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planning unit identifiers in the Marxan planning unit by species sparse (or relational)matrix. Additionally, it can only use a sparse matrix format, and is not compatible with atabular matrix format. Please consult the Marxan website to obtain a copy of thecommand line program “convert_mtx.exe” which converts existing Marxan tabular matrixfiles into a sparse matrix format, compatible with Marxan Optimised.Since Marxan exercises may require several different runs involving the testing ofmultiple parameters, good file management is necessary to maintain organization duringthe analysis. A recommended Marxan working directory should be set up with two subdirectories, one containing the input files, and another containing the output files. Threefiles should reside in the working root folder, including the Input Parameter File,‘input.dat’, the Marxan program executable, ‘Marxan.exe’, and the InEdit executable.The Input Parameter File, ‘input.dat’, must also be stored in the same place as the Marxanprogram executable (see Game and Grantham, 2008).Before we begin discussing how to use the tool to prepare the features and create thesefiles, the user should understand the purpose and contents of each of these files. They aredescribed by Huggins (2005):1. Conservation Feature File (spec.dat)This file holds information about each target, including the goals and names. Onlyid, type and target are essential, all other variables are optional, althoughassigning a high (e.g. 10000) Species Penalty Factor (spf) will help ensure thatyour goals are met. If a column is missing, the default values will be used. Forsome columns, a value of –1 indicates either that the default is to be used or thatvalue is given in the block definition file. The name column can contain spaces orother word separators, but any separator will be replaced by a single space. Ifthere are any duplicate definitions, all but the last one will be ignored. Thecontents of this file are:id Type target spf target2 sepdistanceId of Looks for GoalSpecies Minimum Minimumtarget-block representation penalty clump size separationmustcorrespondto puvspr.datfileCRITICALdefinitionsof the targetDEFAULT (-1) DEFAULT (-1)factor foreach targetDEFAULT (-1)optionalDEFAULT (-1)distanceoptionalDEFAULT (-1)cont..Sepnum name targetoccTarget number of mutuallyseparated PUs in validName in words can includespaces all words must startNumber of occurrencesof the target required.clump optionalwith a letter optionalDEFAULT (-1)DEFAULT (no_name)optionalDEFAULT (-1)The values are separated by commas. The file format looks like:id, type, target, spf, target2, sepdistance, sepnum, name, targetocc334,334,877676.56,10000,443,1000,2,limestone_forest,0335,335,639282.62,63928.26,227,1000,2,alluvial_forest,0TNC Protected Area Tools (PAT) Version 3.0The Nature Conservancy, August 200952
2. Planning Unit File (pu.dat)This file contains all the information related to planning units except for thedistribution of targets. The column headers can include: id, cost, status, xloc andyloc. The id column is the only one that is not optional. The cost and status(ability to “lock-in’) will assume a default value of 1 and 0 respectively if thecolumns are not present. The xloc and yloc columns are critical if there are spatialseparation requirements for any of the targets (separation distance or number).These values represent the location of the planning units, and are usually thecentroids of the polygons. The contents of this file are:id Cost status xloc ylocUnique Of each pu Whether pu is locked in or X centroids of Y centroid ofDEFAULT (1)ID forout of the system pupuDEFAULT (0)CRITICAL for Separation CRITICAL forpuSeparationCRITICALThe values are separated by commas. The file format looks like:id, cost, status1,2.3,02,4.8,0The status of each planning unit can take one of 4 values (Default = 0):Status Meaning0 The PU is not guaranteed to be in the initial or ‘seed’ reserve. However it stillmay be. Its chance of being included in the initial reserve is exactly the‘starting proportion’ from the parameter input file.1 The PU will be included in the ‘seed’ reserve or the initial reserve. It may ormay not be in the final reserve.2 The PU is fixed in the reserve. It starts in the initial reserve and cannot beremoved (locked in).3 The PU is fixed outside of the reser ve. It is not included in the initial reserveand cannot be added (locked out).3. Planning Unit versus Species File (puvspr.dat)This file contains the information on the distribution of targets across the planningunits. It is sometimes called the abundance file. The contents of this file are:SpeciesConservation target idbe a numberCRITICALpuamount– must Planning unit id Number, area, or length ofCRITICALa conservation targetCRITICALThe values are separated by commas. The file format looks like:species,pu,amount26,263,535739.3427,271,228479.37TNC Protected Area Tools (PAT) Version 3.0The Nature Conservancy, August 200953
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 and 44: 3.0 The MARXAN AlgorithmOne of the
Page 45 and 46: 6. All input features must have the
Page 47 and 48: grid of squares or lattice of hexag
Page 49 and 50: • To make "area" and "length" com
Page 51: Sug gested steps for preparing inpu
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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