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b3gbi

Analyze biodiversity trends and spatial patterns from GBIF data cubes, using flexible indicators like richness, evenness, and more.
https://github.com/b-cubed-eu/b3gbi

Category: Biosphere
Sub Category: Biodiversity Data Access and Management

Keywords

biodiversity-indicators data-cubes

Keywords from Contributors

gbif tdwg jekyll oscibio

Last synced: about 4 hours ago
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B-Cubed General Biodiversity Indicators

README.Rmd 

          ---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# b3gbi b3gbi website



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badge](https://b-cubed-eu.r-universe.dev/b3gbi/badges/version)](https://b-cubed-eu.r-universe.dev/b3gbi)
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status](https://www.r-pkg.org/badges/version/b3gbi)](https://CRAN.R-project.org/package=b3gbi)
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Analyze biodiversity trends and spatial patterns from GBIF data cubes, using flexible indicators like richness, evenness, and more.

## Overview

Biodiversity researchers need robust and standardized tools to analyze the vast amounts of data available on platforms like GBIF. The b3gbi package leverages the power of data cubes to streamline biodiversity assessments. It helps researchers gain insights into:

* **Changes Over Time:**  How biodiversity metrics shift throughout the years.
* **Spatial Variations:** Differences in biodiversity across regions, identifying hotspots or areas of concern. 
* **The Impact of Factors:** How different environmental variables or human activities might affect biodiversity patterns. 

## Key Features

b3gbi empowers biodiversity analysis with:

* **Standardized Workflows:**  Simplify the process of calculating common biodiversity indicators from GBIF data cubes.
* **Flexibility:**  Calculate richness, evenness, rarity, taxonomic distinctness, Shannon-Hill diversity, Simpson-Hill diversity, completeness, and more.
* **Analysis Options:** Explore temporal trends or create spatial maps.
* **Visualization Tools:** Generate publication-ready plots of your biodiversity metrics.

## Installation

Install **b3gbi** in R:

``` r
install.packages("b3gbi", repos = c("https://b-cubed-eu.r-universe.dev", "https://cloud.r-project.org"))
```
## Example: Three-Step Workflow

This basic example demonstrates the core workflow: preparing the data cube, calculating an indicator, and plotting the result as a spatial map of species richness for mammals in Denmark.

```{r example, warning = FALSE, message = FALSE}
# Load package
library(b3gbi)

# 1. Load and prepare the GBIF data cube
cube_name <- system.file("extdata", "denmark_mammals_cube_eqdgc.csv", package = "b3gbi")
mammal_data <- process_cube(cube_name)

# 2. Calculate a map of observed richness
map_obs_rich_mammals <- obs_richness_map(mammal_data, level = "country", region = "Denmark", ne_scale = "medium")

# 3. Plot the indicator map
plot(map_obs_rich_mammals, title = "Observed Species Richness: Mammals in Denmark")
```

For a more in-depth introduction, see the tutorial: https://b-cubed-eu.github.io/b3gbi/articles/b3gbi.html.

