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

File List <i>Julia Language code for running simulations</i> 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) <i>R code for plotting results</i> 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) <i>Data files</i> 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. <i>Instructions for running the model</i> 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. <i> </i> <i>R code for plotting results</i> 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. <i>Data files</i> 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 <i>Instructions for sensitivity analyses</i> 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.