Policy Implications of Coupled Economic and Ecological Dynamics in Aquatic Systems

Paper Introducing the marlin package.

renv

This repository is equipped with renv for package management.

To install all dependencies for this project

1. Open R

2. Make sure you have renv installed (if not, install.packages("renv"))

3. Inside R, making sure the working directory is set to the root directory of this repository, run renv::restore()

4. Follow all prompts. This will install local versions of all the dependencies needed for this project

5. If you have trouble installing marlin, see instructions here

Navigating Repo

THe main scripts needed to reproduce results are

1. 00_setup.R
2. 01_coral_case_study.R
3. 02_blue_water_cast_study.R
4. 03_marlin_paper.qmd

The best way to reproduce the results is through the make commands described below. To reproduce results manually, first open 00_setup.R and set parameters as desired. Then, run 01_.. 02_… and 03_.

Knitting to PDF

Note that if you want to knit to PDF you’ll need to have appropriate LaTeX style software installed. I recommend tinytex.

Reproducing results on UNIX machines

This repo is equipped with a make file. To reproduce results this way

1. Make sure you have make installed

2. Open a terminal and make sure the working directory of the terminal is set to the location of this repo

3. Make sure you have all dependencies installed by opening R and running renv::restore()

4. In the terminal, run RUN_NAME="MYRUNNAME" FORMAT="FORMAT" make where MYRUNNAME is the name of the folder you want to create to store results (e.g. v0.1) and FORMAT is one of pdf, html, or docx

5. Wait for a bit! This command will run all the required scripts and knit the paper. Shouldn’t take more than an hour on a reasonable computer with parallel computation capabilities.