Important
This project is the result of the Practice 2 of the training course Reproducible Research in Computational Ecology.
This project aims to download the PanTHERIA database (Jones et al., 2009) and the WWF WildFinder database (World Wildlife Fund 2006). It is structured as a research compendium to be reproducible.
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)
| ├─ count_ecoregions.R # Function to count ecoregions per species
| ├─ dl_wildfinder_data.R # Function to download WildFinder data
| ├─ dl_pantheria_data.R # Function to download PanTHERIA data
| ├─ join_tables.R # Function to merge WildFinder tables
| ├─ plot_counts.R # Function to make the barplot
| ├─ read_data.R # Function to import WildFinder tables
| └─ select_species.R # Function to subset WildFinder species
|
├─ analyses/ # Contains R scripts
| └─ download-data.R # Script to download raw data
|
├─ index.qmd # Quarto report
├─ index.html # Quarto result (html page)
|
└─ 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.
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.
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
This project is released under the GPL-2 license.
Doe J (2024) Download PanTHERIA and WWF WildFinder databases. URL: https://github.com/rdatatoolbox/practice-1
Jones KE, 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.