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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