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4. Block Definition File (block.dat) OPTIONALThis optional file can be used to group targets together or to use the facility thatallows the goal to be set as a proportion without calculating the actual amount inarea, length or number of occurrences. When using this file, the type of eachtarget must be set in the spec.dat file. If no grouping is necessary, the type namescan remain the same as the target id. If you are using a block definition file, it ishighly recommended that you read Game and Grantham (2008) to gain a betterunderstanding of how this file works. The contents of this file are:type targe t target2 targetocc sepnum sepdistance prop spfthe typeTheMini mum The number Target MinimumAn Thefor whichgoal clump ofnumber distance at alternativepenaltythe otherfor the size. If a occurrences of which to target. factorattributestarget clump of a of the target mutually planning This is the for thatare of the number of required. separated units proportiontarget.DEFAULTdefined given planningThis can be planning holding the of the(-1)CRITICALtype. units with used in units in target are totalDEFAULT(-1) the given conjunction valid considered amount oftarget is with or clumps. to be the targetDEFAULT (-1)below this instead ofseparated. whichDEFAULT (-1)size then it ‘target’.must beDEFAULT (-1)does notpreserved.count(N/A)toward thegoal.DEFAULT (-1)The values are separated by commas. The file structure looks like:type,target,target2,targetocc,sepnum,sepdistance,prop,spf1,-1,-1,-1,-1,-1,0.25,100002,-1,-1,-1,-1,-1,0.30,100005. Boundary Length File (bound.dat) OPTIONALThe boundary length file contains information on the boundary costs of adjacentplanning units. Although this is an optional file, it is highly recommended to usesince it helps set the level of fragmentation in the solution. Whereas this cost istypically the actual length of the boundary it can be modified to a ‘cost’ or‘effective length’ value to takeinto account boundaries that are particularlydesirable or undesirable. Bound.dat can be created automatically using theMarxan Input Generator. This table can have tabs or commas between thecolumns. If you see repeating PU ids in the bound file - these are "edge" planningunits and repeating them in the bound.dat file helps to avoid bias in the BLMbecause they have shorter 'shared' boundaries. It is not necessary to specifyboundary lengths for all planning units (where they are not specified, Marxan willassume there is no boundary between planning units). However any missingvalues within the file will prevent Marxan from running, for instance if ‘id1’ andTNC Protected Area Tools (PAT) Version 3.0The Nature Conservancy, August 200954
‘id2’ are set but no value for ‘boundary’ is entered (Game and Grantham, 2008).The contents of the bound.dat file are:id1 id2 boundaryplanning unit id neighboring planning the boundary lengthCRITICALCRITICALunit id or the same asid1 for an irremovableboundaryCRITICALThe values are separated by commas. The file structure looks like:id1,id2,boundary1,2,33453.51,3,334536.23.2.2 Gene rating Hexagons (HexGen)Hexagons are the m ost often used polygon featurethat serve as planning units for Marxan analyses.Ecologists have adopted hexagons because theyhave more facets for connectivity and canrepresent a more continuous and natural surface.The HexGen tool has been designed as a simpleway to generate hexagons based on a user-definedsize and attribute them with customized uniqueIDs.You will not need to create hexagons to run thetutorial data since they are already provided. Inorder to create hexagons for a new Marxananalysis, you must first decide on an extent layer which repreents your maximum extent.HexGen will use your specified extent layer to create a hexagon file that matches thespatial boundaries of your extent layer. This layer represents the total area where youwould like hexagons to be created. Before you click on the HexGen button, make surethat you have the Extent Layer in your map view. Once you click on the HexGen button,follow these steps to create hexagon planning units:1. Specify the Extent Layer you wish to use.2. Choose whether you would like to create the hexagons by specifying an Area orby specifying the Number of hexagons.3. If specifying the area, enter the desired area (in hectares) for each hexagon. Thedefault is 100ha. If specifying the number of hexagons, enter the number ofhexagons you would like to create.4. Enter a starting number for your unit IDs. The default is 1.TNC Protected Area Tools (PAT) Version 3.0The Nature Conservancy, August 200955
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 and 52: Sug gested steps for preparing inpu
Page 53: 2. Planning Unit File (pu.dat)This
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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