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "b3gbi" in publications use:'
type: software
license: MIT
title: 'b3gbi: General Biodiversity Indicators for Biodiversity Data Cubes'
version: 0.8.13
abstract: 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:
- family-names: Dove
  given-names: Shawn
  email: Shawn.Dove@allzool.bio.uni-giessen.de
  orcid: https://orcid.org/0000-0001-9465-5638
repository-code: https://github.com/b-cubed-eu/b3gbi
url: https://b-cubed-eu.github.io/b3gbi/
contact:
- family-names: Dove
  given-names: Shawn
  email: Shawn.Dove@allzool.bio.uni-giessen.de
  orcid: https://orcid.org/0000-0001-9465-5638
keywords:
- biodiversity-indicators
- data-cubes
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2026'
  version: '>= 3.5.0'
- type: software
  title: boot
  abstract: 'boot: Bootstrap Functions'
  notes: Imports
  repository: https://CRAN.R-project.org/package=boot
  authors:
  - family-names: Canty
    given-names: Angelo
    email: cantya@mcmaster.ca
  - family-names: Ripley
    given-names: Brian
    email: Brian.Ripley@R-project.org
  year: '2026'
  doi: 10.32614/CRAN.package.boot
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
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    given-names: Hadley
    email: hadley@posit.co
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    orcid: https://orcid.org/0000-0002-2444-4226
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    given-names: Lionel
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    orcid: https://orcid.org/0000-0002-1416-3412
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    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2026'
  doi: 10.32614/CRAN.package.dplyr
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Imports
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
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- type: software
  title: iNEXT
  abstract: 'iNEXT: Interpolation and Extrapolation for Species Diversity'
  notes: Imports
  url: https://sites.google.com/view/chao-lab-website/software/inext
  repository: https://CRAN.R-project.org/package=iNEXT
  authors:
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  year: '2026'
  doi: 10.32614/CRAN.package.iNEXT
- type: software
  title: labeling
  abstract: 'labeling: Axis Labeling'
  notes: Imports
  repository: https://CRAN.R-project.org/package=labeling
  authors:
  - family-names: Talbot
    given-names: Justin
  year: '2026'
  doi: 10.32614/CRAN.package.labeling
- type: software
  title: magrittr
  abstract: 'magrittr: A Forward-Pipe Operator for R'
  notes: Imports
  url: https://magrittr.tidyverse.org
  repository: https://CRAN.R-project.org/package=magrittr
  authors:
  - family-names: Bache
    given-names: Stefan Milton
    email: stefan@stefanbache.dk
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.magrittr
- type: software
  title: mgrs
  abstract: 'mgrs: Convert ''MGRS'' (''Military Grid Reference System'') Coordinates
    From/To Other Coordinate Systems'
  notes: Imports
  url: https://gitlab.com/hrbrmstr/mgrs
  authors:
  - family-names: Rudis
    given-names: Bob
    email: bob@rud.is
    orcid: https://orcid.org/0000-0001-5670-2640
  year: '2026'
  version: '>= 0.2.4'
- type: software
  title: patchwork
  abstract: 'patchwork: The Composer of Plots'
  notes: Imports
  url: https://patchwork.data-imaginist.com
  repository: https://CRAN.R-project.org/package=patchwork
  authors:
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomasp85@gmail.com
    orcid: https://orcid.org/0000-0002-5147-4711
  year: '2026'
  doi: 10.32614/CRAN.package.patchwork
- type: software
  title: permute
  abstract: 'permute: Functions for Generating Restricted Permutations of Data'
  notes: Imports
  url: https://github.com/gavinsimpson/permute
  repository: https://CRAN.R-project.org/package=permute
  authors:
  - family-names: Simpson
    given-names: Gavin L.
    email: ucfagls@gmail.com
    orcid: https://orcid.org/0000-0002-9084-8413
  year: '2026'
  doi: 10.32614/CRAN.package.permute
- type: software
  title: purrr
  abstract: 'purrr: Functional Programming Tools'
  notes: Imports
  url: https://purrr.tidyverse.org/
  repository: https://CRAN.R-project.org/package=purrr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.purrr
- type: software
  title: readr
  abstract: 'readr: Read Rectangular Text Data'
  notes: Imports
  url: https://readr.tidyverse.org
  repository: https://CRAN.R-project.org/package=readr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Hester
    given-names: Jim
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2026'
  doi: 10.32614/CRAN.package.readr
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.rlang
- type: software
  title: rnaturalearth
  abstract: 'rnaturalearth: World Map Data from Natural Earth'
  notes: Imports
  url: https://docs.ropensci.org/rnaturalearth/
  repository: https://ropensci.r-universe.dev
  authors:
  - family-names: Massicotte
    given-names: Philippe
    email: pmassicotte@hotmail.com
    orcid: https://orcid.org/0000-0002-5919-4116
  - family-names: South
    given-names: Andy
    email: southandy@gmail.com
  year: '2026'
  doi: 10.32614/CRAN.package.rnaturalearth
- type: software
  title: scales
  abstract: 'scales: Scale Functions for Visualization'
  notes: Imports
  url: https://scales.r-lib.org
  repository: https://CRAN.R-project.org/package=scales
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
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    given-names: Dana
  year: '2026'
  doi: 10.32614/CRAN.package.scales
- type: software
  title: sf
  abstract: 'sf: Simple Features for R'
  notes: Imports
  url: https://r-spatial.github.io/sf/
  repository: https://CRAN.R-project.org/package=sf
  authors:
  - family-names: Pebesma
    given-names: Edzer
    email: edzer.pebesma@uni-muenster.de
    orcid: https://orcid.org/0000-0001-8049-7069
  year: '2026'
  doi: 10.32614/CRAN.package.sf
- type: software
  title: stringr
  abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
  notes: Imports
