Predict and Map Oyster Growth Suitability from Environmental
Data
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Documentation for package ‘oystermapR’ version 1.4.0
Help Pages
| add_intertidal_flag | Add an intertidal zone flag to a survey dataframe |
| add_season_column | Detect season for each row in a dataframe |
| add_shellfish_classification | Add shellfish water quality classification to scored result |
| add_suitability_ci | Add bootstrap confidence intervals to suitability scores |
| analyse_connectivity | Analyse spatial connectivity of suitable habitat cells |
| assess_gear_feasibility | Assess gear deployment feasibility at survey locations |
| auto_tidal_correct | Automatically predict and apply tidal correction from harmonic constituents |
| check_exclusions | Check exclusion criteria for all rows in a dataset |
| classify_substrate_from_backscatter | Classify seabed substrate hardness from near-seabed ADCP backscatter |
| compare_species | Compare suitability across multiple oyster species |
| compare_surveys | Compare suitability scores across multiple surveys or monitoring years |
| composite_seasonal | Combine multi-season survey results into a composite suitability score |
| correct_to_chart_datum | Correct survey depths to Chart Datum (LAT) |
| detect_season | Detect meteorological season from date and latitude |
| estimate_chlorophyll_from_backscatter | Estimate chlorophyll-a concentration from ADCP acoustic backscatter |
| estimate_fetch | Estimate effective fetch from a set of lat/lon points and a bearing |
| export_contours | Export optional contour lines as a GeoPackage for QGIS |
| export_geotiff | Export suitability scores as a smooth interpolated GeoTIFF heatmap for QGIS |
| export_qml_style | Export a QGIS colour style (.qml) matching the BioBase orange/red heatmap |
| fetch_live_environmental_data | Fetch live environmental data for a survey extent |
| generate_report | Generate a formatted survey report from predict_oyster() results |
| generate_summary_pdf | Generate a compact printable PDF summary of oystermapR results |
| get_species_tolerances | Get species tolerance parameters |
| get_tolerance_posteriors | Retrieve current posterior tolerance parameters for a species |
| identify_resilient_sites | Identify climate-resilient locations |
| interpolate_survey | Interpolate survey measurements to a regular grid before scoring |
| list_species | List all supported species |
| load_tolerance_update | Load saved Bayesian tolerance updates into session cache |
| merge_sensor_data | Merge multiple sensor datasets into a single survey table |
| oystermapR_help | Print an interactive getting-started guide for oystermapR |
| oystermapR_live_config | Configure live data API credentials for oystermapR |
| parse_opendrift_connectivity | Parse an OpenDrift particle tracking output into a connectivity matrix |
| permutation_importance | Permutation variable importance for suitability model |
| predict_oyster | Predict oyster growth suitability from environmental survey data |
| project_suitability | Project suitability under future climate scenarios |
| qc_survey_data | Run automated quality control on raw survey data |
| read_aanderaa_csv | Read an Aanderaa RCM current meter CSV export |
| read_generic_csv | Read a generic sensor CSV with flexible column mapping |
| read_nortek_adcp | Read and process a Nortek Signature 500 ADCP CSV file |
| read_nortek_aquadopp | Read a Nortek Aquadopp Profiler ASCII export |
| read_rdi_adcp | Read a Teledyne RDI ADCP binary file (PD0 format) |
| read_sonar_tif | Read a bathymetric or sidescan GeoTIFF and convert to oystermapR variables |
| read_soundings_xyz | Read a bathymetric XYZ point cloud and derive depth, slope and roughness |
| reset_tolerance_update | Reset Bayesian tolerance updates for a species |
| save_tolerance_update | Save Bayesian tolerance updates to disk |
| score_anthropogenic_disturbance | Score anthropogenic disturbance at survey locations |
| score_disease_risk | Score locations for disease and parasite risk |
| score_economic_viability | Score economic viability for aquaculture or restoration |
| score_hab_risk | Score harmful algal bloom risk at survey locations |
| score_larval_connectivity | Score larval dispersal connectivity at survey locations |
| score_locations | Score all locations in a dataframe |
| score_predation_risk | Score predation and bioturbation pressure at survey locations |
| score_sediment_stability | Score sediment stability and mobility at survey locations |
| score_settlement | Score locations for spat settlement suitability |
| score_wave_exposure | Score wave exposure from fetch or measured wave height |
| sensitivity_analysis | Partial dependence / sensitivity analysis for a scored variable |
| smooth_suitability | Apply Gaussian kernel smoothing to suitability scores |
| spatial_block_cv | Spatial block cross-validation for suitability model evaluation |
| stack_surveys | Stack multiple survey runs from the same sensor type |
| tidal_port_info | Look up approximate tidal range for major European survey ports |
| update_species_tolerances | Update species tolerance parameters from field observations (Bayesian) |
| validate_against_records | Validate suitability predictions against known presence/absence records |