Shortfalls in the protection of Important Shark and Ray Areas undermine shark conservation efforts in the Central and South American Pacific

This folder contains R code, data and outputs for all analyses in this paper. There are 4 main folders, each of which are given their figure names (Fig. 1, Fig. 2 etc.), to reproduce the figures in the paper.

Authors

Théophile L. Mouton, Adriana Gonzalez-Pestana, Christoph A. Rohner, Ryan Charles, Emiliano García-Rodríguez, Peter M. Kyne, Amanda Batlle-Morera, Giuseppe Notarbartolo di Sciara, Asia O. Armstrong, Enzo Acuñah, Joanna Alfaro-Shigueto, Randall Arauz, Cristopher G. Avalos-Castillo, Ely Augustinus, Sandra Bessudo, Enrique Barraza, Carlos Bustamantea, Elpis J. Chávez, Eduardo Ramon Espinoza, Mario Espinozaa, Ana Hacohen-Domené, Alex R. Hearn, Grettel M. Hernández, Felipe Galván-Magaña, José A. Gonzalez-Leiva, James T. Ketchum, Felipe Ladino, Frida Lara-Lizardi, Jorge Manuel Morales-Saldañaa, Naití Morales Serrano, Jeffry Madrigal-Mesén, Paola A. Mejía-Fallaa, Andrés F. Naviaa, Gabriela M. Ochoa, Marta D. Palacios, César R. Peñaherrera-Palma, Francisco Polanco-Vásquez, Yehudi Rodríguez-Arriatti, Luz E. Saldaña-Ruiz, Oscar Sosa-Nishizaki, Javier Tovar-Ávilaap, Ángel J. Vegaap, Ximena Velez-Zuazo, Melany Villate-Morenoas, Ilena Zanellaat, Rima W. Jabado

R packages

To run the R code contained in this repository, 23 packages are needed to be installed, use the code below to install them:

if (!requireNamespace(tidyverse, quietly = TRUE)) {install.packages(tidyverse)}
if (!requireNamespace(sf, quietly = TRUE)) {install.packages(sf)}
if (!requireNamespace(raster, quietly = TRUE)) {install.packages(raster)}
if (!requireNamespace(ggplot2, quietly = TRUE)) {install.packages(ggplot2)}
if (!requireNamespace(lwgeom, quietly = TRUE)) {install.packages(lwgeom)}
if (!requireNamespace(data.table, quietly = TRUE)) {install.packages(data.table)}
if (!requireNamespace(lubridate, quietly = TRUE)) {install.packages(lubridate)}
if (!requireNamespace(viridis, quietly = TRUE)) {install.packages(viridis)}
if (!requireNamespace(geomtextpath, quietly = TRUE)) {install.packages(geomtextpath)}
if (!requireNamespace(ggpubr, quietly = TRUE)) {install.packages(ggpubr)}
if (!requireNamespace(data.table, quietly = TRUE)) {install.packages(data.table)}
if (!requireNamespace(countrycode, quietly = TRUE)) {install.packages(countrycode)}
if (!requireNamespace(remotes, quietly = TRUE)) {install.packages(remotes)}
if (!requireNamespace(ggflags, quietly = TRUE)) {remotes::install_github('rensa/ggflags')}
if (!requireNamespace(dplyr, quietly = TRUE)) {install.packages(dplyr)}
if (!requireNamespace(lme4, quietly = TRUE)) {install.packages(lme4)}
if (!requireNamespace(sjPlot, quietly = TRUE)) {install.packages(sjPlot)}
if (!requireNamespace(performance, quietly = TRUE)) {install.packages(performance)}
if (!requireNamespace(MuMIn, quietly = TRUE)) {install.packages(MuMIn)}
if (!requireNamespace(visreg, quietly = TRUE)) {install.packages(visreg)}
if (!requireNamespace(grid, quietly = TRUE)) {install.packages(grid)}
if (!requireNamespace(ade4, quietly = TRUE)) {install.packages(ade4)}
if (!requireNamespace(ggrepel, quietly = TRUE)) {install.packages(ggrepel)}

Documentation

The R scripts are as follows:

1. Fig. 1.R - Area charts of temporal trends (1935 - 2023) in marine protected area (A) numbers and (B) size in the Central and South American Pacific.

2. Fig. 2.R - Scatterplots of marine protected area (A) expansion 2010-2023 (B) extent in 2023 and (C) overlaps with ISRAS in the Central and South American Pacific.

The two following scripts need to be ran before, to produce the dataframes necessary to make the plots:

• MPA expansion and extent.R
• ISRAs overlap with MPAs.R

3. Fig. 4.R - Results of Shark Robustness Management Index for Central and South American Pacific MPAs as obtained from Generalised Linear Mixed-effects Models.

4. Fig. 5.R - Principal Component Analysis of the eleven indicators of protection.