Christopher J. Brown, Crow White, Maria Beger, Hedley S. Grantham, Benjamin S. Haloern, Carissa J. Klein, Peter J. Mumby, Vivitskaia J. D. Tulloch, Mary Ruckelshaus, and Hugh P. Possingham. 2015. Fisheries and biodiversity benefits of using static versus dynamic models for designing marine reserve networks. Ecosphere 6:182.

Supplement 1

Julia language, R scripts, and data files for running simulations with the Tun Mustapha Park model.
Ecological Archives C006-044-S1.


File list (downloads)


Christopher J. Brown1,2,11*, Crow White3,4, Maria Beger5, Hedley S. Grantham6,7, Benjamin S. Halpern3,8,9, Carissa J. Klein5, Peter J. Mumby2, Vivitskaia J.D. Tulloch5, Mary Ruckelshaus10 and Hugh P. Possingham5,9

1. The Global Change Institute, The University of Queensland, St Lucia, Queensland, Australia, 4072

2. Marine Spatial Ecology Lab, School of Biological Sciences, The University of Queensland, St Lucia 4072 Australia

3.Bren School of Environmental Science and Management, University of California, Santa Barbara, CA 93106, USA

4. Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA

5. Australian Research Council, Centre of Excellence for Environmental Decisions, School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia 4072

6.The Betty and Gordon Moore Centre for Science and Oceans, Conservation International, 2011 Crystal Driver, Suite 500, Arlington, Virginia, 22202, USA

7. School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia 4072

8. National Center for Ecological Analysis and Synthesis, 735 State St., Suite 300, Santa Barbara, CA 93101, USA

9. Imperial College London, Department of Life Sciences, Silwood Park, Ascot SL5 7PY, Berkshire, England, UK

10. The Natural Capital Project, Department of Biology and the Woods Institute for the Environment at Stanford University; c/o Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112, USA

11. Present address: Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, Queensland, Australia

* E-mail: [email protected]

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)


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


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.