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meet all biodiversity goals, and by selecting planning units that are clustered togetherrather than dispersed (thus reducing outer boundary length). This task is accomplishedby changing the planning units selected and re-evaluating the cost function, throughmultiple iterations. Alternative scenarios can be evaluated by varying the inputs to thetotal cost function. The boundary length cost factor, for example, can be increased ordecreased depending on the assumed importance of a spatially cohesive portfolio of sites(TNC, 2005). Conservation portfolios can be identified that met stated goals forrepresentation of the biodiversity targets. The ultimate objective is to find a portfolio thatmeets stated conservation goals for all target groups in an efficient manner, while alsomeeting the general criteria of reserve design (e.g., connectivity, minimal fragmentation).While this tutorial does not cover all the aspects of Marxan, additional information can befound in Ball and Possingham, (2000).New Marxan User Manual (For Marxan version 1.8.10)The Pacific Marine Analysis and Research Association (PacMARA) and the Universityof Queensland have written an enhanced user manual for Marxan that was released inFebruary 2008 (Game and Grantham, 2008). Previous documentation was a mixture ofmathematical theory and technical input data requirements and did not fully meet theneeds of all tool users. It is highly recommended that all Marxan users download thismanual from http://www.uq.edu.au/marxan/index.html?page=77823&p=1.1.4.2 andreview with detail since it greatly facilitates understanding of the core software wellbeyond what this tutorial is designed for.EXERCISE 3: Running a Sample Marxan AnalysisREMEMBER1. The user needs to have installed ArcGIS 9.3 ArcMap (9.0, 9.1, or 9.2 maynot work. Also please make sure you have installed the latest service pack)2. An ArcInfo Level is required to run the Marxan Tools. In addition, youalso need to have ArcInfo Workstation installed and make sure theCoverage Tools Toolbox is loaded (this is the default). This toolbox isusually found in C:\arcgis\arcexe9x\Toolboxes (If the user has installed itto the default location)3. The user must have the Spatial Analyst Extension and it should beturned on (Tools > Extension)4. The user should have all geometry checked/repaired for each inputfeature file. If problems persist after repairing geometry, convertingshapefiles into coverage format, then back to shapefile format will oftensolve the problem. The Marxan Tools will process geodatabases andshapefiles but NOT grids.5. It is highly recommended to use the Target Prep tool, since it creates allthe necessary fields used in the Marxan Input Generator and dissolveseach target (i.e. there is one table listing for each unique target type).TNC Protected Area Tools (PAT) Version 3.0The Nature Conservancy, August 200944
6. All input features must have the projection defined and all input featuresmust be in the same projection. Do not use Geographic projection (e.g.decimal degrees) since unit areas or lengths will be calculated incorrectly.7. Remember that depending on the size and level of detail requested by theuser, the Marxan Tools may require large amounts of disk space tooperate and may take a considerable amount of time to run.8. You may want to temporarily disable any Virus Checkers since theprogram will be accessing and deploying executable files.9. When using your own data, make sure any entry in the target name fielddoes not contain any special characters (e.g. ñ, ó, œ) or the program mayfail.10. If you have not already, users should register and download Marxan fromhttp://www.uq.edu.au/marxan . You need around 2 MB of free disk spaceto install Marxan and the associated files. When you download Marxanyou will receive the following files:a. Marxan.exe (the Marxan program executable)b. Inedit.exe (a program that allows you to easily generate theInput Parameter File – the file that controls how Marxanworks)c. input.dat (an example Input Parameter File)d. A folder labeled ‘Sample’, containing examples of the otherinput files used to run Marxane. The Marxan User ManualThese files can be saved anywhere on the computer. For simplicity whenrunning Marxan, the executable, ‘Marxan.exe’, should be located in thesame folder as the input files for that project. Rather than continuallymoving files around, Game and Grantham (2008) recommend simplycopying the Marxan executable to each folder containing a Marxanproject.11. It is important to note that there are a number of Marxan variations withmodified functionalities that have been developed over the years (Gameand Grantham, 2008). There is a version that allows probabilisticinformation on threats or the presence of conservation features at sites tobe included in the reserve design problem; and Marxan with Zones, whichis being developed to handle multiple objective zoning The most widelyused version is Marxan 1.8.10 which uses a traditional tabular matrixformat. Users should also be aware of an optimised version 2.0.2 whichuses only uses a sparse matrix format and was redesigned to handle verylarge and complex problems involving greater than 20,000 planning units.This version is sensitive to the order of planning unit identifiers in theplanning unit by species sparse (or relational) matrix and is not compatiblewith the traditional tabular matrix format. Please consult the Marxanwebsite (http://www.uq.edu.au/ marxan) to obtain a copy of the commandline program “convert_mtx.exe” which converts existing Marxan tabularmatrix files into a format compatible with Marxan Optimised.TNC Protected Area Tools (PAT) Version 3.0The Nature Conservancy, August 200945
Page 1 and 2: Protected Area Tools (PAT)TMfor Arc
Page 3 and 4: AcknowledgementsThe idea for the de
Page 5 and 6: Mandatory Requirements Needed to Ru
Page 7 and 8: Installing the Protected Area Tools
Page 9 and 10: The majority of the work that goes
Page 11 and 12: data to spatially represent the spe
Page 13 and 14: 2003, Araújo et al. 2002). In some
Page 15 and 16: 1.1 Setting up the ERS TableSuccess
Page 17 and 18: 1.1.1 Overlay FunctionAnother item
Page 19 and 20: features have been added to the map
Page 21 and 22: the output will automatically defau
Page 23 and 24: Once you click OK in the previous m
Page 25 and 26: unit or feature (i.e. polygon) must
Page 27 and 28: higher elevations and ridges moving
Page 29 and 30: 1.3.4.2 Marine ERS ModelsDeveloping
Page 31 and 32: MODULE 2. Relative Biodiversity Ind
Page 33 and 34: Normalized relative biodiversity in
Page 35 and 36: EXERCISE 2. Calculating the Relativ
Page 37 and 38: the targets (polygons with lots of
Page 39 and 40: Once this step is performed, you ca
Page 41 and 42: This selection routine will choose
Page 43: 3.0 The MARXAN AlgorithmOne of the
Page 47 and 48: grid of squares or lattice of hexag
Page 49 and 50: • To make "area" and "length" com
Page 51 and 52: Sug gested steps for preparing inpu
Page 53 and 54: 2. Planning Unit File (pu.dat)This
Page 55 and 56: ‘id2’ are set but no value for
Page 57 and 58: conservation target files are alrea
Page 59 and 60: An example of what an attribute tab
Page 61 and 62: values. These values will be used i
Page 63 and 64: Occurrence (OCC), Minimum Clump (CL
Page 65 and 66: 3.2.4 Combining Marxan Input FilesI
Page 67 and 68: 2. Click onto the Run Options tab p
Page 69 and 70: This is the folder where the output
Page 71 and 72: 3.4 Joining and Displaying Marxan O
Page 73 and 74: Figure 12. Results of joining the t
Page 75: McPherson, M, S. Schill, G. Raber,

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