Skip to content

Add occurrence validation to run script #18

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
mdales wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Add occurrence validation to run script #18

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion requirements.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ pymer4
pyproj
scikit-image
redlistapi
yirgacheffe>=1.9
yirgacheffe>=1.10
aoh[validation]>=1.0

# GDAL should be installed manually to match the version of the library installed on your machine
Expand Down
12 changes: 12 additions & 0 deletions scripts/run.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,18 @@ aoh-collate-data --aoh_results "${DATADIR}"/aohs/current/ \
echo "Calculating model validation..."
aoh-validate-prevalence --collated_aoh_data "${DATADIR}"/validation/aohs.csv \
--output "${DATADIR}"/validation/model_validation.csv
for TAXA in "${TAXALIST[@]}"
do
echo "Fetching GBIF data for ${TAXA}..."
aoh-fetch-gbif-data --collated_aoh_data "${DATADIR}"/validation/aohs.csv \
--taxa "${TAXA}" \
--output_dir "${DATADIR}"/validation/occurrences/"${TAXA}"
echo "Validating occurrences for ${TAXA}..."
aoh-validate-occurrences --gbif_data_path "${DATADIR}"/validation/occurrences/"${TAXA}" \
--species_data "${DATADIR}"/species-info/"${TAXA}"/current/ \
--aoh_results "${DATADIR}"/aohs/current/"${TAXA}"/ \
--output "${DATADIR}"/validation/occurrences/"${TAXA}".csv
done

# Threats
echo "Generating threat task list..."
Expand Down