Package index • coasts

The Automated Pipeline

Functions that drive the bi-daily GitHub Actions workflow.

ingest_assets(): Ingest Fisheries Asset Metadata
enrich_taxa(): Enrich Taxa with FishBase and SeaLifeBase Biological Data
ingest_pds_trips(): Ingest Pelagic Data Systems (PDS) Trip Data
merge_survey_trips(): Merge GPS Trips with Survey Data
ingest_pds_tracks(): Ingest Pelagic Data Systems (PDS) Track Data
preprocess_pds_tracks(): Preprocess Pelagic Data Systems (PDS) Track Data
predict_pds_tracks(): Predict Fishing Activity from PDS Tracks
aggregate_pds_effort(): Aggregate Predicted Fishing Tracks into an H3 Effort Grid
model_cpue(): Run the Full Spatial CPUE Pipeline

Data Export & Web Readiness

Preparing the analyzed data for the Peskas portal and web maps.

export_geos(): Export Geospatial Data and Regional Metrics to MongoDB
export_fishers_stats(): Export Fisher Performance Statistics to MongoDB
export_portal(): Export Summary Data to MongoDB
export_pds_spatial(): Export Spatial Pipeline Outputs as Web-Ready JSON / GeoJSON

Spatial Utilities

Under-the-hood tools for gridding, mapping, and metric conversion.

assign_h3_indices(): Assign H3 Hexagon Indices to GPS Points
aggregate_h3_effort(): Aggregate Fishing Effort by H3 Hexagon
rollup_h3_resolution(): Roll Up H3 Fishing Effort to a Coarser Resolution
create_spatial_grid(): Convert an H3 Effort Summary to a Spatial Grid
derive_fishing_grounds(): Derive Fishing Ground Polygons from an H3 Effort Grid

Survey & Fleet Analysis

Functions for survey summarization and fleet activity estimation.

calculate_catch_record_usage(): Calculate catch record usage by week
calculate_district_totals(): Calculate District-Level Total Catch and Revenue
calculate_fishery_metrics(): Calculate Fishery Metrics
calculate_monthly_trip_stats(): Calculate Monthly Trip Statistics by District
estimate_fleet_activity(): Estimate Fleet-Wide Activity from Sample Data
summarize_data(): Summarize WorldFish Survey Data
generate_fleet_analysis(): Generate Complete Fleet Activity Analysis Pipeline
prepare_boat_registry(): Prepare Boat Registry Data from Metadata
process_trip_data(): Process Trip Data with District Information
create_usage_heatmap(): Create usage heatmap plot
create_usage_table(): Create interactive reactable

API & Data Ingestion (PDS & Airtable)

Functions interacting with Pelagic Data Systems, Airtable, and KoboToolbox.

airtable_to_df(): Get All Records from Airtable with Pagination
bulk_update_airtable(): Bulk Update Multiple Airtable Records
device_sync(): Sync Data with Airtable (Update + Create)
df_to_airtable(): Create New Airtable Records
update_airtable_record(): Update Single Airtable Record
get_writable_fields(): Get Writable Fields from Airtable Table
pelagic_auth(): Authenticate with Pelagic Analytics API
pelagic_refresh_token(): Refresh Authentication Token
get_pelagic_boats(): Get Boats from Pelagic Analytics API (with server-side filtering)
get_pelagic_devices(): Get Devices from Pelagic Analytics API (with server-side filtering)
ingest_pelagic_boats(): Ingest Pelagic Boats Data and Sync to Airtable
sync_device_users(): Sync Device Users to MongoDB and Update Airtable
get_trips(): Retrieve Trip Details from Pelagic Data API
get_trip_points(): Get Trip Points from Pelagic Data Systems API

Other Utilities and Internals

Additional exported helper functions.

