README.Rmd

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output: github_document
---

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```{r, include = FALSE}
knitr::opts_chunk$set(collapse  = TRUE,
                      comment   = "#>",
                      fig.path  = "man/figures/",
                      out.width = "100%")
```



Mammals & Birds IUCN Range Maps <img src="https://raw.githubusercontent.com/FRBCesab/templates/main/logos/compendium-sticker.png" align="right" style="float:right; height:120px;"/>
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<p align="left">
  • <a href="#overview">Overview</a><br>
  • <a href="#data-sources">Data sources</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 project is dedicated to compute species range size of all Birds and Mammals of the World.



## Data sources

This project uses the following databases:


| Database                  | Usage                                                 | Reference                     | Link                                                                |
| :------------------------ | :---------------------------------------------------- | :---------------------------- | :-----------------------------------------------------------------: |
| IUCN Mammals spatial data | Compute mammal species metrics                 | IUCN (2023)                   | [link](https://www.iucnredlist.org/resources/spatial-data-download) |
| Bird species distribution maps of the world | Compute bird species metrics | BirdLife International (2023) | [link](https://datazone.birdlife.org/species/requestdis)            |
| Natural Earth             | World maps                                            | None                          | [link](https://www.naturalearthdata.com/)

A comprehensive description of all these databases is available [here](https://github.com/frbcesab/iucn-rangemaps/blob/main/data/README.md).


## Workflow

The analysis pipeline follows these steps:

1. Create study area (raster of 0.08333° x 0.08333° resolution)
2. Analyses for Mammals species
    - Import IUCN layer
    - Extract species names
    - Check taxonomy
    - Merge subpopulation w/ parent
    - Compute species range size (count grid cells)
    - Compute species range size (polygons area)
    - Intersect polygons on grid cells (occurrences at cell level)
3. Analyses for Birds species
    - Import BirdLife layers
    - Split spatial layers by Birds family
    - Extract species names
    - Check taxonomy
    - Compute species range size (count grid cells)
    - Compute species range size (polygons area)
    - Intersect polygons on grid cells (occurrences at cell level)


## Content

This repository is structured as follow:

- [`DESCRIPTION`](https://github.com/frbcesab/iucn-rangemaps/blob/main/DESCRIPTION): contains project metadata (authors, description, license, dependencies, etc.).

- [`make.R`](https://github.com/frbcesab/iucn-rangemaps/blob/main/make.R): main R script to set up and run the entire project. Open this file to follow the workflow step by step.

- [`R/`](https://github.com/frbcesab/iucn-rangemaps/blob/main/R): contains R functions developed especially for this project.

- [`data/`](https://github.com/frbcesab/iucn-rangemaps/blob/main/data): contains raw data used in this project. See the [`README`](https://github.com/frbcesab/iucn-rangemaps/blob/main/data/README.md) for further information.

- [`outputs/`](https://github.com/frbcesab/iucn-rangemaps/blob/main/outputs): contains the outputs of the project. See the [`README`](https://github.com/frbcesab/iucn-rangemaps/blob/main/outputs/README.md) for a complete description of the files.



## 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/iucn-rangemaps/tree/main/make.R)
file with:

```{r eval=FALSE}
source("make.R")
```

**Notes**

- All required packages listed in the [`DESCRIPTION`](https://github.com/frbcesab/iucn-rangemaps/blob/main/DESCRIPTION) file will be installed (if necessary)
- All required packages and R functions will be loaded
- Some steps listed in the [`make.R`](https://github.com/frbcesab/iucn-rangemaps/blob/main/make.R) might take time (several hours)




## Citation

Please use the following citation: 

> Casajus N, Loiseau N & Mouquet N (2024) World mammals and birds species richness. URL: <https://github.com/frbcesab/iucn-rangemaps/>.





## Contributing

All types of contributions are encouraged and valued. For more information, 
check out our [Contributor Guidelines](https://github.com/frbcesab/iucn-rangemaps/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.



## 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].

IUCN (2023) The IUCN Red List of Threatened Species. Version 2023-1. Available at: <https://www.iucnredlist.org>. Accessed on [22/03/2024].