{ "_id": "6a1f1f80b401979e7342018d", "Package": "oystermapR", "Title": "Predict and Map Oyster Growth Suitability from Environmental\nData", "Version": "1.0.0", "Authors@R": "person(\"T\", \"Tucker\", email = \"tristantucker48@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"\"))", "Description": "Predicts spatial suitability for oyster growth from\nenvironmental survey data using Analytic Hierarchy Process\n(AHP) weighted scoring. Users supply sensor data (ADCP, CTD,\nbathymetric sonar, sidescan), specify a target species, and\nreceive per-location suitability scores, a GeoTIFF heatmap for\nQGIS, contour lines, and a formatted PDF or HTML report.\nSupported species: Ostrea edulis (European Flat Oyster),\nMagallana gigas (Pacific Oyster), Crassostrea angulata\n(Portuguese Oyster), Ostrea stentina (Denticulate Flat Oyster),\nand Ostrea lurida (Olympia Oyster). Includes season-aware\nscoring, tidal height correction, Bayesian tolerance parameter\nupdating from field observations, spatial block\ncross-validation (Roberts et al. 2017), permutation variable\nimportance, wave exposure and sediment stability modules, HAB\nrisk and anthropogenic disturbance scoring with optional live\nICES data integration, hybrid larval dispersal connectivity\nscoring (union-find Gaussian kernel plus optional\nOpenDrift/FVCOM connectivity matrix), and batch multi-species\ncomparison.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev", "Repository": "https://trissyboats.r-universe.dev", "Date/Publication": "2026-05-01 11:15:13 UTC", "RemoteUrl": "https://github.com/trissyboats/oystermapr", "RemoteRef": "HEAD", "RemoteSha": "2e26744637fb401e2e5de5e756232a259a0d6858", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-16 08:06:39 UTC", "User": "root" }, "Author": "T Tucker [aut, cre]", "Maintainer": "T Tucker ", "MD5sum": "9b7727c5b82b8b23540633d6e7696f4e", "_user": "trissyboats", "_type": "src", "_file": "oystermapR_1.0.0.tar.gz", "_fileid": "1f31b048966925dd70cda8910d62a913cf3a6aa4e25fa67dfc5aeaa008128cab", "_filesize": 622803, "_sha256": "1f31b048966925dd70cda8910d62a913cf3a6aa4e25fa67dfc5aeaa008128cab", "_created": "2026-05-16T08:06:39.000Z", "_published": "2026-06-02T18:22:56.425Z", "_distro": "noble", "_jobs": [ { "job": 79142120931, "time": 156, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7031840254" }, { "job": 79142121487, "time": 150, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7031839583" }, { "job": 79142121751, "time": 158, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7031861436" }, { "job": 79142121346, "time": 164, "config": 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downloadables", "time": 1777634113 }, "_maintainer": { "name": "T Tucker", "email": "tristantucker48@gmail.com", "login": "trissyboats", "uuid": 226574646 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "dplyr", "version": ">= 1.0.0", "role": "Imports" }, { "package": "terra", "version": ">= 1.7.18", "role": "Imports" }, { "package": "sf", "version": ">= 1.0.0", "role": "Imports" }, { "package": "rlang", "version": ">= 1.0.0", "role": "Imports" }, { "package": "cli", "version": ">= 3.0.0", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.4.0", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "version": ">= 2.20", "role": "Suggests" }, { "package": "tinytex", "role": "Suggests" }, { "package": "httr", 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"extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/oystermapR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/trissyboats/oystermapr", "_realowner": "trissyboats", "_cranurl": true, "_releases": [ { "version": "1.4.0", "date": "2026-05-15" } ], "_exports": [ "add_intertidal_flag", "add_season_column", "add_shellfish_classification", "add_suitability_ci", "analyse_connectivity", "assess_gear_feasibility", "auto_tidal_correct", "check_exclusions", "classify_substrate_from_backscatter", "compare_species", "compare_surveys", "composite_seasonal", "correct_to_chart_datum", "detect_season", "estimate_chlorophyll_from_backscatter", "estimate_fetch", "export_contours", "export_geotiff", "export_qml_style", "fetch_live_environmental_data", "generate_report", "get_species_tolerances", "get_tolerance_posteriors", "identify_resilient_sites", "interpolate_survey", "list_species", "load_tolerance_update", "merge_sensor_data", "oystermapR_help", "oystermapR_live_config", "parse_opendrift_connectivity", "permutation_importance", "predict_oyster", "project_suitability", "qc_survey_data", "read_generic_csv", "read_nortek_adcp", "read_sonar_tif", "read_soundings_xyz", "reset_tolerance_update", "save_tolerance_update", "score_anthropogenic_disturbance", "score_disease_risk", "score_economic_viability", "score_hab_risk", "score_larval_connectivity", "score_locations", "score_predation_risk", "score_sediment_stability", "score_settlement", "score_wave_exposure", "sensitivity_analysis", "smooth_suitability", "spatial_block_cv", "stack_surveys", "tidal_port_info", "update_species_tolerances", "validate_against_records" ], "_help": [ { "page": "add_intertidal_flag", "title": "Add an intertidal zone flag to a survey dataframe", "topics": [ "add_intertidal_flag" ] }, { "page": "add_season_column", "title": "Detect season for each row in a dataframe", "topics": [ "add_season_column" ] }, { "page": "add_shellfish_classification", "title": "Add shellfish water quality classification to scored result", "topics": [ "add_shellfish_classification" ] }, { "page": "add_suitability_ci", "title": "Add bootstrap confidence intervals to suitability scores", "topics": [ "add_suitability_ci" ] }, { "page": "analyse_connectivity", "title": "Analyse spatial connectivity of suitable habitat cells", "topics": [ "analyse_connectivity" ] }, { "page": "assess_gear_feasibility", "title": "Assess gear deployment feasibility at survey locations", "topics": [ "assess_gear_feasibility" ] }, { "page": "auto_tidal_correct", "title": "Automatically predict and apply tidal correction from harmonic constituents", "topics": [ "auto_tidal_correct" ] }, { "page": "check_exclusions", "title": "Check exclusion criteria for all rows in a dataset", "topics": [ "check_exclusions" ] }, { "page": "classify_substrate_from_backscatter", "title": "Classify seabed substrate hardness from near-seabed ADCP backscatter", "topics": [ "classify_substrate_from_backscatter" ] }, { "page": "compare_species", "title": "Compare suitability across multiple oyster species", "topics": [ "compare_species" ] }, { "page": "compare_surveys", "title": "Compare suitability scores across multiple surveys or monitoring years", "topics": [ "compare_surveys" ] }, { "page": "composite_seasonal", "title": "Combine multi-season survey results into a composite suitability score", "topics": [ "composite_seasonal" ] }, { "page": "correct_to_chart_datum", "title": "Correct survey depths to Chart Datum (LAT)", "topics": [ "correct_to_chart_datum" ] }, { "page": "detect_season", "title": "Detect meteorological season from date and latitude", "topics": [ "detect_season" ] }, { "page": "estimate_chlorophyll_from_backscatter", "title": "Estimate chlorophyll-a concentration from ADCP acoustic backscatter", "topics": [ "estimate_chlorophyll_from_backscatter" ] }, { "page": "estimate_fetch", "title": "Estimate effective fetch from a set of lat/lon points and a bearing", "topics": [ "estimate_fetch" ] }, { "page": "export_contours", "title": "Export optional contour lines as a GeoPackage for QGIS", "topics": [ "export_contours" ] }, { "page": "export_geotiff", "title": "Export suitability scores as a smooth interpolated GeoTIFF heatmap for QGIS", "topics": [ "export_geotiff" ] }, { "page": "export_qml_style", "title": "Export a QGIS colour style (.qml) matching the BioBase orange/red heatmap", "topics": [ "export_qml_style" ] }, { "page": "fetch_live_environmental_data", "title": "Fetch live environmental data for a survey extent", "topics": [ "fetch_live_environmental_data" ] }, { "page": "generate_report", "title": "Generate a formatted survey report from predict_oyster() results", "topics": [ "generate_report" ] }, { "page": "get_species_tolerances", "title": "Get species tolerance parameters", "topics": [ "get_species_tolerances" ] }, { "page": "get_tolerance_posteriors", "title": "Retrieve current posterior tolerance parameters for a species", "topics": [ "get_tolerance_posteriors" ] }, { "page": "identify_resilient_sites", "title": "Identify climate-resilient locations", "topics": [ "identify_resilient_sites" ] }, { "page": "interpolate_survey", "title": "Interpolate survey measurements to a regular grid before scoring", "topics": [ "interpolate_survey" ] }, { "page": "list_species", "title": "List all supported species", "topics": [ "list_species" ] }, { "page": "load_tolerance_update", "title": "Load saved Bayesian tolerance updates into session