{ "_id": "6ad9286e992ad85420b5f4b0", "Type": "Package", "Package": "b3gbi", "Title": "General Biodiversity Indicators for Biodiversity Data Cubes", "Version": "1.1.3", "Authors@R": "c(\nperson(\"Shawn\", \"Dove\", email = \"Shawn.Dove@allzool.bio.uni-giessen.de\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-9465-5638\")),\nperson(\"Ward\", \"Langeraert\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5900-8109\")),\nperson(\"Peter\", \"Desmet\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8442-8025\")),\nperson(\"University of Giessen\", role = \"cph\"),\nperson(\"European Union\", role = \"fnd\",\ncomment = \"Horizon Europe Research and Innovation Programme, grant 101059592\")\n)", "Description": "Calculate general biodiversity indicators from species\noccurrence cubes, such as those produced by the 'GBIF' (Global\nBiodiversity Information Facility) occurrence cube service\n. Indicators\ninclude observed and coverage-based rarefied species richness\nand Hill numbers (via 'iNEXT'), evenness, rarity, taxonomic\ndistinctness, occupancy, turnover and sample completeness, and\ncan be calculated over time (time series) or space (maps), with\nbootstrap confidence intervals. Cubes using the EEA reference\ngrid, MGRS, the extended quarter-degree grid (EQDGC) or ISEA3H\ngrids are supported. 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"hill0_map", "hill0_ts", "hill1_map", "hill1_ts", "hill2_map", "hill2_ts", "list_species", "mgrs_to_latlong_bbox", "newness_map", "newness_ts", "obs_richness_map", "obs_richness_ts", "occ_density_map", "occ_density_ts", "occ_turnover_ts", "pielou_evenness_map", "pielou_evenness_ts", "plot_map", "plot_mv", "plot_species_map", "plot_species_ts", "plot_ts", "prepare_indicator_bootstrap", "process_cube", "relative_occupancy_map", "relative_occupancy_ts", "replace_na", "spec_occ_map", "spec_occ_ts", "spec_range_map", "spec_range_ts", "spec_richness_density_map", "spec_richness_density_ts", "sum_by_taxon", "tax_distinct_map", "tax_distinct_ts", "total_occ_map", "total_occ_ts", "williams_evenness_map", "williams_evenness_ts" ], "_datasets": [ { "name": "available_indicators", "title": "Indicators Available for Use in the Package", "object": "available_indicators", "class": [ "available_indicators", "list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_cube_1", "title": "Cube of GBIF Mammal Occurrences in Denmark", "object": "example_cube_1", "class": [ "processed_cube" ], "fields": [], "table": false, "tojson": false }, { "name": "example_indicator_map1", "title": "Map of Observed Species Richness for Mammals in Denmark", "object": "example_indicator_map1", "class": [ "indicator_map", "obs_richness" ], "fields": [], "table": false, "tojson": false }, { "name": "example_indicator_ts1", "title": "Time Series of Observed Species Richness for Mammals in Denmark", "object": "example_indicator_ts1", "class": [ "indicator_ts", "obs_richness" ], "fields": [], "table": false, "tojson": false }, { "name": "example_indicator_ts2", "title": "Time Series of Cumulative Species Richness for Bryophytes in South Africa", "object": "example_indicator_ts2", "class": [ "indicator_ts", "cum_richness" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "add_ci", "title": "Add Confidence Intervals to an Indicator Object", "topics": [ "add_ci" ] }, { "page": "area_rarity_map", "title": "Calculate Rarity Over Time or Space", "topics": [ "ab_rarity_map", "ab_rarity_ts", "area_rarity_map", "area_rarity_ts" ] }, { "page": "available_indicators", "title": "Indicators Available for Use in the Package", "topics": [ "available_indicators" ] }, { "page": "calc_ci", "title": "Calculate Confidence Intervals for a Biodiversity Indicator", "topics": [ "calc_ci", "calc_ci.ab_rarity", "calc_ci.area_rarity", "calc_ci.default", "calc_ci.hill0", "calc_ci.hill1", "calc_ci.hill2", "calc_ci.newness", "calc_ci.occ_density", "calc_ci.pielou_evenness", "calc_ci.spec_occ", "calc_ci.spec_range", "calc_ci.spec_richness_density", "calc_ci.total_occ", "calc_ci.williams_evenness" ] }, { "page": "calc_map", "title": "Calculate Biodiversity Indicators Over Space", "topics": [ "calc_map", "calc_map.ab_rarity", "calc_map.area_rarity", "calc_map.completeness", "calc_map.hill0", "calc_map.hill1", "calc_map.hill2", "calc_map.newness", "calc_map.obs_richness", "calc_map.occ_density", "calc_map.pielou_evenness", "calc_map.relative_occupancy", "calc_map.spec_occ", "calc_map.spec_range", "calc_map.spec_richness_density", "calc_map.tax_distinct", "calc_map.total_occ", "calc_map.williams_evenness" ] }, { "page": "calc_ts", "title": "Calculate Biodiversity Indicators Over Time", "topics": [ "calc_ts", "calc_ts.ab_rarity", "calc_ts.area_rarity", "calc_ts.completeness", "calc_ts.cum_richness", "calc_ts.default", "calc_ts.hill0", "calc_ts.hill1", "calc_ts.hill2", "calc_ts.newness", "calc_ts.obs_richness", "calc_ts.occ_density", "calc_ts.occ_turnover", "calc_ts.pielou_evenness", "calc_ts.relative_occupancy", "calc_ts.spec_occ", "calc_ts.spec_range", "calc_ts.spec_richness_density", "calc_ts.tax_distinct", "calc_ts.total_occ", "calc_ts.williams_evenness" ] }, { "page": "completeness_map", "title": "Calculate