Ecological Archives C006-044-S2

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. http://dx.doi.org/10.1890/es14-00429.1

Mathematical code, written in the program Matlab, for conducting the California MPA case study analysis.
Ecological Archives C006-044-S2.

Christopher J. Brown^1,2,11*, Crow White^3,4, Maria Beger⁵, Hedley S. Grantham^6,7, Benjamin S. Halpern^3,8,9, Carissa J. Klein⁵, Peter J. Mumby², Vivitskaia J.D. Tulloch⁵, Mary Ruckelshaus¹⁰ and Hugh P. Possingham^5,9

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]

Short-term case-study (folder v9 ga NPV fullN fix1)

BinaryTabuMonteCarlo_PointLimit.m (MD5: 069b0975e3970338bc17f079a53b895a)

BinaryTabuMonteCarlo.m (MD5: ab10685d98a5f80af5d52bebb3af36cc)

connect_RedSeaUrchin.mat (MD5: 3dd2aa330869182d45bcc1e7ac4ce1b3)

Fleet_v1.m (MD5: 6245a8898a58c02416f687f4463c2013)

MOPmodel_loop1.m (MD5: dd0ab2893f60679adf5ddbc75994b958)

MOPmodel2.m (MD5: 060cfc23c503344f615618d7fae97f6f)

MPA_EF_v1.m (MD5: afaaa7bd17e462c105a5c4696478dd3c)

OptFsum.m (MD5: 1c52a9cfa4e6f9f6adaa91b8e17331d6)

Patches.mat (MD5: 942ceb31cde9277847f9e61b6fac1a3f)

Payoff_Conservation_EFvalue_STATIC1.m (MD5: 884aff36cbea043067de7b42f1efc64c)

Payoff_Conservation_EFvalue_v1.m (MD5: 8f4304eff81d9ac766bebb45311cbe7a)

STATIC1_v1.m (MD5: baa7296232d57c47d1f3f661b55e8ec6)

tuneAlphaCR.m (MD5: 72fc5bac58ddd4daf48836e9ea8a264b)

tuneRmax.m (MD5: 61e855f083d88cd6c53cba18d8b6f78f)

urchinHab135.mat (MD5: b07077150d5ea4733c80f2ebc65b668a)

wapr.m (MD5: 19b797c30b11aba20b390bb03054b234)

Long-term case-study (folder v9 ga T100)

BinaryTabuMonteCarlo_PointLimit.m (MD5: 069b0975e3970338bc17f079a53b895a)

BinaryTabuMonteCarlo.m (MD5: ab10685d98a5f80af5d52bebb3af36cc)

connect_RedSeaUrchin.mat (MD5: 3dd2aa330869182d45bcc1e7ac4ce1b3)

Fleet_v1.m (MD5: 6245a8898a58c02416f687f4463c2013)

MOPmodel_loop1.m (MD5: 15378bd64be805454b33d3ea4ae848d0)

MOPmodel2.m (MD5: b857cafc564ea35043e0701458d9fd8f)

MPA_EF_v1.m (MD5: afaaa7bd17e462c105a5c4696478dd3c)

OptFsum.m (MD5: 1c52a9cfa4e6f9f6adaa91b8e17331d6)

Patches.mat (MD5: 942ceb31cde9277847f9e61b6fac1a3f)

Payoff_Conservation_EFvalue_STATIC1.m (MD5: 884aff36cbea043067de7b42f1efc64c)

Payoff_Conservation_EFvalue_v1.m (MD5: 8f4304eff81d9ac766bebb45311cbe7a)

STATIC1_v1.m (MD5: 9572ae1a22019a66d93f3d4644d543d1)

tuneAlphaCR.m (MD5: 72fc5bac58ddd4daf48836e9ea8a264b)

tuneRmax.m (MD5: 61e855f083d88cd6c53cba18d8b6f78f)

urchinHab135.mat (MD5: b07077150d5ea4733c80f2ebc65b668a)

wapr.m (MD5: 19b797c30b11aba20b390bb03054b234)

1. Open Matlab
2. Navigate to the appropriate directory
2a. For the short-term case study analysis, navigate into the folder "v9 ga NPV fullN fix1"
2b. For the long-term case study analysis, navigate into the folder "v9 ga T100" (Note: running this code takes ~15 days on a standard desktop computer)
3. Open the file MOPmodel_loop1.m in Matlab and run it
4. When complete, the analysis will produce figures of the results and save the results as "data_save_NPV" (for the short-term analysis) or "data_save_equil" (for the long-term analysis)