🎓 Practice 1 - Research Compendium

Important

This project is the result of the Practice 1 of the training course Reproducible Research in Computational Ecology.

This project aims to download the PanTHERIA database (Kate et al., 2009) and the WWF WildFinder database (World Wildlife Fund 2006). It is structured as a research compendium to be reproducible.

Content

This project is structured as follow:

.
├─ README.md                                  # Presentation of the project
├─ DESCRIPTION                                # Project metadata
├─ LICENSE.md                                 # License of the project
|
├─ data/                                      # Contains raw data
|  ├─ pantheria/                              # PanTHERIA database
|  |  └─ PanTHERIA_1-0_WR05_Aug2008.txt
|  |
|  └─ wildfinder/                             # WWF WildFinder database
|     ├─ wildfinder-ecoregions_list.csv
|     ├─ wildfinder-ecoregions_species.csv
|     └─ wildfinder-mammals_list.csv
|
├─ R/                                         # Contains R functions (only)
|  ├─ dl_pantheria_data.R                     # Function to download PanTHERIA data
|  └─ dl_wildfinder_data.R                    # Function to download WildFinder data
|
├─ analyses/                                  # Contains R scripts
|  └─ download-data.R                         # Script to download raw data
|
└─ make.R                                     # Script to setup & run the project

Note

The folder data/ is not present in this repository (listed in the .gitignore) but we provide the code to locally download raw data.

Installation

To install this compendium:

• Fork this repository using the GitHub interface.
• Open RStudio IDE and create a New Project from Version Control to Clone your fork.

Usage

Open this project in RStudio IDE and launch analyses by running:

source("make.R")

• All packages will be automatically installed and loaded
• Raw data will be saved in the data/ directory

License

This project is released under the GPL-2 license.

Citation

Doe J (2024) Download PanTHERIA and WWF WildFinder databases. URL: https://github.com/rdatatoolbox/practice-1

References

Kate EJ, Bielby J, Cardillo M et al. (2009) PanTHERIA: A species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology, 90, 2648. DOI: 10.1890/08-1494.1

World Wildlife Fund (2006) WildFinder: Online database of species distributions. Version Jan-06. URL: https://www.worldwildlife.org/pages/wildfinder-database.