add_version(): Add timestamp and sha string to a file name
aggregate_daily_effort(): Aggregate GPS Points to a Reference Grid
aggregate_h3_effort(): Aggregate Fishing Effort by H3 Hexagon
aggregate_pds_effort(): Aggregate Predicted Fishing Tracks into an H3 Effort Grid
airtable_to_df(): Get All Records from Airtable with Pagination
assign_h3_indices(): Assign H3 Hexagon Indices to GPS Points
backup_tracks(): Backup Pelagic Tracks (Fallback)
bulk_update_airtable(): Bulk Update Multiple Airtable Records
calculate_catch_record_usage(): Calculate catch record usage by week
calculate_district_totals(): Calculate District-Level Total Catch and Revenue
calculate_fishery_metrics(): Calculate Fishery Metrics
calculate_monthly_trip_stats(): Calculate Monthly Trip Statistics by District
cloud_storage_authenticate(): Authenticate to a Cloud Storage Provider
create_reference_grid(): Create a Deterministic Reference Grid
create_spatial_grid(): Convert an H3 Effort Summary to a Spatial Grid
create_usage_heatmap(): Create usage heatmap plot
create_usage_table(): Create interactive reactable
derive_fishing_grounds(): Derive Fishing Ground Polygons from an H3 Effort Grid
device_sync(): Sync Data with Airtable (Update + Create)
df_to_airtable(): Create New Airtable Records
download_cloud_file(): Download File from Cloud Storage
download_parquet_from_cloud(): Download Parquet File from Cloud Storage
enrich_taxa(): Enrich Taxa with FishBase and SeaLifeBase Biological Data
estimate_fleet_activity(): Estimate Fleet-Wide Activity from Sample Data
expand_taxonomic_info(): Expand Taxa to FishBase / SeaLifeBase Species Matches
export_fishers_stats(): Export Fisher Performance Statistics to MongoDB
export_frame_data(): Export Fishing Frame Gear Composition as Web-Ready JSON
export_geos(): Export Geospatial Data and Regional Metrics to MongoDB
export_pds_spatial(): Export Spatial Pipeline Outputs as Web-Ready JSON / GeoJSON
export_portal(): Export Summary Data to MongoDB
fetch_asset(): Fetch and Filter Asset Data from Airtable
fetch_assets(): Fetch Multiple Asset Tables from Airtable
generate_app_usage_report(): Generate complete app usage report
generate_fleet_analysis(): Generate Complete Fleet Activity Analysis Pipeline
generate_track_summaries(): Generate Grid Summaries for Track Data
get_fisher_summaries(): Aggregate Fisher Catch Events by Trip
get_kobo_data(): Retrieve Data from Kobotoolbox API
get_pelagic_boats(): Get Boats from Pelagic Analytics API (with server-side filtering)
get_pelagic_devices(): Get Devices from Pelagic Analytics API (with server-side filtering)
get_trip_points(): Get Trip Points from Pelagic Data Systems API
get_trips(): Retrieve Trip Details from Pelagic Data API
get_writable_fields(): Get Writable Fields from Airtable Table
ingest_assets(): Ingest Fisheries Asset Metadata
ingest_pds_tracks(): Ingest Pelagic Data Systems (PDS) Track Data
ingest_pds_trips(): Ingest Pelagic Data Systems (PDS) Trip Data
ingest_pelagic_boats(): Ingest Pelagic Boats Data and Sync to Airtable
mdb_collection_pull(): Retrieve Data from MongoDB
mdb_collection_push(): Push Data to MongoDB Collection
merge_survey_trips(): Merge GPS Trips with Survey Data
model_cpue(): Run the Full Spatial CPUE Pipeline
pelagic_auth(): Authenticate with Pelagic Analytics API
pelagic_refresh_token(): Refresh Authentication Token
plot_cpue_map(): Create an Interactive Leaflet Map of Spatial CPUE by Species
plot_effort_map(): Create an Interactive Leaflet Map of Fishing Effort by Year
predict_pds_tracks(): Predict Fishing Activity from PDS Tracks
prep_fishing_points(): Project Fishing GPS Points to a Metric CRS
prepare_boat_registry(): Prepare Boat Registry Data from Metadata
prepare_usage_summary(): Prepare usage summary table
preprocess_pds_tracks(): Preprocess Pelagic Data Systems (PDS) Track Data
preprocess_track_data(): Preprocess Track Data into Spatial Grid Summary
process_trip_data(): Process Trip Data with District Information
pull_catch_events(): Pull catch events data from MongoDB
pull_users_data(): Pull users data from MongoDB
read_config(): Read configuration file
rollup_h3_resolution(): Roll Up H3 Fishing Effort to a Coarser Resolution
summarize_data(): Summarize WorldFish Survey Data
sync_device_users(): Sync Device Users to MongoDB and Update Airtable
update_airtable_record(): Update Single Airtable Record
upload_cloud_file(): Upload File to Cloud Storage
upload_parquet_to_cloud(): Upload Data as Parquet File to Cloud Storage