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islasgeci/bycatch_code

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By Conservación de Islas

•Updated 4 months ago

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islasgeci/bycatch_code repository overview

⁠bycatch — seabird bycatch risk assessment

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Assess where seabirds forage, where fishing vessels operate, and where they overlap — to prevent bycatch.

bycatch converts GPS tracking data from seabird colonies into maps of foraging areas, identifies potential key biodiversity areas (KBAs), and overlays them with fishing vessel GPS data to pinpoint high-risk overlap zones.

⁠What you need

  • Seabird GPS data (CSV with dates, positions, and individual IDs).
  • Colony location and configuration (coordinates, buffer distances, trip duration).
  • Fishing vessel GPS data (optional, for overlap analysis).

Run inside the provided Docker container — all paths use /workdir/....

⁠Quick start

# Inside the Docker container:

# 1. Cache individual KDE for a colony (fast, no bootstrap)
Rscript -e "bycatch::create_individual_kde(bycatch::get_domain_specific_options())" \
  --config-path /workdir/config.json \
  --data-path /workdir/data/trips.csv \
  --output-path /workdir/output/individual_kde.rds \
  --percentage-distribution 50 \
  --trips-summary-path /workdir/data/trips_summary.csv

# 2. Run the expensive bootstrap assessment (repAssess) once
Rscript -e "bycatch::create_representative_assessment(bycatch::get_domain_specific_options())" \
  --rds-path /workdir/output/individual_kde.rds \
  --output-path /workdir/output/assessment.rds \
  --percentage-distribution 50 \
  --n-iterations 100

# 3. Render the assessment diagnostic plot
Rscript -e "bycatch::render_representative_assessment(bycatch::get_domain_specific_options())" \
  --rds-path /workdir/output/assessment.rds \
  --output-path /workdir/output/assessment.png

# 4. Identify potential KBAs from the cached assessment
Rscript -e "bycatch::create_potential_kba(bycatch::get_domain_specific_options())" \
  --rds-path /workdir/output/assessment.rds \
  --output-path /workdir/output/kba.gpkg \
  --percentage-distribution 50 \
  --population-size 10

# 5. Render a KBA map from the pre-computed GeoPackage
Rscript -e "bycatch::render_potential_kba(bycatch::get_domain_specific_options())" \
  --gpkg-path /workdir/output/kba.gpkg \
  --output-path /workdir/output/kba.png

# 6. Render an individual KDE map from the cached RDS
Rscript -e "bycatch::render_individual_kde(bycatch::get_domain_specific_options())" \
  --rds-path /workdir/output/individual_kde.rds \
  --output-path /workdir/output/individual_kde.png

For a complete reference of all commands and parameters, see DOCS.md⁠.

⁠Outputs

FormatWhatExample
PNGStatic maps and figuresKBA map, individual KDE map
GeoPackage (.gpkg)Vector polygons for GISKBA boundaries
CSVTabular dataTrip summaries, filtered data
RDSCached computation resultsIndividual KDE cache, assessment cache

⁠Coming soon

  • Overlap analysis between seabird KBA polygons and fishing vessel tracks.
  • Multi-colony comparisons.
  • Customizable map projections.

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