Changes in version 1.4.0 (2026-05-15)                  

New species (9 added; 14 total)

  - crassostrea_virginica — Eastern Oyster (NW Atlantic); high data
    quality.
  - saccostrea_glomerata — Sydney Rock Oyster (E Australia); medium data
    quality.
  - magallana_sikamea — Kumamoto Oyster (Japan / Pacific NW); low data
    quality.
  - magallana_ariakensis — Suminoe Oyster (E Asia); low data quality.
  - crassostrea_hongkongensis — Hong Kong Oyster (S China Sea); high
    data quality; note on historical misidentification as C. plicatula /
    C. rivularis included in species metadata.
  - crassostrea_nippona — Iwagaki Oyster (Japan / Korea); medium data
    quality.
  - crassostrea_belcheri — Tropical Rock Oyster (SE Asia); low data
    quality.
  - ostrea_chilensis — Chilean Oyster (S Chile / New Zealand); low data
    quality.
  - ostrea_denselamellosa — Korean Flat Oyster (E Asia); low data
    quality.

New sensor readers (3 added)

  - read_nortek_aquadopp() — reads Nortek Aquadopp ASCII export (ENU or
    beam files); handles moored (fixed lat/lon) and vessel-mounted (GPS
    in file) deployments.
  - read_rdi_adcp() — reads Teledyne RDI binary PD0 files via
    oce::read.adp.rdi(); falls back to WinRiver ASCII CSV with
    VelEast_binN columns.
  - read_aanderaa_csv() — reads Aanderaa Data Studio CSV exports;
    auto-detects speed unit (cm/s vs m/s); handles "Horisontal Speed"
    column name variant.

Vignette

  - Added example-bay-survey vignette: complete eight-step pipeline
    using simulated Example Bay data (ADCP, single-beam soundings, CTD),
    covering data ingest, QC, suitability prediction, risk scoring, and
    GeoTIFF export.
  - Added three example data files to inst/extdata/:
    example_bay_adcp.csv, example_bay_soundings.xyz,
    example_bay_ctd.csv.

Citation and documentation

  - inst/REFERENCES.md expanded: added citations for all 9 new species;
    added Horn (1981) for terrain derivative methods; confirmed every
    referenced source in the package has a corresponding entry.
  - Fixed pre-existing omission of Ostrea lurida from the species table
    in the bundled user-guide PDF.

                        Changes in version 1.2.0                        

Live data integration

  - oystermapR_live_config() — stores credentials for CMEMS, ICES,
    EMODnet, and FSA in a session-scoped environment; credentials are
    never written to disk.
  - fetch_live_environmental_data() — pulls salinity, temperature,
    current speed, chlorophyll, HAB presence, and substrate from
    external APIs and merges the result onto an existing survey
    dataframe by rounded lat/lon grid keys.
  - CMEMS integration updated to copernicusmarine CLI v2.x: credentials
    via environment variables, removed --force-download /
    --output-format csv, --log-level changed to WARN; all output is
    NetCDF parsed with ncdf4.
  - Multi-candidate dataset ID fallback: NWS north-west shelf regional
    product preferred; falls back to global 0.083-degree product
    automatically.

Sensor ingest (new readers)

  - read_soundings_xyz() — reads bathymetric sounding XYZ files; derives
    slope and rugosity via terra::terrain.
  - read_sonar_tif() updated to normalise backscatter intensity to
    substrate_hardness in the range [0, 1]; reprojects to WGS84 if
    needed.

Bug fixes

  - qc_survey_data() — fixed crash when apply_flags = TRUE:
    cli::cli_inform bullet-prefix argument was incorrectly passed as a
    named function argument instead of a named element of the message
    character vector.
  - devtools::document() warnings resolved: non-ASCII characters
    replaced with \\uXXXX escapes in R source; roxygen #' lines now use
    plain ASCII to avoid unknown-macro warnings in compiled .Rd files.

                        Changes in version 1.1.0                        

Season-aware scoring and tidal correction

  - detect_season() / add_season_column() — automatic season detection
    from a datetime column; used internally by predict_oyster() to apply
    season-specific tolerance weights.
  - auto_tidal_correct() / correct_to_chart_datum() — corrects depth
    readings to chart datum using harmonic tidal prediction (nodal
    factors, UKHO-style harmonics).
  - add_intertidal_flag() — flags survey points that fall within the
    intertidal zone based on tidal range.

Habitat and risk modules

  - score_hab_risk() — HAB (Harmful Algal Bloom) risk scoring with
    optional live ICES biotoxin data integration.
  - score_anthropogenic_disturbance() — disturbance scoring
    incorporating shipping density, aquaculture lease proximity, and
    dredging history layers.
  - score_wave_exposure() / score_sediment_stability() — fetch-based
    wave exposure and Shields criterion sediment stability scoring.
  - add_shellfish_classification() — appends EU/UK shellfish harvesting
    classification zone (A/B/C/Prohibited) from spatial polygon layers.

Reporting

  - generate_summary_pdf() — produces a self-contained four-page A4 PDF
    using only grDevices::pdf() and ggplot2; no LaTeX or pandoc
    dependency.

Validation

  - validate_against_records() now returns Brier score and F1 alongside
    AUC, TSS, sensitivity, and specificity.
  - spatial_block_cv() spatial block cross-validation added.

                        Changes in version 1.0.0                        

Initial CRAN release.

Core prediction pipeline

  - predict_oyster() — AHP-weighted suitability scoring from tabular
    sensor data, with automatic column name matching, season detection,
    hard exclusion checks, and optional GeoTIFF + contour export for
    QGIS.
  - check_exclusions() / score_locations() — modular exclusion and
    scoring steps for programmatic use.
  - export_geotiff() / export_qml_style() — raster and QGIS colour-ramp
    export.

Species supported

Ostrea edulis, Magallana gigas, Crassostrea angulata, Ostrea stentina,
Ostrea lurida. See list_species().

Sensor ingest

  - read_nortek_adcp() — Nortek Signature 500 ADCP CSV parser.
  - read_sonar_tif() — Ping 3DSS / BioBase bathymetric raster reader.
  - merge_sensor_data() / ingest_sensors() — spatial merge of
    multi-sensor datasets.

Validation and diagnostics

  - validate_against_records() — AUC, TSS, Brier score, F1,
    sensitivity/specificity vs known presence/absence records.
  - spatial_block_cv() — spatial block cross-validation (Roberts et
    al. 2017).
  - permutation_importance() — variable importance by AUC drop.
  - sensitivity_analysis() — partial dependence curves.

Bayesian tolerance updating

  - update_species_tolerances() — MAP + Laplace or RWMH MCMC updating of
    optimal-range parameters from field observations.
  - get_tolerance_posteriors(), save_tolerance_update(),
    load_tolerance_update(), reset_tolerance_update().

Risk and disturbance modules

  - score_predation_risk(), score_hab_risk(),
    score_anthropogenic_disturbance(), score_wave_exposure(),
    score_sediment_stability(), add_shellfish_classification().

Larval connectivity

  - score_larval_connectivity() — hybrid union-find Gaussian kernel +
    optional OpenDrift/FVCOM connectivity matrix scoring.
  - parse_opendrift_connectivity() — converts OpenDrift CSV output to
    connectivity matrix format.

Multi-species and seasonal comparison

  - compare_species(), compare_surveys(), composite_seasonal().