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b3gbi

B-Cubed General Biodiversity Indicators

https://github.com/b-cubed-eu/b3gbi

Science Score: 44.0%

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    Scientific vocabulary similarity
    Low similarity (19.4%) to scientific vocabulary

Keywords

biodiversity-indicators data-cubes
Last synced: 6 months ago · JSON representation ·

Repository

B-Cubed General Biodiversity Indicators

Basic Info
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  • Stars: 6
  • Watchers: 4
  • Forks: 2
  • Open Issues: 9
  • Releases: 24
Topics
biodiversity-indicators data-cubes
Created over 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Codemeta

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



[![repo status](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
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badge](https://b-cubed-eu.r-universe.dev/b3gbi/badges/version)](https://b-cubed-eu.r-universe.dev/b3gbi)
[![CRAN
status](https://www.r-pkg.org/badges/version/b3gbi)](https://CRAN.R-project.org/package=b3gbi)
[![R-CMD-check](https://github.com/b-cubed-eu/b3gbi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/b-cubed-eu/b3gbi/actions/workflows/R-CMD-check.yaml)
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[![name status
badge](https://b-cubed-eu.r-universe.dev/badges/:name?color=6CDDB4)](https://b-cubed-eu.r-universe.dev/)



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, 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"))
```

You can install the development version from
[GitHub](https://github.com/) with:

``` r
# install.packages("remotes")
remotes::install_github("b-cubed-eu/b3gbi")
```

## Example

This is a basic example which shows you how to calculate and plot a map of species richness for a data cube containing GBIF occurrence data on amphibians in Europe:

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

# Load GBIF data cube
cube_name <- system.file("extdata", "denmark_mammals_cube_eqdgc.csv", package = "b3gbi")

# Prepare cube
mammal_data <- process_cube(cube_name)

# Calculate diversity metric
map_obs_rich_mammals <- obs_richness_map(mammal_data, level = "country", region = "Denmark", ne_scale = "medium")

# Plot diversity metric
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.

Owner

  • Name: B-Cubed
  • Login: b-cubed-eu
  • Kind: organization

Biodiversity Building Blocks for Policy

Citation (CITATION.cff) 

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.5.0
# 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: 0.7.0
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:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2025'
  institution:
    name: R Foundation for Statistical Computing
  version: '>= 3.5.0'
- type: software
  title: boot
  abstract: 'boot: Bootstrap Functions (Originally by Angelo Canty for S)'
  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: ripley@stats.ox.ac.uk
  year: '2025'
- 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
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2025'
- 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
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  - family-names: van den Brand
    given-names: Teun
    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2025'
- type: software
  title: iNEXT
  abstract: 'iNEXT: Interpolation and Extrapolation for Species Diversity'
  notes: Imports
  url: http://chao.stat.nthu.edu.tw/wordpress/software_download/
  repository: https://CRAN.R-project.org/package=iNEXT
  authors:
  - family-names: Hsieh
    given-names: T. C.
  - family-names: Ma
    given-names: K. H.
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    given-names: Anne
  year: '2025'
- 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: '2025'
- 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@rstudio.com
  year: '2025'
- 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
  repository: https://b-cubed-eu.r-universe.dev
  authors:
  - family-names: Rudis
    given-names: Bob
    email: bob@rud.is
    orcid: https://orcid.org/0000-0001-5670-2640
  year: '2025'
  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: '2025'
- 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: '2025'
- 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@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Henry
    given-names: Lionel
    email: lionel@rstudio.com
  year: '2025'
- 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: '2025'
- 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: '2025'
- type: software
  title: rnaturalearth
  abstract: 'rnaturalearth: World Map Data from Natural Earth'
  notes: Imports
  url: https://docs.ropensci.org/rnaturalearth/
  repository: https://CRAN.R-project.org/package=rnaturalearth
  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: '2025'
- 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
  - family-names: Seidel
    given-names: Dana
  year: '2025'
- 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: '2025'
- 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: '2025'
- 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: '2025'
- type: software
  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: '2025'
- 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: '2025'
- type: software
  title: bold
  abstract: 'bold: Interface to Bold Systems API'
  notes: Suggests
  url: https://docs.ropensci.org/bold/
  repository: https://b-cubed-eu.r-universe.dev
  authors:
  - family-names: Dubois
    given-names: Salix
    email: salixdubois+bold@gmail.com
  - family-names: Chamberlain
    given-names: Scott
    email: myrmecocystus@gmail.com
    orcid: https://orcid.org/0000-0003-1444-9135
  year: '2025'
  version: '>= 1.3.0'
- 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
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
- 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: '2025'
- 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: '2025'
- type: software
  title: rnaturalearthdata
  abstract: 'rnaturalearthdata: World Vector Map Data from Natural Earth Used in ''rnaturalearth'''
  notes: Suggests
  url: https://github.com/ropenscilabs/rnaturalearthdata
  repository: https://CRAN.R-project.org/package=rnaturalearthdata
  authors:
  - family-names: South
    given-names: Andy
    email: southandy@gmail.com
  year: '2025'
- 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: '2025'
- 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: '2025'
  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: '2025'
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CodeMeta (codemeta.json) 

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}

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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