APPENDIX 1. Overview of steps for setting up and running MARXAN

1. Select an appropriate study area boundary: Keep in mind that your choice here can have a dramatic impact on your ultimate MARXAN results. Inclusion of an area with certain biological resources will draw focus away from other areas containing those same resources.

2. Create planning units GIS layer: These can be ownership parcels, uniform polygons (e.g. hexagonal grid), or other appropriate spatial units. Because MARXAN calculates the boundaries of conservation reserves, it is critical that the planning unit dataset used has clean boundaries between the units (e.g. no sliver polygons). A common problem with using parcel datasets is that they include roads as having a width in the map, which prevents adjoining parcels from being considered contiguous. To avoid this problem we removed the roads and extended parcel boundary lines to the centerlines of the roads to allow parcels to be considered adjacent to each other that would not otherwise be considered adjacent because a road right of way was between them.

3. Attribute planning units GIS layer and create planning unit MARXAN file: Each planning unit requires at a minimum three attributes: unique identification number, cost, and conservation status (already conserved, available to be conserved, or excluded from analysis). The cost can be either a true monetary cost of the unit or a proxy, such as the area of the unit. (See how the monetary cost was estimated for each parcel based on parcel size in the main text) Create a planning unit text file using either manually in Excel (for further information see MARXAN user’s manual section 3.2) or using automated tools designed for creating MARXAN input files (e.g. PANDA http://www.mappamondogis.it/panda_en.htm or CLUZ http://www.mosaic-conservation.org/cluz/).

4. Select conservation targets and create conservation feature target file: These targets could be vegetation types, species occurrences, species’ habitat, etc. In the Elkhorn Slough project, vegetation land cover types were the targets, while in the Pleasant Grove project habitat for selected focal species was additionally used. It is then necessary to create a conservation feature target text file manually using Excel that identifies the amount of each conservation target that is to be included in the final reserve selection.

5. Create a planning unit versus conservation feature text file: This can be accomplished manually by determining the amount of each of the conservation targets falling within the boundaries of each planning unit using a variety of GIS overlay techniques (e.g. zonal statistics or intersect), then converting this information into a text file format (for further information see MARXAN user’s manual section 3.6). Alternatively, this can be accomplished using automated tools designed for creating MARXAN input files (e.g. PANDA or CLUZ).

6. Create a boundary length text file. The automated tools designed for creating MARXAN input files (e.g. PANDA or CLUZ) should be used to create the boundary length text file.

7. Create a MARXAN input parameter file. This includes information about where the input files are located, where the output files from the analysis should be placed, as well as a variety of parameters that tell MARXAN how to run the analysis. These parameters include the boundary modifier, the number of runs, number of iterations, and the type of optimization algorithm that should be used. In general, the default parameters are good to use unless otherwise noted. However, the boundary length modifier needs to be analyzed for a range of values, which are used to identify which single value from the range boundary modifiers is appropriate to use The type of optimization algorithm used for these analyses was simulated annealing, which seems to offer the best balance between analysis power and computing efficiency. The MARXAN input file can be created using the user-friendly inedit.exe program included with the MARXAN tool. The input parameter file created using this program should be called input.dat. Alternatively, the input parameters can be set using the automated tools designed for creating MARXAN input files (e.g. PANDA or CLUZ).

8. Run MARXAN model. All of the input files should be located in a single directory (identified as the input directory in the input.dat file) along with the marxan.exe program. To run the model simply double click the marxan.exe program and if all of the input files are set up correctly, a box will appear and output messages about the model runs. Alternatively, the MARXAN model can be run using the automated tools designed for creating MARXAN input files (e.g. PANDA or CLUZ).

9. Output files: summed runs, best run, summary statistics

10. Displaying results and interpretation of output files: Using the summed runs gives you the best estimation of how important any given parcel is for meeting the conservation targets set for the analysis. For more information on the use of MARXAN, see methods manual (Ball and Possingham 2000) and literature at the MARXAN website: http://www.uq.edu.au/marxan/.