diff --git a/.github/prehooks/commit-msg b/.github/prehooks/commit-msg
new file mode 100755
index 00000000..ad0b4422
--- /dev/null
+++ b/.github/prehooks/commit-msg
@@ -0,0 +1,62 @@
+#!/bin/bash
+
+# ==================================================================== #
+# TITLE:                                                               #
+# AMR: An R Package for Working with Antimicrobial Resistance Data     #
+#                                                                      #
+# SOURCE CODE:                                                         #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# PLEASE CITE THIS SOFTWARE AS:                                        #
+# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
+# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
+# Journal of Statistical Software, 104(3), 1-31.                       #
+# https://doi.org/10.18637/jss.v104.i03                                #
+#                                                                      #
+# Developed at the University of Groningen and the University Medical  #
+# Center Groningen in The Netherlands, in collaboration with many      #
+# colleagues from around the world, see our website.                   #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
+# ==================================================================== #
+
+# Path to the commit message file
+COMMIT_MSG_FILE="$1"
+
+# Read the original commit message
+COMMIT_MSG=$(cat "$COMMIT_MSG_FILE")
+
+# Check if commit should skip checks
+if [[ "$COMMIT_MSG" =~ no-?checks?|no-?verify ]]; then
+  echo "Not modifying commit message:"
+  echo "Commit message contains 'no-check' or 'no-verify'."
+  echo ""
+  exit 0
+fi
+
+# Read the version number from the temporary file
+if [ -f ".git/commit_version.tmp" ]; then
+  currentversion=$(cat .git/commit_version.tmp)
+  rm -f .git/commit_version.tmp
+else
+  echo "Version number file not found."
+  currentversion=""
+fi
+
+# Prepend the version number to the commit message if available
+if [ -n "$currentversion" ]; then
+  echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_FILE"
+else
+  echo "No version number to prepend to commit message."
+fi
+
+exit 0
diff --git a/.github/prehooks/pre-commit b/.github/prehooks/pre-commit
index 8eaf689f..73332421 100755
--- a/.github/prehooks/pre-commit
+++ b/.github/prehooks/pre-commit
@@ -29,10 +29,86 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-# always add these:
-git add data-raw/*
-git add man/*
-git add R/sysdata.rda
-git add NAMESPACE
+# Check if commit should skip checks
+COMMIT_MSG_FILE=".git/COMMIT_EDITMSG"
+if [ -f "$COMMIT_MSG_FILE" ]; then
+  COMMIT_MSG=$(cat "$COMMIT_MSG_FILE")
+  if [[ "$COMMIT_MSG" =~ no-?checks?|no-?verify ]]; then
+    echo "Not running prehook:"
+    echo "Commit message contains 'no-check' or 'no-verify'."
+    echo ""
+    exit 0
+  fi
+fi
+
+echo "Running prehook..."
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# Run the R script and stage the modified files
+if command -v Rscript > /dev/null; then
+  if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
+    Rscript -e "source('data-raw/_pre_commit_checks.R')"
+    currentpkg=$(Rscript -e "cat(pkgload::pkg_name())")
+    echo "- Adding changed files in ./data-raw and ./man to this commit"
+    git add data-raw/*
+    git add man/*
+    git add R/sysdata.rda
+    git add NAMESPACE
+  else
+    echo "- R package 'pkgload', 'devtools', or 'dplyr' 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//')
+
+# Assume main branch to be 'main' or 'master'
+defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
+if [ "$currenttag" = "" ]; then
+  currenttag="0.0.1"
+  currentcommit=$(git rev-list --count ${defaultbranch})
+  echo "- No git tags found, creating one in format 'v(x).(y).(z)' - currently ${currentcommit} previous commits in '${defaultbranch}'"
+else
+  currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
+  echo "- Latest tag is '${currenttagfull}', with ${currentcommit} previous commits in '${defaultbranch}'"
+fi
+
+# Combine tag and commit number
+currentversion="$currenttag.$((currentcommit + 9001))"
+echo "- ${currentpkg} pkg version set to ${currentversion}"
+
+# Update version number and date in DESCRIPTION
+sed -i -- "s/^Version: .*/Version: ${currentversion}/" DESCRIPTION
+sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
+echo "- Updated version number and date in ./DESCRIPTION"
+rm -f DESCRIPTION--
 git add DESCRIPTION
-git add NEWS.md
+
+# Update version number in NEWS.md
+if [ -e "NEWS.md" ]; then
+  if [ "$currentpkg" = "your" ]; then
+    currentpkg=""
+  fi
+  sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
+  echo "- Updated version number in ./NEWS.md"
+  rm -f NEWS.md--
+  git add NEWS.md
+else
+  echo "- No NEWS.md found!"
