Package: b3gbi 0.4.2

Shawn Dove

b3gbi: General Biodiversity Indicators for Biodiversity Data Cubes

Calculate general biodiversity indicators from GBIF data cubes. Includes many common indicators such as species richness and evenness, which can be calculated over time (trends) or space (maps).

Authors:Shawn Dove [aut, cre]

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b3gbi.pdf |b3gbi.html✨
b3gbi/json (API)
NEWS

# 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 site:https://b-cubed-eu.github.io

Datasets:

On CRAN:

biodiversity-indicatorsdata-cubes

5.81 score 3 stars 34 scripts 43 exports 80 dependencies

Last updated 1 hours agofrom:bb3e83543d. Checks:4 OK, 4 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 20 2025
R-4.5-winOKFeb 20 2025
R-4.5-macOKFeb 20 2025
R-4.5-linuxOKFeb 20 2025
R-4.4-winNOTEFeb 20 2025
R-4.4-macNOTEFeb 20 2025
R-4.3-winNOTEFeb 20 2025
R-4.3-macNOTEFeb 20 2025

Exports:%>%ab_rarity_mapab_rarity_tsarea_rarity_maparea_rarity_tscalc_cicalc_mapcalc_tscompute_indicator_workflowcum_richness_tsget_observed_yearshill0_maphill0_tshill1_maphill1_tshill2_maphill2_tslist_speciesnewness_mapnewness_tsobs_richness_mapobs_richness_tsocc_density_mapocc_density_tsocc_turnover_tspielou_evenness_mappielou_evenness_tsplot_mapplot_species_mapplot_species_tsplot_tsprocess_cubeprocess_cube_oldspec_occ_mapspec_occ_tsspec_range_mapspec_range_tstax_distinct_maptax_distinct_tstotal_occ_maptotal_occ_tswilliams_evenness_mapwilliams_evenness_ts

Dependencies:askpassbitbit64bootclassclassIntclicliprcodetoolscolorspacecpp11crayoncurlDBIdigestdplyre1071fansifarverfurrrfuturegenericsggplot2globalsgluegtablehmshttriNEXTisobandjsonliteKernSmoothlabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvmgrsmimemunsellnlmeopensslparallellypatchworkpermutepillarpkgconfigplyrprettyunitsprogressproxypurrrR6RColorBrewerRcppreadrreshape2rlangrnaturalearths2scalessfstringistringrsysterratibbletidyrtidyselecttzdbunitsutf8vctrsviridisLitevroomwithrwk

Tutorial

Shawn Dove

Rendered fromb3gbi.Rmdusingknitr::rmarkdownon Feb 20 2025.

Last update: 2025-01-13
Started: 2024-04-12

Readme and manuals

Help Manual

Help pageTopics
Calculate Abundance-Based Rarity Over Spaceab_rarity_map
Calculate Abundance-Based Rarity Over Timeab_rarity_ts
Calculate Area-Based Rarity Over Spacearea_rarity_map
Calculate Area-Based Rarity Over Timearea_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.newness calc_ci.occ_density calc_ci.pielou_evenness calc_ci.spec_occ calc_ci.spec_range calc_ci.tax_distinct calc_ci.total_occ calc_ci.williams_evenness
Calculate Biodiversity Indicators Over Spacecalc_map calc_map.ab_rarity calc_map.area_rarity calc_map.newness calc_map.obs_richness calc_map.occ_density calc_map.pielou_evenness calc_map.spec_occ calc_map.spec_range 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.cum_richness calc_ts.newness calc_ts.obs_richness calc_ts.occ_density calc_ts.occ_turnover calc_ts.pielou_evenness calc_ts.spec_occ calc_ts.spec_range calc_ts.tax_distinct calc_ts.total_occ calc_ts.williams_evenness
Calculate Biodiversity Indicators Over Space or Timecompute_indicator_workflow
Calculate Cumulative Species Richnesscum_richness_ts
Cube of GBIF Mammal Occurrences in Denmarkexample_cube_1
Time Series of Observed Species Richness for Mammals in Denmarkexample_indicator_ts1
Time Series of Cumulative Species Richness for Insects in Europeexample_indicator_ts2
Calculate confidence intervals for list of 'boot' objectsget_bootstrap_ci
Extract Years With Observations from an Indicator Mapget_observed_years
Calculate Estimated Species Richness Over Spacehill0_map
Calculate Estimated Species Richness Over Timehill0_ts
Calculate Hill-Shannon Diversity Over Spacehill1_map
Calculate Hill-Shannon Diversity Over Timehill1_ts
Calculate Hill-Simpson Diversity Over Spacehill2_map
Calculate Hill-Simpson Diversity Over Timehill2_ts
Extract Species Names.list_species
Calculate Mean Year of Occurrence Over Spacenewness_map
Calculate Mean Year of Occurrence Over Timenewness_ts
Calculate Observed Species Richness Over Spaceobs_richness_map
Calculate Observed Species Richness Over Timeobs_richness_ts
Calculate Occurrence Density Over Spaceocc_density_map
Calculate Occurrence Density Over Timeocc_density_ts
Calculate Occupancy Turnover Over Timeocc_turnover_ts
Calculate Pielou's Evenness Over Spacepielou_evenness_map
Calculate Pielou's Evenness Over Timepielou_evenness_ts
Plot Biodiversity Indicator Mapplot_map
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
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 Objectprint.processed_cube_dsinfo
Print a Simulated Data Cube Objectprint.sim_cube
Process GBIF Data Cubesprocess_cube process_cube_old
Calculate Species Occurrences Over Spacespec_occ_map
Calculate Number of Occurrences for One or More Species Over Timespec_occ_ts
Plot Species Ranges Over Spacespec_range_map
Calculate Range Size (Number of Cells Occupied) for One or More Species Over Timespec_range_ts
Calculate Taxonomic Distinctness Over Spacetax_distinct_map
Calculate Taxonomic Distinctness Over Timetax_distinct_ts
Calculate Total Occurrences Over Spacetotal_occ_map
Calculate Total Occurrences Over Timetotal_occ_ts
Calculate Williams' Evenness Over Spacewilliams_evenness_map
Calculate Williams' Evenness Over Timewilliams_evenness_ts