workflow.md

Create Africa map

Instruction for downloading spatial data and creating our customised Africa map (with regions and marine areas) are found in $SCRIPTDIR/inc/bash/Data-download.sh

Then we run this script to summarise the locations of strategic assessments and areas of systematic assessments.

Rscript --vanilla $SCRIPTDIR/inc/R/prepare-spatial-data.R

upload to cloud repository

We will upload these spatial files to google drive:

Rscript --vanilla $SCRIPTDIR/inc/R/google-drive-upload.R

Create map figure for Manuscript

Rscript --vanilla $SCRIPTDIR/inc/R/Africa-map.R

Calculate EFG areas

source env/project-env.sh
mkdir -p $SCRIPTDIR/Data/area-calc
Rscript --vanilla $SCRIPTDIR/inc/R/zenodo-download.R

source $HOME/venv/gis/bin/activate
cd $SCRIPTDIR/Data/area-calc
tar -xjvf all-maps-raster-geotiff.tar.bz2
cp $SCRIPTDIR/Data/Africa.gpkg $SCRIPTDIR/Data/area-calc
mkdir -p $SCRIPTDIR/Data/area-calc/tmpdir
mkdir -p $SCRIPTDIR/Data/area-calc/areas-per-country
python $SCRIPTDIR/inc/python/calculate-hist.py
rm *tif.aux.xml
rm *tif
rm -r tmpdir 

upload to cloud repository

We will test upload to google drive:

Rscript --vanilla $SCRIPTDIR/inc/R/google-drive-upload.R

Create plots for Manuscript

Rscript --vanilla $SCRIPTDIR/inc/R/EFG-plot.R

Summarise data for table

This code needs some fixes:

Rscript --vanilla $SCRIPTDIR/inc/R/List-RLE-assessments.R