+fi
+echo ""
+
+# Save the version number for use in the commit-msg hook
+echo "${currentversion}" > .git/commit_version.tmp
+
+exit 0
diff --git a/.github/prehooks/prepare-commit-msg b/.github/prehooks/prepare-commit-msg
deleted file mode 100755
index 7e458886..00000000
--- a/.github/prehooks/prepare-commit-msg
+++ /dev/null
@@ -1,126 +0,0 @@
-#!/bin/bash
-
-# ==================================================================== #
-# TITLE:                                                               #
-# AMR: An R Package for Working with Antimicrobial Resistance Data     #
-#                                                                      #
-# SOURCE CODE:                                                         #
-# https://github.com/msberends/AMR                                     #
-#                                                                      #
-# PLEASE CITE THIS SOFTWARE AS:                                        #
-# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
-# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
-# Journal of Statistical Software, 104(3), 1-31.                       #
-# https://doi.org/10.18637/jss.v104.i03                                #
-#                                                                      #
-# Developed at the University of Groningen and the University Medical  #
-# Center Groningen in The Netherlands, in collaboration with many      #
-# colleagues from around the world, see our website.                   #
-#                                                                      #
-# This R package is free software; you can freely use and distribute   #
-# it for both personal and commercial purposes under the terms of the  #
-# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
-# the Free Software Foundation.                                        #
-# We created this package for both routine data analysis and academic  #
-# research and it was publicly released in the hope that it will be    #
-# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-#                                                                      #
-# Visit our website for the full manual and a complete tutorial about  #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
-# ==================================================================== #
-
-########################################
-# This script runs before every commit #
-########################################
-
-COMMIT_MSG_FILE=".git/COMMIT_EDITMSG"
-
-# Read the commit message
-if [ -f "$COMMIT_MSG_FILE" ]; then
-  COMMIT_MSG=$(cat "$COMMIT_MSG_FILE")
-else
-  echo "Commit message file not found."
-  exit 1
-fi
-
-# Check the commit message and skip checks if needed
-if [[ "$COMMIT_MSG" =~ no-?checks?|no-?verify ]]; then
-  echo "Not running prehook:"
-  echo "Commit message contains 'no-check' or 'no-verify'."
-  echo ""
-  exit 0
-fi
-
-echo "Running prehook..."
-
-# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-if command -v Rscript > /dev/null; then
-  if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
-    Rscript -e "source('data-raw/_pre_commit_checks.R')"
-    currentpkg=$(Rscript -e "cat(pkgload::pkg_name())")
-    echo "- Adding changed files in ./data-raw and ./man to this commit"
-    git add data-raw/*
-    git add man/*
-    git add R/sysdata.rda
-    git add NAMESPACE
-  else
-    echo "- R package 'pkgload', 'devtools', or 'dplyr' 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//')
-# assume main branch to be 'main' or 'master', pick the right name:
-defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
-if [ "$currenttag" = "" ]; then
-  # there is no tag, so set tag to 0.0.1 and commit index to current count
-  currenttag="0.0.1"
-  currentcommit=$(git rev-list --count ${defaultbranch})
-  echo "- no git tags found, create one in format 'v(x).(y).(z)' - curently ${currentcommit} previous commits in '${defaultbranch}'"
-else
-  # there is a tag, so base version number on that
-  currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
-  echo "- latest tag is '${currenttagfull}', with ${currentcommit} previous commits in '${defaultbranch}'"
-fi
-# 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
-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: $(date '+%Y-%m-%d')/" DESCRIPTION
-echo "- updated version number and date in ./DESCRIPTION"
-# remove leftover on macOS
-rm -f DESCRIPTION--
-# add to commit
-git add DESCRIPTION
-
-# set version number to NEWS file
-if [ -e "NEWS.md" ]; then
-  if [ "$currentpkg" = "your" ]; then
-    currentpkg=""
-  fi
-  sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
-  echo "- updated version number in ./NEWS.md"
-  # remove leftover on macOS
-  rm -f NEWS.md--
-  # add to commit
-  git add NEWS.md
-else
-  echo "- no NEWS.md found!"
-fi
-echo ""
-
-# Prepend the version number to the commit message
-echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_FILE"