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.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.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.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.--force-download / --output-format csv,
--log-level changed to WARN; all output is NetCDF parsed with ncdf4.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.compare_species(), compare_surveys(), composite_seasonal().