Supplement 1. Julia language, R scripts, and data files for running simulations with the Tun Mustapha Park model.

File List
Julia Language code for running simulations

Dynamic_optimisation_multiple_runs.jl (MD5: bbfdd827661655716a7055a8ada89bac)

Fishmod_Functions.jl (MD5: dd46b17a2797e1a946af24576369d592)

FishMod_types.jl (MD5: d25a1899f3944bdfe240e06254c01d80)

FishParams_TMP.jl (MD5: 3043b385595906bd89e0ada5578eeaaa)

Generate_initial_conditions.jl (MD5: 40c248c35563c41ce1d99af6e0c82960)

Opt_Functions.jl (MD5: 4b27c3226a0259d38f48b7a209ce8246)

R code for plotting results

MR_plots.R (MD5: 27baadd28c4e5f98a9139b870d11c96e)

stitchresults.R (MD5: 1501a32eb479349248391231a13a331c)

Tradeoffs_plot_Static_Dynamic_TMP.R (MD5: fd0edf6815d6581352cd385e142eb41c)

Tradeoffs_plot_static_naive_informed_TMP_SCB.R (MD5: a82c6c5e77ab766cb7d7ed3d83edebaa)

Data files

AllGridRefsTMPL.csv (MD5: ceebd23d4b88e7b919b49b2d5b003e2a)

bath100.asc (MD5: bc76ddcaaea50986a9e774aba1a4d742)

HabitatGridRefsTMPL.csv (MD5: 92603a8750926d77c20aac26ca993ec2)

HabitatNamesL.csv (MD5: 5908ab79e7b33f10fd91f5c8e8cd2510)

HabitatQualityL.csv (MD5: 0c1ec278d961995979782803e0e5b2ee)

NHabitatsTMPL.csv (MD5: 5e889ebb8c87d8507c2c7d7a322e40fb)

Description
Julia language (v0.3.2) was used to run model simulations and optimise marine reserves.

Working directories will need to be updated for your computer.

R was used for plotting results.

Instructions for running the model

Fishmod_Functions.jl specifies functions for running the model

Opt_Functions.jl specifies functions for optimisations

FishMod_types.jl type declarations for the model

FishParams_TMP.jl parameters file

Generate_initial_conditions.jl Generates initial conditions. Must be run and results saved before optimisations can be conducted.

Dynamic_optimisation_multiple_runs.jl Runs static and dynamic optimisations for multiple scenarios and saves results.

R code for plotting results

stitchresults.R

Stitches together results from multiple runs of different habitat protection targets into one file.

MR_plots.R Make a map of the marine reserves

Tradeoffs_plot_static_naive_informed_TMP_SCB.R Plot static naïve vs. informed tradeoffs.

Tradeoffs_plot_Static_Dynamic_TMP.R Plot static informed vs. dynamic tradeoffs.

Data files

AllGridRefsTMPL.csv Grid cell definitions

bath100.asc Depths for the TMP region

HabitatGridRefsTMPL.csv Habitat types in each grid cell

HabitatNamesL.csv Habitat names

HabitatQualityL.csv Maximum coral trout recruitment rate in each habitat type

NHabitatsTMPL.csv Number of habitat types

Instructions for sensitivity analyses

To run our sensitivity analyses with different dispersal distances. Update the disperal distance parameter 'mlarv' in the parameters file and re-run 'Generate_initial_conditions.jl' to get initial conditions and dispersal distance. Then run the optimisations.