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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE,
comment = "#>",
fig.path = "figures/readme/",
out.width = "100%")
```
Birds of Western Palearctic <img src="figures/readme/compendium-sticker.png" align="right" style="float:right; height:120px;"/>
=========================================================
<!-- badges: start -->
[](https://www.repostatus.org/#active)
[](https://choosealicense.com/licenses/gpl-2.0/)
<!-- badges: end -->
<p align="left">
• <a href="#overview">Overview</a><br>
• <a href="#data-sources">Data sources</a><br>
• <a href="#workflow">Workflow</a><br>
• <a href="#content">Content</a><br>
• <a href="#installation">Installation</a><br>
• <a href="#usage">Usage</a><br>
• <a href="#citation">Citation</a><br>
• <a href="#contributing">Contributing</a><br>
• <a href="#acknowledgments">Acknowledgments</a><br>
• <a href="#references">References</a>
</p>
## Overview
This repository is structured as a research compendium and shares the material used to...
## Data sources
This project uses the following databases:
| Database | Usage | Reference | Link |
| :--------------------------------------------- | :------------------------------------------- | :---------------------------- | :----: |
| WWF Terrestrial Ecoregions of the World | Create Western Palearctic region | Olson _et al._ (2001) | [link](https://www.worldwildlife.org/publications/terrestrial-ecoregions-of-the-world) |
| Natural Earth | Create Western Palearctic region | None | [link](https://www.naturalearthdata.com) |
| BirdLife | Get bird species distribution | BirdLife International (2023) | [link](https://datazone.birdlife.org/species/requestdis) |
## Workflow
This is a work in progress...
## Content
This repository is structured as follow:
- [`DESCRIPTION`](https://github.com/frbcesab/birdlife-wp/tree/main/DESCRIPTION):
contains project metadata (authors, date, dependencies, etc.)
- [`make.R`](https://github.com/frbcesab/birdlife-wp/tree/main/make.R):
main R script to run the entire project
- [`R/`](https://github.com/frbcesab/birdlife-wp/tree/main/R):
contains R functions developed especially for this project
- **{{ LIST ADDITIONAL FILES/FOLDER }}**
## Installation
To install this compendium:
- [Fork](https://docs.github.com/en/get-started/quickstart/contributing-to-projects)
this repository using the GitHub interface.
- [Clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository)
your fork using `git clone fork-url` (replace `fork-url` by the URL of your fork).
Alternatively, open [RStudio IDE](https://posit.co/products/open-source/rstudio/)
and create a New Project from Version Control.
## Usage
Launch the [`make.R`](https://github.com/frbcesab/birdlife-wp/tree/main/make.R)
file with:
```{r eval=FALSE}
source("make.R")
```
**Notes**
- All required packages listed in the `DESCRIPTION` file will be installed (if necessary)
- All required packages and R functions will be loaded
- Some analyses listed in the `make.R` might take time
## Citation
Please use the following citation:
> Casajus N & Barnagaud JY (2025) Geographical characterics of birds of Western Palearctic. URL: <https://github.com/frbcesab/birdlife-wp/>.
## Contributing
All types of contributions are encouraged and valued. For more information,
check out our [Contributor Guidelines](https://github.com/frbcesab/birdlife-wp/blob/main/CONTRIBUTING.md).
Please note that this project is released with a
[Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.
## Acknowledgments
This project has been developed for the
[FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/)
research group
[Acoucene](https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/acoucene/)
that aims to model and project the impacts of the anthropocene on soundscapes with birds as an acoustic ecological indicator.
## References
BirdLife International and Handbook of the Birds of the World (2023) Bird species distribution maps of the world. Version 2023-1. Available at: <http://datazone.birdlife.org/species/requestdis>. Accessed on [22/03/2024].
Olson DM, Dinerstein E, Wikramanayake ED _et al._ (2001) Terrestrial ecoregions of the World: A new map of life on Earth. **Bioscience**, 51, 933-938. DOI: [10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2](https://doi.org/10.1641/0006-3568(2001)051[0933:TEOTWA]2.0.CO;2).