Package: b3gbi 1.1.3.9000

Shawn Dove

b3gbi: General Biodiversity Indicators for Biodiversity Data Cubes

Calculate general biodiversity indicators from species occurrence cubes, such as those produced by the 'GBIF' (Global Biodiversity Information Facility) occurrence cube service <https://techdocs.gbif.org/en/data-use/data-cubes>. Indicators include observed and coverage-based rarefied species richness and Hill numbers (via 'iNEXT'), evenness, rarity, taxonomic distinctness, occupancy, turnover and sample completeness, and can be calculated over time (time series) or space (maps), with bootstrap confidence intervals. Cubes using the EEA reference grid, MGRS, the extended quarter-degree grid (EQDGC) or ISEA3H grids are supported. For details see Dove (2026) <doi:10.21105/joss.10963>.

Authors:Shawn Dove [aut, cre], Ward Langeraert [ctb], Peter Desmet [ctb], University of Giessen [cph], European Union [fnd]

b3gbi_1.1.3.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
b3gbi/json (API)

# Install 'b3gbi' in R:
install.packages('b3gbi', repos = c('https://b-cubed-eu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/b-cubed-eu/b3gbi/issues

Pkgdown/docs site:https://b-cubed-eu.github.io

Datasets:

On CRAN:

Conda:

biodiversity-indicatorsdata-cubes

8.75 score 10 stars 1 packages 127 scripts 56 exports 63 dependencies

Last updated from:1452bd7455. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK240
source / vignettesOK357
linux-releaseOK285
macos-releaseOK221
macos-oldrelOK209
windows-develOK253
windows-releaseOK226
windows-oldrelOK231
wasm-releaseOK184

Exports:%>%ab_rarity_mapab_rarity_tsadd_ciarea_rarity_maparea_rarity_tscalc_cicalc_mapcalc_tscompleteness_mapcompleteness_tscompute_indicator_workflowconvert_eqdgc_latlongcreate_sf_from_utmcum_richness_tsget_observed_yearshill0_maphill0_tshill1_maphill1_tshill2_maphill2_tslist_speciesmgrs_to_latlong_bboxnewness_mapnewness_tsobs_richness_mapobs_richness_tsocc_density_mapocc_density_tsocc_turnover_tspielou_evenness_mappielou_evenness_tsplot_mapplot_mvplot_species_mapplot_species_tsplot_tsprepare_indicator_bootstrapprocess_cuberelative_occupancy_maprelative_occupancy_tsreplace_naspec_occ_mapspec_occ_tsspec_range_mapspec_range_tsspec_richness_density_mapspec_richness_density_tssum_by_taxontax_distinct_maptax_distinct_tstotal_occ_maptotal_occ_tswilliams_evenness_mapwilliams_evenness_ts

Dependencies:askpassbitbit64bootclassclassIntclicliprcpp11crayoncurlDBIdplyre1071farvergenericsggplot2gluegtablehmshttriNEXTisobandjsonliteKernSmoothlabelinglifecyclemagrittrmimeopensslpillarpkgconfigplyrprettyunitsprogressproxypurrrR6RColorBrewerRcppreadrreshape2rlangrnaturalearths2S7scalessfstringistringrsysterratibbletidyrtidyselecttzdbunitsutf8vctrsviridisLitevroomwithrwk

A Gentle Introduction to b3gbi: Data Cubes to Biodiversity Indicators
Introduction | Package Installation | Step 1: Data Ingestion with process_cube() | Key process_cube() Arguments | Example: Import Data and Filter by Time | Step 2: Indicator Calculation | Available Indicators | Core Arguments for Wrapper Functions | Example: Observed Species Richness Map | Example: Total Occurrences Time Series | Step 3: Visualization with plot() | Plotting the Map | Plotting the Time Series
Rendered fromb3gbi.Rmdusingknitr::rmarkdown

