Package: oystermapR 1.0.0

oystermapR: Predict and Map Oyster Growth Suitability from Environmental Data

Predicts spatial suitability for oyster growth from environmental survey data using Analytic Hierarchy Process (AHP) weighted scoring. Users supply sensor data (ADCP, CTD, bathymetric sonar, sidescan), specify a target species, and receive per-location suitability scores, a GeoTIFF heatmap for QGIS, contour lines, and a formatted PDF or HTML report. Supported species: Ostrea edulis (European Flat Oyster), Magallana gigas (Pacific Oyster), Crassostrea angulata (Portuguese Oyster), Ostrea stentina (Denticulate Flat Oyster), and Ostrea lurida (Olympia Oyster). Includes season-aware scoring, tidal height correction, Bayesian tolerance parameter updating from field observations, spatial block cross-validation (Roberts et al. 2017), permutation variable importance, wave exposure and sediment stability modules, HAB risk and anthropogenic disturbance scoring with optional live ICES data integration, hybrid larval dispersal connectivity scoring (union-find Gaussian kernel plus optional OpenDrift/FVCOM connectivity matrix), and batch multi-species comparison.

Authors:T Tucker [aut, cre]

oystermapR_1.0.0.tar.gz
oystermapR_1.0.0.zip(r-4.7)oystermapR_1.0.0.zip(r-4.6)oystermapR_1.0.0.zip(r-4.5)
oystermapR_1.0.0.tgz(r-4.6-any)oystermapR_1.0.0.tgz(r-4.5-any)
oystermapR_1.0.0.tar.gz(r-4.7-any)oystermapR_1.0.0.tar.gz(r-4.6-any)
oystermapR_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
oystermapR/json (API)
NEWS

# Install 'oystermapR' in R:
install.packages('oystermapR', repos = c('https://trissyboats.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/trissyboats/oystermapr/issues

On CRAN:

Conda:

2.70 score 9 scripts 58 exports 28 dependencies

Last updated from:2e26744637. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE156
source / vignettesOK231
linux-release-x86_64NOTE150
macos-release-arm64NOTE164
macos-oldrel-arm64NOTE158
windows-develNOTE120
windows-releaseNOTE109
windows-oldrelNOTE114
wasm-releaseOK156

Exports:add_intertidal_flagadd_season_columnadd_shellfish_classificationadd_suitability_cianalyse_connectivityassess_gear_feasibilityauto_tidal_correctcheck_exclusionsclassify_substrate_from_backscattercompare_speciescompare_surveyscomposite_seasonalcorrect_to_chart_datumdetect_seasonestimate_chlorophyll_from_backscatterestimate_fetchexport_contoursexport_geotiffexport_qml_stylefetch_live_environmental_datagenerate_reportget_species_tolerancesget_tolerance_posteriorsidentify_resilient_sitesinterpolate_surveylist_speciesload_tolerance_updatemerge_sensor_dataoystermapR_helpoystermapR_live_configparse_opendrift_connectivitypermutation_importancepredict_oysterproject_suitabilityqc_survey_dataread_generic_csvread_nortek_adcpread_sonar_tifread_soundings_xyzreset_tolerance_updatesave_tolerance_updatescore_anthropogenic_disturbancescore_disease_riskscore_economic_viabilityscore_hab_riskscore_larval_connectivityscore_locationsscore_predation_riskscore_sediment_stabilityscore_settlementscore_wave_exposuresensitivity_analysissmooth_suitabilityspatial_block_cvstack_surveystidal_port_infoupdate_species_tolerancesvalidate_against_records

Dependencies:classclassIntcliDBIdplyre1071genericsglueKernSmoothlifecyclemagrittrMASSpillarpkgconfigproxyR6Rcpprlangs2sfterratibbletidyselectunitsutf8vctrswithrwk

