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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().These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.