sandra-neubert/larvalexportmpas

Larval Export from MPAs

This repository provides the code to the study "Investigating effects of larval export from marine protected areas on fisheries using a global bioeconomic size-spectrum model". Briefly, we couple Lagrangian particle tracking to simulate passive larval movement with the global, spatially-resolved bioeconomic trophic size-spectrum model BOATS to estimate fish biomass and harvest. We then explore a 30✕30 MPA scenario that maximises economic benefit to test how much incorporating larval movement in a marine ecosystem model could offset the projected loss to fisheries upon MPA implementation.
The code can be divided into four main sections:

• Particle Tracking: Preprocessing scripts for particle tracking can be found in Analysis/Notebooks and Analysis/PythonScripts. Near-global particle tracking is done with Parcels by Delandmeter and van Sebille (2019), performed with Analysis/Movement/PythonScripts/HPCParticleTrackingScript.py and requires a high perfomance computer.
• Calculating the transition matrix with movement probabilities: The output of the particle tracking was processed to monthly transition matrices in R using the scripts in Analysis/Movement/RScripts/ProbabilityMatrix, specifically the script Calculate_ProbMatPTGlobalCompile25Y.R.
• Global bioeconomic modelling simulations: We used the publicly available BiOeconomic mArine Trophic Size-spectrum model (BOATS) by Carozza et al. (2016, 2017) to simulate whether egg/larval movement can offset lost fishing following MPA implementation. The version of BOATS including egg/larval movement can be found in Analysis/BOATS/sneubert-boats_v1 with instructions on how to run the model in the doc folder. Running BOATS as available here also requires a high performance computer.
• Analysis of simulations: BOATS outputs were analysed in MATLAB using the scripts available in the folders prepareOutput_SN and plotting_scripts_SN. The output was further analysed in R with the scripts in Analysis/Movement/RScripts/AnalysisBOATSoutput using a Generalised Linear Model (GLM folder) and by assessing the changes in individual Large Marine Ecosystems (LME folder).