Readme and manuals

Help Manual

Help pageTopics
Add an intertidal zone flag to a survey dataframeadd_intertidal_flag
Detect season for each row in a dataframeadd_season_column
Add shellfish water quality classification to scored resultadd_shellfish_classification
Add bootstrap confidence intervals to suitability scoresadd_suitability_ci
Analyse spatial connectivity of suitable habitat cellsanalyse_connectivity
Assess gear deployment feasibility at survey locationsassess_gear_feasibility
Automatically predict and apply tidal correction from harmonic constituentsauto_tidal_correct
Check exclusion criteria for all rows in a datasetcheck_exclusions
Classify seabed substrate hardness from near-seabed ADCP backscatterclassify_substrate_from_backscatter
Compare suitability across multiple oyster speciescompare_species
Compare suitability scores across multiple surveys or monitoring yearscompare_surveys
Combine multi-season survey results into a composite suitability scorecomposite_seasonal
Correct survey depths to Chart Datum (LAT)correct_to_chart_datum
Detect meteorological season from date and latitudedetect_season
Estimate chlorophyll-a concentration from ADCP acoustic backscatterestimate_chlorophyll_from_backscatter
Estimate effective fetch from a set of lat/lon points and a bearingestimate_fetch
Export optional contour lines as a GeoPackage for QGISexport_contours
Export suitability scores as a smooth interpolated GeoTIFF heatmap for QGISexport_geotiff
Export a QGIS colour style (.qml) matching the BioBase orange/red heatmapexport_qml_style
Fetch live environmental data for a survey extentfetch_live_environmental_data
Generate a formatted survey report from predict_oyster() resultsgenerate_report
Get species tolerance parametersget_species_tolerances
Retrieve current posterior tolerance parameters for a speciesget_tolerance_posteriors
Identify climate-resilient locationsidentify_resilient_sites
Interpolate survey measurements to a regular grid before scoringinterpolate_survey
List all supported specieslist_species
Load saved Bayesian tolerance updates into session cacheload_tolerance_update
Merge multiple sensor datasets into a single survey tablemerge_sensor_data
Print an interactive getting-started guide for oystermapRoystermapR_help
Configure live data API credentials for oystermapRoystermapR_live_config
Parse an OpenDrift particle tracking output into a connectivity matrixparse_opendrift_connectivity
Permutation variable importance for suitability modelpermutation_importance
Predict oyster growth suitability from environmental survey datapredict_oyster
Project suitability under future climate scenariosproject_suitability
Run automated quality control on raw survey dataqc_survey_data
Read a generic sensor CSV with flexible column mappingread_generic_csv
Read and process a Nortek Signature 500 ADCP CSV fileread_nortek_adcp
Read a bathymetric or sidescan GeoTIFF and convert to oystermapR variablesread_sonar_tif
Read a bathymetric XYZ point cloud and derive depth, slope and roughnessread_soundings_xyz
Reset Bayesian tolerance updates for a speciesreset_tolerance_update
Save Bayesian tolerance updates to disksave_tolerance_update
Score anthropogenic disturbance at survey locationsscore_anthropogenic_disturbance
Score locations for disease and parasite riskscore_disease_risk
Score economic viability for aquaculture or restorationscore_economic_viability
Score harmful algal bloom risk at survey locationsscore_hab_risk
Score larval dispersal connectivity at survey locationsscore_larval_connectivity
Score all locations in a dataframescore_locations
Score predation and bioturbation pressure at survey locationsscore_predation_risk
Score sediment stability and mobility at survey locationsscore_sediment_stability
Score locations for spat settlement suitabilityscore_settlement
Score wave exposure from fetch or measured wave heightscore_wave_exposure
Partial dependence / sensitivity analysis for a scored variablesensitivity_analysis
Apply Gaussian kernel smoothing to suitability scoressmooth_suitability
Spatial block cross-validation for suitability model evaluationspatial_block_cv
Stack multiple survey runs from the same sensor typestack_surveys
Look up approximate tidal range for major European survey portstidal_port_info
Update species tolerance parameters from field observations (Bayesian)update_species_tolerances
Validate suitability predictions against known presence/absence recordsvalidate_against_records