R: Predict and Map Oyster Growth Suitability from Environmental Data

# Predict and Map Oyster Growth Suitability from Environmental Data

## Documentation for package ‘oystermapR’ version 1.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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
area_summary | Fine-scale habitat area summary for restoration and science
assess_gear_feasibility | Assess gear deployment feasibility at survey locations
auto_tidal_correct | Automatically predict and apply tidal correction from harmonic constituents
calculate_aragonite | Calculate aragonite saturation state from seawater carbonate chemistry
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
plot_tolerance | Plot the tolerance scoring curve for a species and variable
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
variable_impact | Summarise variable-level impact on suitability scores