRIPTION"
 # remove leftover on macOS
-rm -f DESCRIPTION--
+rm DESCRIPTION--
 # add to commit
 git add DESCRIPTION
 
@@ -62,7 +62,7 @@ if [ -e "NEWS.md" ]; then
   sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
   echo ">>  - updated NEWS.md"
   # remove leftover on macOS
-  rm -f NEWS.md--
+  rm NEWS.md--
   # add to commit
   git add NEWS.md
 else

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.1.9026
+Version: 1.8.1.9021
-Date: 2022-08-25
+Date: 2022-08-21
 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

@@ -1,4 +1,4 @@
-# your 1.8.1.9026
+# AMR 1.8.1.9021
 
 ### New
 * EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.

_pkgdown.yml

@@ -32,7 +32,7 @@ template:
   assets: "pkgdown/logos" # use logos in this folder
   bslib:
     code_font: {google: "Fira Code"}
-    # body-text-align: "justify"
+    body-text-align: "justify"
     line-height-base: 1.75
     # the green "success" colour of this bootstrap theme should be the same as the green in our logo
     success: "#128f76"
@@ -47,9 +47,9 @@ template:
 news:
   one_page: true
   cran_dates: true
-
+  
 footer:
-  structure:
+  structure: 
     left: [devtext]
     right: [logo]
   components:
@@ -99,9 +99,9 @@ navbar:
       - text: "Get properties of an antibiotic"
         icon: "fa-capsules"
         href: "reference/ab_property.html" # reference instead of an article
-      # - text: "Other: benchmarks"
+      - text: "Other: benchmarks"
-      #   icon: "fa-shipping-fast"
+        icon: "fa-shipping-fast"
-      #   href: "articles/benchmarks.html"
+        href: "articles/benchmarks.html"
     - text: "Manual"
       icon: "fa-book-open"
       href: "reference/index.html"
@@ -128,7 +128,7 @@ reference:
     - "`as.mo`"
     - "`mo_property`"
     - "`mo_source`"
-
+    
   - title: "Preparing data: antibiotics"
     desc: >
       Use these functions to get valid properties of antibiotics from any input or to clean your input.
@@ -138,7 +138,7 @@ reference:
     - "`ab_property`"
     - "`ab_from_text`"
     - "`atc_online_property`"
-
+    
   - title: "Preparing data: antimicrobial resistance"
     desc: >
       With `as.mic()` and `as.disk()` you can transform your raw input to valid MIC or disk diffusion values.
@@ -150,7 +150,7 @@ reference:
     - "`as.disk`"
     - "`eucast_rules`"
     - "`custom_eucast_rules`"
-
+    
   - title: "Analysing data: antimicrobial resistance"
     desc: >
       Use these function for the analysis part. You can use `susceptibility()` or `resistance()` on any antibiotic column.
@@ -190,7 +190,7 @@ reference:
     - "`example_isolates_unclean`"
     - "`rsi_translation`"
     - "`WHONET`"
-
+    
   - title: "Other: miscellaneous functions"
     desc: >
       These functions are mostly for internal use, but some of
@@ -208,7 +208,7 @@ reference:
     - "`mo_matching_score`"
     - "`pca`"
     - "`random`"
-
+  
   - title: "Other: statistical tests"
     desc: >
       Some statistical tests or methods are not part of base R and were added to this package for convenience.
@@ -224,3 +224,4 @@ reference:
       in a future version.
     contents:
     - "`AMR-deprecated`"
+