set up Git LFS for large files

.gitattributes

@@ -0,0 +1,6 @@
+*.dta filter=lfs diff=lfs merge=lfs -text
+*.sas filter=lfs diff=lfs merge=lfs -text
+*.sav filter=lfs diff=lfs merge=lfs -text
+data-raw/*.dta filter=lfs diff=lfs merge=lfs -text
+data-raw/*.sas filter=lfs diff=lfs merge=lfs -text
+data-raw/*.sav filter=lfs diff=lfs merge=lfs -text

.github/prehooks/post-checkout

@@ -0,0 +1,3 @@
+#!/bin/sh
+command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting .git/hooks/post-checkout.\n"; exit 2; }
+git lfs post-checkout "$@"

.github/prehooks/post-commit

@@ -0,0 +1,3 @@
+#!/bin/sh
+command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting .git/hooks/post-commit.\n"; exit 2; }
+git lfs post-commit "$@"

.github/prehooks/post-merge

@@ -0,0 +1,3 @@
+#!/bin/sh
+command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting .git/hooks/post-merge.\n"; exit 2; }
+git lfs post-merge "$@"

.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/*
@@ -59,6 +59,9 @@ git add DESCRIPTION
 
 # set version number to NEWS file
 if [ -e "NEWS.md" ]; then
+  if [ "$currentpkg" = "your" ]; then
+    currentpkg=""
+  fi
   sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
   echo ">>  - updated NEWS.md"
   # remove leftover on macOS

.github/prehooks/pre-commit.save

@@ -0,0 +1,71 @@
+#!/bin/sh
+
+echo "Running pre-commit hook..."
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+echo ">>  Updating R documentation..."
+if command -v Rscript > /dev/null; then
+  if [ "$(Rscript -e 'cat(all(c('"'roxygen2'"', '"'pkgload'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
+    Rscript -e "suppressMessages(roxygen2::roxygenise())"
+    currentpkg=`Rscript -e "cat(pkgload::pkg_name())"`
+    git add man/*
+    echo ">>  done."
+  else
+    echo ">>  R packages 'roxygen2' and 'pkgload' are not installed!"
+    currentpkg="your"
+  fi
+else
+  echo ">>  R is not available on your system!"
+  currentpkg="your"
+fi
+echo ">>  "
+
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+echo ">>  Updating semantic versioning and date..."
+
+# get tags from remote, and remove tags not on remote:
+git fetch origin --prune --prune-tags --quiet
+currenttagfull=`git describe --tags --abbrev=0`
+currenttag=`git describe --tags --abbrev=0 | sed 's/v//'`
+if [ "$currenttag" = "" ]; then
+  # there is no tag, so set tag to 0.0.1 and commit index to current count
+  echo ">>  - no git tags found, create some using v(x).(y).(z)"
+  currenttag="0.0.1"
+  currentcommit=`git rev-list --count HEAD`
+else
+  # there is a tag, so base version number on that
+  currentcommit=`git rev-list --count ${currenttagfull}..HEAD`
+  if (( "$currentcommit" == 0 )); then
+    # tag is new, so this must become the version number
+    currentversion="$currenttag"
+  fi
+  echo ">>  - latest tag is '${currenttagfull}', with ${currentcommit} previous commits"
+fi
+if [ "$currentversion" = "" ]; then
+  # combine tag (e.g. 1.2.3) and commit number (like 5) increased by 9000 to indicate beta version
+  currentversion="$currenttag.$((currentcommit + 9001))" # results in e.g. 1.2.3.9005
+fi
+echo ">>  - ${currentpkg} pkg version set to ${currentversion}"
+
+# set version number and date to DESCRIPTION file
+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--
+# add to commit
+git add DESCRIPTION
+
+# set version number to NEWS file
+if [ -e "NEWS.md" ]; then
+  sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
+  echo ">>  - updated NEWS.md"
+  # remove leftover on macOS
+  rm -f NEWS.md--
+  # add to commit
+  git add NEWS.md
+else
+  echo ">>  - no NEWS.md found!"
+fi
+echo ">>  "

.github/prehooks/pre-push

@@ -0,0 +1,3 @@
+#!/bin/sh
+command -v git-lfs >/dev/null 2>&1 || { echo >&2 "\nThis repository is configured for Git LFS but 'git-lfs' was not found on your path. If you no longer wish to use Git LFS, remove this hook by deleting .git/hooks/pre-push.\n"; exit 2; }
+git lfs pre-push "$@"

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.1.9026
-Date: 2022-08-25
+Version: 1.8.1.9027
+Date: 2022-08-26
 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 1.8.1.9027
 
 ### 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.

vignettes/datasets.Rmd

@@ -25,7 +25,7 @@ knitr::opts_chunk$set(
 library(AMR)
 library(dplyr)
 
-options(knitr.kable.NA = '')
+options(knitr.kable.NA = "")
 
 structure_txt <- function(dataset) {
   paste0("A data set with ",
@@ -94,8 +94,6 @@ All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCA
 
 On this page, we explain how to download them and how the structure of the data sets look like. 
 
-<p class="dataset-within-r">If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.</p>
-
 ## Microorganisms (currently accepted names)
 
 `r structure_txt(microorganisms)`
@@ -104,8 +102,6 @@ This data set is in R available as `microorganisms`, after you load the `AMR` pa
 
 `r download_txt("microorganisms")`
 
-**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.** Advice? Use R instead.
-
 ### Source
 
 Our full taxonomy of microorganisms is based on the authoritative and comprehensive: