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().
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