From 157d1b5cc9ff5ab61a5b9cf4e5a311ed334a335f Mon Sep 17 00:00:00 2001
From: Michael Dales <mwd24@cam.ac.uk>
Date: Fri, 16 May 2025 20:15:20 +0100
Subject: [PATCH 1/3] Install R bits required for validation

---
 Dockerfile       | 7 +++++++
 requirements.txt | 1 +
 2 files changed, 8 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 1d4f490..ade1030 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -15,8 +15,11 @@ FROM ghcr.io/osgeo/gdal:ubuntu-small-3.10.0
 RUN apt-get update -qqy && \
 	apt-get install -qy \
 		git \
+		cmake \
 		python3-pip \
+		r-base \
 		libpq-dev \
+		libtirpc-dev \
 	&& rm -rf /var/lib/apt/lists/* \
 	&& rm -rf /var/cache/apt/*
 
@@ -29,6 +32,10 @@ RUN pip install gdal[numpy]==3.10.0
 COPY requirements.txt /tmp/
 RUN pip install -r /tmp/requirements.txt
 
+RUN mkdir /root/R
+ENV R_LIBS_USER=/root/R
+RUN Rscript -e 'install.packages(c("lme4","lmerTest","emmeans"), repos="https://cloud.r-project.org")'
+
 COPY ./ /root/star
 WORKDIR /root/star
 RUN chmod 755 ./scripts/run.sh
diff --git a/requirements.txt b/requirements.txt
index 8f1b0d3..7c9a8ef 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,6 +4,7 @@ geopandas
 postgis
 psycopg2
 psutil
+pymer4
 pyproj
 scikit-image
 requests

From 37aca753bd9a3d20b724da9878af51c5f08eb8df Mon Sep 17 00:00:00 2001
From: Michael Dales <mwd24@cam.ac.uk>
Date: Fri, 16 May 2025 20:23:34 +0100
Subject: [PATCH 2/3] Fix typo in run.sh that stopped threats being processed

---
 scripts/run.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/run.sh b/scripts/run.sh
index 25d5668..2ce4863 100755
--- a/scripts/run.sh
+++ b/scripts/run.sh
@@ -108,7 +108,7 @@ echo "Generating threat task list..."
 python3 ./utils/threats_generator.py --input ${DATADIR}/species-info --datadir ${DATADIR} --output ${DATADIR}/threatbatch.csv
 
 echo "Generating threat rasters..."
-littlejohn -j ${THREADS} -o ${DATADIR}/threatbatch.log -c ${DATADIR}/threatcatch.csv ${VIRTUAL_ENV}/bin/python3 -- ./threats/threat_processing.py
+littlejohn -j ${THREADS} -o ${DATADIR}/threatbatch.log -c ${DATADIR}/threatbatch.csv ${VIRTUAL_ENV}/bin/python3 -- ./threats/threat_processing.py
 
 echo "Summarising threats..."
 python3 ./threats/threat_summation.py --threat_rasters ${DATADIR}/threat_rasters --output ${DATADIR}/threat_results

From f56795c29b98f6d729d329f348fcc1b35e6b8dac Mon Sep 17 00:00:00 2001
From: Michael Dales <mwd24@cam.ac.uk>
Date: Fri, 16 May 2025 20:33:01 +0100
Subject: [PATCH 3/3] Add R to github action

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index aad935b..8fd17a0 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -22,7 +22,7 @@ jobs:
       - name: Install system
         run: |
           apt-get update -qqy
-          apt-get install -y git python3-pip libpq5 libpq-dev
+          apt-get install -y git python3-pip libpq5 libpq-dev r-base libtirpc-dev
       - uses: actions/checkout@v4
         with:
           submodules: 'true'