Ecological erosion and expanding extinction risk of sharks and rays
In this repository, you will find the R codes to support the analyses in the publication.
Cite this article as Dulvy and Pacoureau, et al. 2024.
Dulvy NK†, Pacoureau N†, Matsushiba JH, Yan HF, VanderWright WJ, Rigby CL, Finucci B, Sherman CS, Jabado RW, Carlson JK, Pollom RA, Charvet P, Pollock CM, Hilton-Taylor C and Simpfendorfer CA. (2024)  Science 386, eadn1477. DOI: 10.1126/science.adn1477
† These authors contributed equally to this work.

 READ THE FULL ARTICLE AT https://www.science.org/doi/10.1126/science.adn1477

Time-series and trait data are publicly available on https://www.sharkipedia.org/ (Mull, C. G., Pacoureau, N., Pardo, S. A., Ruiz, L. S., García-Rodríguez, E., Finucci, B., ... & Dulvy, N. K. (2022). Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series. Scientific Data, 9(1), 559.)


Boosted_Regression_Tree_Analysis is the folder for the Boosted Regression Tree analysis. It contains:
- Source code contains with Libraries and User-defined functions
- Data (Red List Index ([RLI] and covariates)
- Analysis script

Functional_richness_analysis is the folder for the Simulations of the loss of functional diversity analysis. It contains:
- a script to perform the functional richness analysis
- two functions

General_data is the folder with species names, IUCN categories and covariates.

Global_Chondrichthyan_Catch_and_Effort is the folder for the catch reconstructions and fishing effort analysis. It contains:
- a script to perform the analysis
- a stan model
- two dataset of global catch and effort

Red_List_Index_and_Sankey_plot is the folder for the Red List Index (RLI) over time analysis. It contains:
- a script to calculate the RLI (as well as bootstrapped uncertainty) and do a Sankey plot
- RLI values