Design of R packages for indicator calculation. Milestone 28
This document outlines the integration and maintenance of R package software for calculating biodiversity indicators from occurrence cubes within the B3 project. We propose the b3verse, which is not an R package but the name for a collection of related R packages that streamline indicator calculation, organize code, and simplify package management. Currently, six packages are included in the b3verse:
1. rgbif: Download occurrence cubes (data generation)
2. gcube: Simulation of occurrence cubes (data generation)
3. b3gbi: Calculate general biodiversity indicators from occurrence cubes (indicator calculation)
4. pdindicatoR: Calculate phylogenetic indicators from occurrence cubes (indicator calculation)
5. impIndicator: Calculate alien impact indicators from occurrence cubes (indicator calculation)
6. dubicube: Calculation of robustness measures for occurrence cubes and uncertainty calculation for indicators (uncertainty estimation)
All packages will be accessible and maintained via an R-universe platform, ensuring continuous updates, easy distribution, and efficient installation.
An indicator calculation workflow is proposed, integrating the different b3verse packages. Occurrence cubes can be downloaded from GBIF data with rgbif or simulated using gcube, then processed with b3gbi to standardize input data. Indicator calculations follow using specialized packages (b3gbi, pdindicator or impIndicator), with dubicube supporting uncertainty estimation.
1. rgbif: Download occurrence cubes (data generation)
2. gcube: Simulation of occurrence cubes (data generation)
3. b3gbi: Calculate general biodiversity indicators from occurrence cubes (indicator calculation)
4. pdindicatoR: Calculate phylogenetic indicators from occurrence cubes (indicator calculation)
5. impIndicator: Calculate alien impact indicators from occurrence cubes (indicator calculation)
6. dubicube: Calculation of robustness measures for occurrence cubes and uncertainty calculation for indicators (uncertainty estimation)
All packages will be accessible and maintained via an R-universe platform, ensuring continuous updates, easy distribution, and efficient installation.
An indicator calculation workflow is proposed, integrating the different b3verse packages. Occurrence cubes can be downloaded from GBIF data with rgbif or simulated using gcube, then processed with b3gbi to standardize input data. Indicator calculations follow using specialized packages (b3gbi, pdindicator or impIndicator), with dubicube supporting uncertainty estimation.
Details
| Number of pages | 10 |
|---|---|
| Type | Report not published by INBO |
| Category | Research |
| Language | English |
Bibtex
@misc{b91815d5-6962-49ce-943d-19b993b9d4c4,
title = "Design of R packages for indicator calculation",
abstract = "This document outlines the integration and maintenance of R package software for calculating biodiversity indicators from occurrence cubes within the B3 project. We propose the b3verse, which is not an R package but the name for a collection of related R packages that streamline indicator calculation, organize code, and simplify package management. Currently, six packages are included in the b3verse:
1. rgbif: Download occurrence cubes (data generation)
2. gcube: Simulation of occurrence cubes (data generation)
3. b3gbi: Calculate general biodiversity indicators from occurrence cubes (indicator calculation)
4. pdindicatoR: Calculate phylogenetic indicators from occurrence cubes (indicator calculation)
5. impIndicator: Calculate alien impact indicators from occurrence cubes (indicator calculation)
6. dubicube: Calculation of robustness measures for occurrence cubes and uncertainty calculation for indicators (uncertainty estimation)
All packages will be accessible and maintained via an R-universe platform, ensuring continuous updates, easy distribution, and efficient installation.
An indicator calculation workflow is proposed, integrating the different b3verse packages. Occurrence cubes can be downloaded from GBIF data with rgbif or simulated using gcube, then processed with b3gbi to standardize input data. Indicator calculations follow using specialized packages (b3gbi, pdindicator or impIndicator), with dubicube supporting uncertainty estimation.",
author = "Ward Langeraert and Peter Desmet and Toon Van Daele",
year = "2025",
month = mar,
day = "19",
doi = "",
language = "English",
publisher = "Instituut voor Natuur- en Bosonderzoek",
address = "Belgium,
type = "Other"
}
