oystermapR 1.5.0

Ocean acidification scoring (pH + aragonite saturation)

• pH scoring added to all 17 species tolerance profiles with species-specific thresholds. Ostrea edulis (most sensitive): optimal 7.9–8.3; poor below 7.6. Cupped/Pacific species slightly more tolerant; brackish C. iredalei lowest thresholds.
• calculate_aragonite() — new exported function. Computes aragonite saturation state (Ω_arag) from pH, total alkalinity, temperature, and salinity with no external package dependencies. Uses Lueker et al. (2000) K1/K2, Dickson (1990) KB, Millero (1995) KW, Mucci (1983) Ksp_arag, Uppstrom (1974) [B_T], Riley & Tongudai (1967) [Ca²⁺]. Validated: T=12 °C, S=35, pH=8.1, TA=2300 µmol/kg → Ω≈2.54.
• Aragonite auto-calculation: if ph and alkalinity columns are present in the survey data, predict_oyster() automatically computes omega_aragonite before scoring — no preprocessing step required.
• Omega_aragonite scoring added to all 17 species tolerance profiles.
• Sample data updated: inst/extdata/sample_survey.csv and inst/extdata/example_bay_ctd.csv now include ph and alkalinity columns with realistic values for their respective locations.

Visualisation and spatial tools

• plot_tolerance(species, variable) — new exported function. Draws the suitability scoring curve for any species/variable combination directly from the tolerance specification, no dataset required. Colour-coded zone backgrounds (green = optimal, orange = poor/acceptable, red = excluded). For seasonal variables (temperature), pass season = "all" to overlay all four curves. Falls back to base R plot() if ggplot2 is not installed.

• area_summary(result) — new exported function. Converts point-based suitability output to fine-scale area estimates in m² (primary unit) and ha (secondary). Designed for restoration ecology and science where sub-hectare precision matters. Key features:

  • Auto-estimates survey cell size from median nearest-neighbour spacing; accepts explicit cell_size_m for known grids (ROV, AUV, ADCP tracklines).
  • Per-class breakdown: n_points, area m², area ha, % of total, % of suitable area, mean and median suitability.
  • Totals: surveyed area, suitable (High + Moderate) area, % suitable.
  • Contiguous patch analysis (terra::patches()) identifies individual High/Moderate habitat patches by size, with a viable flag against a configurable minimum area threshold (default 100 m² = 0.01 ha, aligned with OSPAR oyster reef restoration guidance). Largest/smallest/median patch size printed to console.
  • Cell size cap at 500 m prevents inflated estimates from sparse transect spacing on large offshore surveys.

• Note: compare_species() and sensitivity_analysis() were already implemented in batch_compare.R and variable_importance.R respectively.

Variable impact diagnostic (variable_impact())

• variable_impact(result, species) — new exported function. Returns a ranked summary table showing for each environmental variable: species importance rank, normalised weight (%), mean score across non-excluded points, net weighted contribution to the suitability score, and data coverage (% of points with data). Sort by "mean_contribution" (default, highest-impact variables first), "mean_score" (lowest-scoring = likely bottlenecks), or "pct_coverage" (sparsest data layers). Primary diagnostic for QA and survey planning.

Tolerance improvements (all 17 species)

• Dissolved oxygen added to scored for all 17 species (rank 5). DO was previously only used as a hard exclusion threshold. Sites are now credited for better oxygen conditions within the acceptable range — a site at 9 mg/L scores higher than one at 5 mg/L. Species-specific optimal ranges applied (e.g. O. edulis 6–10 mg/L; C. iredalei 4–8 mg/L).
• Salinity added to scored for 6 species that lacked it (ostrea_edulis, magallana_gigas, crassostrea_angulata, ostrea_stentina, ostrea_lurida, ostrea_angasi). Salinity was exclusion-only for these species; sites at optimal salinity now score higher than sites at merely acceptable salinity.
• dissolved_oxygen and salinity added to col_aliases — these variables are now recognised from standard column names (e.g. do, do_mgl, sal, salinity_psu) and properly matched to the scored entries.
• O. edulis depth optimal_min corrected from 0 m to 2 m with poor_min = 0. O. edulis is a subtidal species; intertidal sites (0–2 m) now score in the “poor” rather than “optimal” zone, consistent with published habitat assessments (Pogoda et al. 2023).

Data completeness overlay

• n_layers_scored — new integer output column from predict_oyster(). Counts the number of environmental variables that contributed to the suitability score at each location. Use alongside data_completeness (fraction) to identify points where the score rests on few data inputs.
• GeoTIFF band 5: export_geotiff() now writes n_layers_scored as a fifth raster band. Load it as a thematic overlay in QGIS to visualise data coverage spatially alongside the suitability heatmap.

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.

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.

oystermapR 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.

oystermapR 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.

oystermapR 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().