Last update: 2026-09-25
Started: 2024-04-12

Uncertainty in Biodiversity Indicators
Introduction 🛡️ | The Two-Step Workflow | Example: Total Occurrences with Uncertainty | Bootstrapping Levels | 1. Cube-Level Bootstrapping (bootstrap_level = "cube") | 2. Indicator-Level Bootstrapping (bootstrap_level = "indicator") | Automatic Indicator Configuration | Advanced Configuration | Types of Confidence Intervals | Customizing the Bootstrap Process | Overriding Indicator Defaults | Supported Indicators | Special Case: Hill Diversity Indicators | Exclusions | Data Exploration with dubicube 🔍 | Summary
Rendered fromuncertainty.Rmdusingknitr::rmarkdown

Last update: 2026-09-25
Started: 2026-06-22

Readme and manuals

Help Manual

Help pageTopics
Add Confidence Intervals to an Indicator Objectadd_ci
Calculate Rarity Over Time or Spaceab_rarity_map ab_rarity_ts area_rarity_map area_rarity_ts
Indicators Available for Use in the Packageavailable_indicators
Calculate Confidence Intervals for a Biodiversity Indicatorcalc_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
Calculate Biodiversity Indicators Over Spacecalc_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
Calculate Biodiversity Indicators Over Timecalc_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
Calculate Completeness (Sample Coverage) Over Space or Timecompleteness_map completeness_ts
Calculate Biodiversity Indicators Over Space or Timecompute_indicator_workflow
Convert extended quarter-degree grid cell codes to latitude and longitudeconvert_eqdgc_latlong
Create an sf object from UTM coordinates, handling multiple zones correctly.create_sf_from_utm
Calculate Cumulative Species Richnesscum_richness_ts
Cube of GBIF Mammal Occurrences in Denmarkexample_cube_1
Map of Observed Species Richness for Mammals in Denmarkexample_indicator_map1
Time Series of Observed Species Richness for Mammals in Denmarkexample_indicator_ts1
Time Series of Cumulative Species Richness for Bryophytes in South Africaexample_indicator_ts2
Extract Years With Observationsget_observed_years
Calculate Estimated Hill Diversity Over Space or Timehill0_map hill0_ts hill1_map hill1_ts hill2_map hill2_ts
Extract Species Names.list_species
Create a Longitude/Latitude Bounding Box from MGRS Datamgrs_to_latlong_bbox
Calculate Mean Year of Occurrence Over Time or Spacenewness_map newness_ts
Calculate Observed Species Richness Over Space or Timeobs_richness_map obs_richness_ts
Calculate Occurrence Density Over Space or Timeocc_density_map occ_density_ts
Calculate Occupancy Turnoverocc_turnover_ts
Calculate Evenness Over Time or Spacepielou_evenness_map pielou_evenness_ts williams_evenness_map williams_evenness_ts
Plot Biodiversity Indicator Mapplot_map
Plot Interactive Biodiversity Indicator Mapplot_mv
Plot Occurrence Map or Range Map of Individual Speciesplot_species_map
Plot Occurrence Trends or Range Size Trends for Individual Speciesplot_species_ts
Plot Biodiversity Indicator Trendplot_ts
Prepare bootstrap and confidence interval parameters for an indicatorprepare_indicator_bootstrap
Print Available Indicatorsprint.available_indicators
Print an Indicator Map Objectprint.indicator_map
Print an Indicator Time Series Objectprint.indicator_ts
Print a Processed Data Cube Objectprint.processed_cube
Print a Processed Data Cube Object with Dataset Informationprint.processed_cube_dsinfo
Print a Simulated Data Cube Objectprint.sim_cube
Process GBIF Data Cubesprocess_cube
Calculate Species Relative Occupancy Over Space or Timerelative_occupancy_map relative_occupancy_ts
Replace NA Values in Indicator Objectsreplace_na
Calculate Species Occurrences Over Space or Timespec_occ_map spec_occ_ts
Calculate Species Ranges Over Space or Timespec_range_map spec_range_ts
Calculate Species Richness Density Over Space or Timespec_richness_density_map spec_richness_density_ts
Sum Observations by Taxonomic Ranksum_by_taxon
Calculate Taxonomic Distinctness Over Space or Timetax_distinct_map tax_distinct_ts
Calculate Total Occurrences Over Space or Timetotal_occ_map total_occ_ts