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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

Added

  • (none)

Changed

  • (none)

Fixed

  • (none)

0.10.4 - 2026-05-31

Fixed

  • create_individual_kde() now uses the Area-Restricted Search scale (scaleARS) from First Passage Time analysis as the KDE smoothing parameter, instead of the log of the median foraging range (mag). The --smoothing-method CLI flag was never consumed by any function and has been removed from get_domain_specific_options(). Passing it now fails with "long flag is invalid".

0.10.3 - 2026-05-22

Fixed

  • render_potential_kba() no longer crashes with a GEOS TopologyException when KBA polygons produced by findSite contain self-intersections. Invalid geometries are now repaired via sf::st_make_valid before reaching track2KBA::mapSite.

0.10.2 - 2026-05-21

Fixed

  • render_potential_kba() no longer crashes with S2 geometry validation errors on polygons containing duplicate vertices.

0.10.1 - 2026-05-21

Changed

  • render_representative_assessment() output visualization now includes confidence bands (meanPred ± est_asym × sdInclude), fitted regression curve, and representativeness percentage label. Previously showed only a scatter plot of raw observations.

0.10.0 - 2026-05-20

Added

  • --trips-summary-path (-y) CLI flag for get_domain_specific_options().

Changed

  • create_individual_kde() rewritten. Output changed from GeoPackage (UDPolygons only) to RDS (KDE_surface, UDPolygons, tracks). Pipeline now uses import_trips → compute_project_returning_tracks → import_trips_summary → compute_scale_parameters → compute_individual_kde. Accepts new --trips-summary-path flag; --smoothing-method is no longer consumed.
  • create_representative_assessment() now reads an individual KDE RDS, runs repAssess, and writes an RDS with assessment_summary, assessment_detail, and KDE_surface. No longer writes CSV or datapackage.json.
  • create_potential_kba() now reads KDE_surface directly from a cached assessment RDS instead of recomputing KDE from raw data. Drops --config-path, --data-path, --smoothing-method options.
  • render_individual_kde() now reads from an RDS file (--rds-path) instead of a GeoPackage (--gpkg-path).
  • create_trips_summary() now uses import_trips(filter_returning = FALSE) internally. No change to its CLI interface.

Removed

  • create_processed_data() — its logic (compose compute_individual_kde + compute_representative_assessment) is now embedded in create_representative_assessment.

0.9.1 - 2026-05-17

Fixed

  • get_domain_specific_options() now defines --gpkg-path (-g) and --rds-path (-r) flags for render_individual_kde, render_potential_kba, render_representative_assessment, create_potential_kba, and create_representative_assessment. Previously, passing these flags via get_domain_specific_options() failed with "long flag is invalid".

0.9.0 - 2026-05-16

Added

  • create_individual_kde(options) — reads GPS data and configuration, computes individual kernel density estimates, and saves UDPolygons as a GeoPackage file.
  • create_processed_data(options) — runs the full bootstrap pipeline (individual KDE + repAssess) exactly once and caches the assessment results as an RDS file. This is the only exported function that runs the expensive bootstrap.
  • create_potential_kba(options) — reads a cached RDS file, recomputes individual KDE from raw data, identifies potential KBAs, and saves the result as a GeoPackage file. Requires a pre-computed RDS cache (from create_processed_data).
  • create_representative_assessment(options) — reads a cached RDS file and writes the full iteration data as a Tabular Data Package (CSV + datapackage.json with field schemas).

Changed

  • filter_data_between_dates() renamed to create_filtered_gps_between_dates().
  • process_fisheries_data() renamed to create_filtered_fisheries().
  • write_trips_summary() renamed to create_trips_summary().
  • write_trips() renamed to create_trips().
  • render_representative_assessment() no longer runs the R6 compute pipeline. It now takes rds-path and output-path only — reads a pre-computed cache instead of raw data.
  • render_potential_kba() no longer runs the R6 compute pipeline or calls track2KBA::mapSite. It now takes gpkg-path and output-path only — reads a pre-computed GeoPackage instead of raw data.
  • render_individual_kde() no longer runs the R6 compute pipeline or calls track2KBA::mapKDE. It now takes gpkg-path and output-path only — reads a pre-computed GeoPackage instead of raw data.

Removed

  • No exported functions were removed.

0.8.0 - 2026-05-11

Changed

  • Exported function render_potential_kba() replaces internal plot_potential_site(); internal method get_site() renamed to compute_potential_kba().
  • plot_representative_assess() renamed to render_representative_assessment(); internal method get_assessment() renamed to compute_representative_assessment().
  • plot_individual_kernels() renamed to render_individual_kde(); internal method calculate_space_use() renamed to estimate_space_use().

Removed

  • Command plot_usage_area_by_individual() no longer available.
  • Internal method get_site() removed from Track2KBA_Wrapper.

0.7.0 - 2026-01-30

Added

  • Command filter_data_between_dates() filters GPS data between two dates. The dates given are included in the output file.

0.6.0 - 2026-01-14

Added

  • New argument smoothing-method to select the method used to compute the smoothing parameter h in the following CLI commands:
    • plot_representative_assess()
    • plot_usage_area_by_individual()
    • plot_individual_kernels()

Fixed

  • Added population-size option in get_domain_specific_options().

0.5.0 - 2025-12-19

Changed

  • Function write_trips_summary() now receives a CSV file from write_trips() output. Before, we calculated the trips twice.
  • Function plot_individual_kernels() now receives a CSV file from write_trips() output. Before, we calculated the trips twice.
  • Function plot_representative_assess() now receives a CSV file from write_trips() output. Before, we calculated the trips twice.

0.4.0 - 2025-12-11

Added

  • formatDT = "ymd_HMS" in order to remove the parse date-time warning.

0.3.0 - 2025-06-25

Added

  • Command process_fisheries_data() filters raw fisheries GPS data based on date and geographic boundaries.

0.2.0 - 2025-05-28

Added

  • New command plot_usage_area_by_individual() to write a usage area map for tracked individuals.

0.1.0 - 2024-10-03