oystermapR 1.4.0

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

Initial CRAN release.

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.

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

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.

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.

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().

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

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.