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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 = "man/figures/",
out.width = "100%")
```
# World fish occurrences at ecoregion level <img src="https://raw.githubusercontent.com/FRBCesab/templates/main/logos/compendium-sticker.png" align="right" style="float:right; height:120px;"/>
<!-- badges: start -->
[](https://choosealicense.com/licenses/mit/)
<!-- 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 project is dedicated to retrieve, clean and check GBIF occurrences for all fish species of the World (n = 35,035 species). Occurrences are aggregated at the ecoregion level (Spalding _et al._, 2007) for marine species and at the drainage basin level (Tedesco _et al._, 2017) for freshwater species.
## Data sources
This project uses the following databases:
| Database | Usage | Reference | Link |
| :-------------- | :------------------------------------------- | :------------------------ | :----: |
| Fishbase | Get fish species accepted names | Froese R & Pauly D (2000) | [link](https://www.fishbase.se/) |
| GBIF | Get fish occurrences at World scale | GBIF.org (2024) | [link](https://www.gbif.org/) |
| MEOW | Aggregate occurrences for marine species | Spalding _et al._ (2007) | [link](https://www.worldwildlife.org/publications/marine-ecoregions-of-the-world-a-bioregionalization-of-coastal-and-shelf-areas) |
| Drainage basins | Aggregate occurrences for freshwater species | Tedesco _et al._ (2017) | [link](https://figshare.com/collections/A_global_database_on_freshwater_fish_species_occurrences_in_drainage_basins/3739145) |
| Natural Earth | World maps | None | [link](https://www.naturalearthdata.com) |
A comprehensive description of all these databases is available [here](https://github.com/phenofish/gbif-ecoregions/blob/main/data/README.md).
## Workflow
The analysis pipeline follows these steps:
1. Find GBIF accepted names & identifiers from Fishbase accepted names
2. Download GBIF occurrences
3. Clean and check GBIF occurrences
4. Intersect occurrences w/ marine ecoregions layer (marine species)
5. Intersect occurrences w/ drainage basins layer (terrestrial species)
6. Export layers in [`outputs/`](https://github.com/phenofish/gbif-ecoregions/blob/main/outputs)
7. Compute marine and freshwater species richness
8. Export World maps in [`figures/`](https://github.com/phenofish/gbif-ecoregions/blob/main/figures)
## Content
This repository is structured as follow:
- [`DESCRIPTION`](https://github.com/phenofish/gbif-ecoregions/blob/main/DESCRIPTION): contains project metadata (authors, description, license, dependencies, etc.).
- [`make.R`](https://github.com/phenofish/gbif-ecoregions/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/phenofish/gbif-ecoregions/blob/main/R): contains R functions developed especially for this project.
- [`data/`](https://github.com/phenofish/gbif-ecoregions/blob/main/data): contains raw data used in this project. See the [`README`](https://github.com/phenofish/gbif-ecoregions/blob/main/data/README.md) for further information.
- [`analyses/`](https://github.com/phenofish/gbif-ecoregions/blob/main/analyses): contains R scripts to run the workflow. The order to run these scripts is explained in the [`make.R`](https://github.com/phenofish/gbif-ecoregions/blob/main/make.R) and the description of each script is available in the header of each file.
- [`outputs/`](https://github.com/phenofish/gbif-ecoregions/blob/main/outputs): contains the outputs of the project. See the [`README`](https://github.com/phenofish/gbif-ecoregions/blob/main/outputs/README.md) for a complete description of the files.
- [`figures/`](https://github.com/phenofish/gbif-ecoregions/blob/main/figures): contains the figures used to validate et visualize the outputs.
## 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/phenofish/gbif-ecoregions/blob/main/make.R)
file with:
```{r eval=FALSE}
source("make.R")
```
**Notes**
- All required packages listed in the [`DESCRIPTION`](https://github.com/phenofish/gbif-ecoregions/blob/main/DESCRIPTION) file will be installed (if necessary)
- All required packages and R functions will be loaded
- Each script in [`analyses/`](https://github.com/phenofish/gbif-ecoregions/blob/main/analyses) can be run independently
- Some steps listed in the [`make.R`](https://github.com/phenofish/gbif-ecoregions/blob/main/make.R) might take time (several hours)
## Citation
Please use the following citation:
> Casajus N & Loiseau N (2024) A database on World fish species occurrences at ecoregion and drainage basin level. URL: <https://github.com/phenofish/gbif-ecoregions/>.
## Contributing
All types of contributions are encouraged and valued. For more information,
check out our [Contributor Guidelines](https://github.com/phenofish/gbif-ecoregions/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
[Phenofish](https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/phenofish/)
that aims to create a global database of fish functional traits integrating
physiology and ecology across World aquatic ecosystems.
## References
Froese R & Pauly D (2000) FishBase 2000: Concepts, designs and data sources. ICLARM, Los Banos, Philippines. URL: <https://www.fishbase.se/>.
GBIF.org (2024) GBIF Home Page. Available from: <https://www.gbif.org> [17 February 2024].
Spalding MD _et al._ (2007) Marine Ecoregions of the World: A Bioregionalization of Coastal and Shelf Areas. **BioScience**, 57(7), 573-583. DOI: <https://doi.org/10.1641/B570707>.
Tedesco P _et al._ (2017) A global database on freshwater fish species occurrence in drainage basins. **Scientific Data**, 4, 170141. DOI: <https://doi.org/10.1038/sdata.2017.141>.