Simualtion and analysis code for Marine reserves can provide buffering against environmental fluctuations to overexploited but not sustainably harvested fisheries
Contact: dpkilduff@ucdavis.edu
This repo contains code for the submitted manuscript Marine reserves can provide buffering against environmental fluctuations to overexploited but not sustainably harvested fisheries by Will White, Patrick Kilduff, Louis Botsford, and Alan Hastings
These instructions assum that the analyst has installed R (R version 4.3.1 was used for this study) and optionally RStudio.
Clone the project or download and unzip the project file from GitHub.
To install all the packages used by the project, open a new R session and run the following lines from the REPL:
install.packages("renv")
renv::restore() # installs specified versions of all packages in the `renv.lock` file
then run
targets::tar_make()
to run the simulations using the R targets package for analytical pipelines.
Note: running 5 simulations for the parameter set used in the manuscript produces an approx. 29GB duckdb database with 12 tables.
After running the simulations, figures can be created by running the code in the file ms_figures_supp_figs.qmd. To render the file ms_figures_supp_figs.qmd, install Quarto or, if using RStudio, use the Run --> Run all.