Completeness (Sample Coverage) Over Space or Time", "topics": [ "completeness_map", "completeness_ts" ] }, { "page": "compute_indicator_workflow", "title": "Calculate Biodiversity Indicators Over Space or Time", "topics": [ "compute_indicator_workflow" ] }, { "page": "convert_eqdgc_latlong", "title": "Convert extended quarter-degree grid cell codes to latitude and longitude", "topics": [ "convert_eqdgc_latlong" ] }, { "page": "create_sf_from_utm", "title": "Create an sf object from UTM coordinates, handling multiple zones correctly.", "topics": [ "create_sf_from_utm" ] }, { "page": "cum_richness_ts", "title": "Calculate Cumulative Species Richness", "topics": [ "cum_richness_ts" ] }, { "page": "example_cube_1", "title": "Cube of GBIF Mammal Occurrences in Denmark", "topics": [ "example_cube_1" ] }, { "page": "example_indicator_map1", "title": "Map of Observed Species Richness for Mammals in Denmark", "topics": [ "example_indicator_map1" ] }, { "page": "example_indicator_ts1", "title": "Time Series of Observed Species Richness for Mammals in Denmark", "topics": [ "example_indicator_ts1" ] }, { "page": "example_indicator_ts2", "title": "Time Series of Cumulative Species Richness for Bryophytes in South Africa", "topics": [ "example_indicator_ts2" ] }, { "page": "get_observed_years", "title": "Extract Years With Observations", "topics": [ "get_observed_years" ] }, { "page": "hill0_map", "title": "Calculate Estimated Hill Diversity Over Space or Time", "topics": [ "hill0_map", "hill0_ts", "hill1_map", "hill1_ts", "hill2_map", "hill2_ts" ] }, { "page": "list_species", "title": "Extract Species Names.", "topics": [ "list_species" ] }, { "page": "mgrs_to_latlong_bbox", "title": "Create a Longitude/Latitude Bounding Box from MGRS Data", "topics": [ "mgrs_to_latlong_bbox" ] }, { "page": "newness_map", "title": "Calculate Mean Year of Occurrence Over Time or Space", "topics": [ "newness_map", "newness_ts" ] }, { "page": "obs_richness_map", "title": "Calculate Observed Species Richness Over Space or Time", "topics": [ "obs_richness_map", "obs_richness_ts" ] }, { "page": "occ_density_map", "title": "Calculate Occurrence Density Over Space or Time", "topics": [ "occ_density_map", "occ_density_ts" ] }, { "page": "occ_turnover_ts", "title": "Calculate Occupancy Turnover", "topics": [ "occ_turnover_ts" ] }, { "page": "pielou_evenness_map", "title": "Calculate Evenness Over Time or Space", "topics": [ "pielou_evenness_map", "pielou_evenness_ts", "williams_evenness_map", "williams_evenness_ts" ] }, { "page": "plot_map", "title": "Plot Biodiversity Indicator Map", "topics": [ "plot_map" ] }, { "page": "plot_mv", "title": "Plot Interactive Biodiversity Indicator Map", "topics": [ "plot_mv" ] }, { "page": "plot_species_map", "title": "Plot Occurrence Map or Range Map of Individual Species", "topics": [ "plot_species_map" ] }, { "page": "plot_species_ts", "title": "Plot Occurrence Trends or Range Size Trends for Individual Species", "topics": [ "plot_species_ts" ] }, { "page": "plot_ts", "title": "Plot Biodiversity Indicator Trend", "topics": [ "plot_ts" ] }, { "page": "prepare_indicator_bootstrap", "title": "Prepare bootstrap and confidence interval parameters for an indicator", "topics": [ "prepare_indicator_bootstrap" ] }, { "page": "print.available_indicators", "title": "Print Available Indicators", "topics": [ "print.available_indicators" ] }, { "page": "print.indicator_map", "title": "Print an Indicator Map Object", "topics": [ "print.indicator_map" ] }, { "page": "print.indicator_ts", "title": "Print an Indicator Time Series Object", "topics": [ "print.indicator_ts" ] }, { "page": "print.processed_cube", "title": "Print a Processed Data Cube Object", "topics": [ "print.processed_cube" ] }, { "page": "print.processed_cube_dsinfo", "title": "Print a Processed Data Cube Object with Dataset Information", "topics": [ "print.processed_cube_dsinfo" ] }, { "page": "print.sim_cube", "title": "Print a Simulated Data Cube Object", "topics": [ "print.sim_cube" ] }, { "page": "process_cube", "title": "Process GBIF Data Cubes", "topics": [ "process_cube" ] }, { "page": "relative_occupancy_map", "title": "Calculate Species Relative Occupancy Over Space or Time", "concept": [ "species-based indicators" ], "topics": [ "relative_occupancy_map", "relative_occupancy_ts" ] }, { "page": "replace_na", "title": "Replace NA Values in Indicator Objects", "topics": [ "replace_na" ] }, { "page": "spec_occ_map", "title": "Calculate Species Occurrences Over Space or Time", "concept": [ "species-based indicators" ], "topics": [ "spec_occ_map", "spec_occ_ts" ] }, { "page": "spec_range_map", "title": "Calculate Species Ranges Over Space or Time", "concept": [ "species-based indicators" ], "topics": [ "spec_range_map", "spec_range_ts" ] }, { "page": "spec_richness_density_map", "title": "Calculate Species Richness Density Over Space or Time", "topics": [ "spec_richness_density_map", "spec_richness_density_ts" ] }, { "page": "sum_by_taxon", "title": "Sum Observations by Taxonomic Rank", "topics": [ "sum_by_taxon" ] }, { "page": "tax_distinct_map", "title": "Calculate 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