cache", "topics": [ "load_tolerance_update" ] }, { "page": "merge_sensor_data", "title": "Merge multiple sensor datasets into a single survey table", "topics": [ "merge_sensor_data" ] }, { "page": "oystermapR_help", "title": "Print an interactive getting-started guide for oystermapR", "topics": [ "oystermapR_help" ] }, { "page": "oystermapR_live_config", "title": "Configure live data API credentials for oystermapR", "topics": [ "oystermapR_live_config" ] }, { "page": "parse_opendrift_connectivity", "title": "Parse an OpenDrift particle tracking output into a connectivity matrix", "topics": [ "parse_opendrift_connectivity" ] }, { "page": "permutation_importance", "title": "Permutation variable importance for suitability model", "topics": [ "permutation_importance" ] }, { "page": "predict_oyster", "title": "Predict oyster growth suitability from environmental survey data", "topics": [ "predict_oyster" ] }, { "page": "project_suitability", "title": "Project suitability under future climate scenarios", "topics": [ "project_suitability" ] }, { "page": "qc_survey_data", "title": "Run automated quality control on raw survey data", "topics": [ "qc_survey_data" ] }, { "page": "read_generic_csv", "title": "Read a generic sensor CSV with flexible column mapping", "topics": [ "read_generic_csv" ] }, { "page": "read_nortek_adcp", "title": "Read and process a Nortek Signature 500 ADCP CSV file", "topics": [ "read_nortek_adcp" ] }, { "page": "read_sonar_tif", "title": "Read a bathymetric or sidescan GeoTIFF and convert to oystermapR variables", "topics": [ "read_sonar_tif" ] }, { "page": "read_soundings_xyz", "title": "Read a bathymetric XYZ point cloud and derive depth, slope and roughness", "topics": [ "read_soundings_xyz" ] }, { "page": "reset_tolerance_update", "title": "Reset Bayesian tolerance updates for a species", "topics": [ "reset_tolerance_update" ] }, { "page": "save_tolerance_update", "title": "Save Bayesian tolerance updates to disk", "topics": [ "save_tolerance_update" ] }, { "page": "score_anthropogenic_disturbance", "title": "Score anthropogenic disturbance at survey locations", "topics": [ "score_anthropogenic_disturbance" ] }, { "page": "score_disease_risk", "title": "Score locations for disease and parasite risk", "topics": [ "score_disease_risk" ] }, { "page": "score_economic_viability", "title": "Score economic viability for aquaculture or restoration", "topics": [ "score_economic_viability" ] }, { "page": "score_hab_risk", "title": "Score harmful algal bloom risk at survey locations", "topics": [ "score_hab_risk" ] }, { "page": "score_larval_connectivity", "title": "Score larval dispersal connectivity at survey locations", "topics": [ "score_larval_connectivity" ] }, { "page": "score_locations", "title": "Score all locations in a dataframe", "topics": [ "score_locations" ] }, { "page": "score_predation_risk", "title": "Score predation and bioturbation pressure at survey locations", "topics": [ "score_predation_risk" ] }, { "page": "score_sediment_stability", "title": "Score sediment stability and mobility at survey locations", "topics": [ "score_sediment_stability" ] }, { "page": "score_settlement", "title": "Score locations for spat settlement suitability", "topics": [ "score_settlement" ] }, { "page": "score_wave_exposure", "title": "Score wave exposure from fetch or measured wave height", "topics": [ "score_wave_exposure" ] }, { "page": "sensitivity_analysis", "title": "Partial dependence / sensitivity analysis for a scored variable", "topics": [ "sensitivity_analysis" ] }, { "page": "smooth_suitability", "title": "Apply Gaussian kernel smoothing to suitability scores", "topics": [ "smooth_suitability" ] }, { "page": "spatial_block_cv", "title": "Spatial block cross-validation for suitability model evaluation", "topics": [ "spatial_block_cv" ] }, { "page": "stack_surveys", "title": "Stack multiple survey runs from the same sensor type", "topics": [ "stack_surveys" ] }, { "page": "tidal_port_info", "title": "Look up approximate tidal range for major European survey ports", "topics": [ "tidal_port_info" ] }, { "page": "update_species_tolerances", "title": "Update species tolerance parameters from field observations (Bayesian)", "topics": [ "update_species_tolerances" ] }, { "page": "validate_against_records", "title": "Validate suitability predictions against known presence/absence records", "topics": [ 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