  url: https://stringr.tidyverse.org
  repository: https://CRAN.R-project.org/package=stringr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.stringr
- type: software
  title: tibble
  abstract: 'tibble: Simple Data Frames'
  notes: Imports
  url: https://tibble.tidyverse.org/
  repository: https://CRAN.R-project.org/package=tibble
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2026'
  doi: 10.32614/CRAN.package.tibble
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  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Imports
  url: https://tidyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=tidyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
  - family-names: Girlich
    given-names: Maximilian
  year: '2026'
  doi: 10.32614/CRAN.package.tidyr
- type: software
  title: units
  abstract: 'units: Measurement Units for R Vectors'
  notes: Imports
  url: https://r-quantities.github.io/units/
  repository: https://CRAN.R-project.org/package=units
  authors:
  - family-names: Pebesma
    given-names: Edzer
    email: edzer.pebesma@uni-muenster.de
    orcid: https://orcid.org/0000-0001-8049-7069
  - family-names: Mailund
    given-names: Thomas
    email: mailund@birc.au.dk
  - family-names: Kalinowski
    given-names: Tomasz
  - family-names: Ucar
    given-names: Iñaki
    email: iucar@fedoraproject.org
    orcid: https://orcid.org/0000-0001-6403-5550
  year: '2026'
  doi: 10.32614/CRAN.package.units
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
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  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2026'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: mapview
  abstract: 'mapview: Interactive Viewing of Spatial Data in R'
  notes: Suggests
  url: https://r-spatial.github.io/mapview/
  repository: https://CRAN.R-project.org/package=mapview
  authors:
  - family-names: Appelhans
    given-names: Tim
    email: tim.appelhans@gmail.com
  - family-names: Detsch
    given-names: Florian
    email: fdetsch@web.de
  - family-names: Reudenbach
    given-names: Christoph
    email: reudenbach@geo.uni-marburg.de
  - family-names: Woellauer
    given-names: Stefan
    email: stephan.woellauer@geo.uni-marburg.de
  year: '2026'
  doi: 10.32614/CRAN.package.mapview
- type: software
  title: mockery
  abstract: 'mockery: Mocking Library for R'
  notes: Suggests
  url: https://github.com/r-lib/mockery
  repository: https://CRAN.R-project.org/package=mockery
  authors:
  - family-names: Finkelstein
    given-names: Noam
  - family-names: Bartnik
    given-names: Lukasz
  - family-names: Hester
    given-names: Jim
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.mockery
- type: software
  title: mockr
  abstract: 'mockr: Mocking in R'
  notes: Suggests
  url: https://krlmlr.github.io/mockr/
  repository: https://CRAN.R-project.org/package=mockr
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
  year: '2026'
  doi: 10.32614/CRAN.package.mockr
- type: software
  title: RColorBrewer
  abstract: 'RColorBrewer: ColorBrewer Palettes'
  notes: Suggests
  repository: https://CRAN.R-project.org/package=RColorBrewer
  authors:
  - family-names: Neuwirth
    given-names: Erich
    email: erich.neuwirth@univie.ac.at
  year: '2026'
  doi: 10.32614/CRAN.package.RColorBrewer
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2026'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: rnaturalearthdata
  abstract: 'rnaturalearthdata: World Vector Map Data from Natural Earth Used in ''rnaturalearth'''
  notes: Suggests
  url: https://docs.ropensci.org/rnaturalearthdata/
  repository: https://CRAN.R-project.org/package=rnaturalearthdata
  authors:
  - family-names: South
    given-names: Andy
    email: southandy@gmail.com
    orcid: https://orcid.org/0000-0003-4051-6135
  - family-names: Michael
    given-names: Schramm
    email: mpschramm@gmail.com
  - family-names: Massicotte
    given-names: Philippe
    email: pmassicotte@hotmail.com
    orcid: https://orcid.org/0000-0002-5919-4116
  year: '2026'
  doi: 10.32614/CRAN.package.rnaturalearthdata
- type: software
  title: rnaturalearthhires
  abstract: 'rnaturalearthhires: High Resolution World Vector Map Data from Natural
    Earth used in rnaturalearth'
  notes: Suggests
  url: https://docs.ropensci.org/rnaturalearthhires
  authors:
  - family-names: South
    given-names: Andy
    email: southandy@gmail.com
    orcid: https://orcid.org/0000-0003-4051-6135
  - family-names: Michael
    given-names: Schramm
    email: mpschramm@gmail.com
  - family-names: Massicotte
    given-names: Philippe
    email: pmassicotte@hotmail.com
    orcid: https://orcid.org/0000-0002-5919-4116
  year: '2026'
- type: software
  title: taxize
  abstract: 'taxize: Taxonomic Information from Around the Web'
  notes: Suggests
  url: https://docs.ropensci.org/taxize/
  repository: https://CRAN.R-project.org/package=taxize
  authors:
  - family-names: Chamberlain
    given-names: Scott
    email: myrmecocystus@gmail.com
  - family-names: Szoecs
    given-names: Eduard
  - family-names: Foster
    given-names: Zachary
    email: zacharyfoster1989@gmail.com
  - family-names: Arendsee
    given-names: Zebulun
  year: '2026'
  doi: 10.32614/CRAN.package.taxize
  version: '>= 0.9.99'
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2026'
  doi: 10.32614/CRAN.package.testthat
  version: '>= 3.0.0'

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Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • dplyr * depends
  • ggplot2 * depends
  • furrr * imports
  • future * imports
  • iNEXT * imports
  • magrittr * imports
  • permute * imports
  • purrr * imports
  • readr * imports
  • rnaturalearth * imports
  • sf * imports
  • taxize * imports
  • tibble * imports
  • tidyr * imports
  • units * imports
  • vegan * imports
  • testthat >= 3.0.0 suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.5.0 composite
  • actions/checkout v4 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v4 composite
  • actions/upload-artifact v4 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite

Score: 4.836281906951478