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USER MANUAL and TUTORIAL

1. 1 DEFAULT 1 DEFAULT 1 each target optional e dar DEFAULT 1 DEFAULT 1 CRITICAL cont Sepnum name targetocc Target number of mutually Name in words can include Number of occurrences separated PUs in valid spaces all words must start of the target required clump optional with a letter optional optional DEFAULT 1 DEFAULT no_name DEFAULT 1 The values are separated by commas The file format looks like id type target spf target2 sepdistance sepnum name targetocc 334 334 877676 56 10000 443 1000 2 limestone_forest 0 335 335 639282 62 63928 26 227 1000 2 alluvial_forest 0O TNC Protected Area Tools PAT Version 3 0 52 The Nature Conservancy August 2009 2 Planning Unit File pu dat This file contains all the information related to planning units except for the distribution of targets The column headers can include id cost status xloc and yloc 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 O respectively if the columns are not present The x oc and yloc columns are critical if there are spatial separation requirements for any of the targets separation distance or number These values represent the location of the planning units and are usually the centroids of the polygons The contents of this file are id Cost_ status lo yor Unique Of each pu Whether pu is locked in or X centroids of Y
2. 4 743687 479 659515 515 Meters TNC Protected Area Tools PAT Version 3 0 25 The Nature Conservancy August 2009 mean and a color ramp Before clicking OK press the Classify button to see the MEAN Statistic histogram summary The mean value of the MEAN field will be displayed in the Classification Statistics box This represents the mean risk value for all the habitat polygons This number could be used as a cut off point in determining a threshold for habitats which may be more impacted because of the intensity and influence distances of the underlying risk element features For example if the mean value is 12 55 all planning units polygons that exceed this may be high risk candidate units or potentially impacted at higher risk levels based on the ERS model and the spatial extents of the risk element features One could exclude these features in the map view by clicking on Data Exclusion in the Classification dialog box and specifying this threshold limit as a selection formula e g zstat MEAN gt 12 55 1 3 4 Creating Freshwater and Marine Environmental Risk Surfaces As previously mentioned ERS models can also be customized to represent risks to habitats in freshwater and marine realms Experts in these realms must identify what risk elements are impacting the health of these systems and rank them accordingly in their intensity value and influence distance For example freshwater habitats may be impacted by features such
3. defined When using grids the grid value is used as the intensity value Sample Data Tydixton Park Watershed Jamaica The sample spatial data used in these tutorial exercises comes from the Tydixton Park watershed in central Jamaica The data contains habitat features representing lines rivers points endemic species locations and polygons forest types In addition to habitats species there are shapefiles representing various socio economic activities or habitat risk elements These include agriculture mining roads and urban areas The other files are the planning units hexagons protected areas and the boundaries of the Tydixton Park watershed All of these files will be used to conduct a preliminary protected area gap assessment based on the results of the three exercises As with any input file that is used in PAT each data file must have any geometry errors corrected and projection information defined These sample datasets have been projected to Lambert Conformal Conic using the Jamaican Datum 2001 JAD2001 La Sample Modeks Folder Eo rick_ag_small_scale shp Shapefile ES risk_ag_sugarcane shp Shapet ile it Ei risk_baunite_mines sho Shapefile 7 EB risk_quanries sho Shapefie El risk_roads shp Shapefile E risk_towns shp Shapefde El risk_urban_arveas cho Shapefde Ei target line habitats cho Shapefde Ef rarget peent spaces cho Shapefde EX target_pelygon habitats cho Shapefde El eydixton planning _units shp Shap
4. 15 KErOv aY EUC UON a aa 17 1 2 Adding and Assigning the Intensity and Influence Distance to Each Risk I Fe Ae A esra e E e N 18 LO exe Cutie be ERS Modul ssoi non iarutaatomoriistnecdteaue 18 1 3 1 Launch the ERS Module and Specify Input Layers and Output Parameters 19 1 3 2 Specify the Intensity Influence Distance Decay Type Overlay and Weight Toreach Risk Element ve ciachsnecedavesactncaiconddavisedenuarperedusigss a a a 22 1 3 3 Viewing the ERS Results and Summarizing Spatial Statistics 24 1 3 4 Creating Freshwater and Marine Environmental Risk Surfaces 26 MODULE 2 Relative Biodiversity Index RBI Calculator 0 0 ceseeeeeeeeeeeeeeees 31 EXERCISE 2 Calculating the Relative Biodiversity Index RBI ce eeeeeeeeees 34 ZA RUNS tne RBI M d l zarana ntcudivaladieasiulnssniluentletenitaialehrdianes 35 2a nemen FR Db CS US eea e E n 37 MODULES Maram Toob erenn a a a 42 30 The MARXAN Als orth ea a a E eaten 43 EXERCISE 3 Running a Sample Marxan Analysis cccccccsssseeeeeeeeeeeeeeaeeeseeeeees 44 32 Matxananput Pile Prepatat Oi eonenn unes a ieharth ea aagaees tah eb ascumeeanteaares 49 3 2 Marxian An DU File Seeonee a a apes a a a 51 5 2 2 Genetauins Hexac Ons CHC KEM ese sities sea aisha nseteasete a Scostitensa ecto stances 55 32 Markan Par Set Pie enseri A oveteri minor mae 56 9 225 Maian Input Generator MI aioe Obi a Babe utah 61 5 2 4 Combining Marxin Input Flesini A 65 5
5. 2 0 RU Convert Matix FING serena a a anit aircbenes 65 3 3 Setting up the input dat file with Inedit and Executing Marxan 0008 66 De Oe VT Med ess oie aces late madinuuraeisaantare ican ieee 66 3o Ranne NM E21 21 MORE MET een a a ont iar amr ven nt Pentre Wane ec nC mae me Cet rt Ooty ete 70 3 4 Joining and Displaying Marxan Output ccccccccccccccsssssssecceceeeeeeeeesseeceeeeeeeeas 71 54 2 Joni Marxian Output Files aie ccc osen e town eeeed ete awa 71 3 4 2 Displaying and Analyzing Marxan Results ccccsssssesececceeeeeesseseeeeeees 12 S Uo ol e S ee E E E E E A E E S E EEE ee 74 TNC Protected Area Tools PAT Version 3 0 2 The Nature Conservancy August 2009 Acknowledgements The idea for the development of the Protected Area Tools PAT to assist countries struggling with methods for conducting national protected area gap assessments was conceived at the Mesoamerica and Caribbean Geospatial Alliance meeting in Port of Spain Trinidad in May 2004 The design and development of the system was executed by The Nature Conservancy s Mesoamerica amp Caribbean Science Program and funded by The World Bank s Development Grant Facility DGF Project The DGF Project was designed to help the Inter American Biodiversity Information Network IABIN establish the Connectivity Program whose main objective is to encourage the integration of biological and geospatial data The objective of IABIN is to prom
6. 2009 1 2 Adding and Assigning the Intensity and Influence Distance to Each Risk Element Feature Prior to executing the ERS model all risk elements must first have intensity and influence distance values assigned As explained in the previous section creating an ERS risk matrix is helpful when comparing intensity and influence distance values and ranking risk potential between risk elements The user has the option of entering these values manually using the ERS tool or defining these values in a field within the corresponding shapefile or geodatabase For large and complex datasets it is always easier to define the values using attribute fields The intensity and influence distance fields should be defined as integer types and given a name that the user can recognize If the risk element has a class definition listed in the attribute table it is important to assign the correct values to each corresponding class type The risk matrix can help you when it is time to calculate these fields Remember that a raster dataset will be created for each unique combination of risk element class intensity and influence distance values If you have a large number of classes intensity and influence distance values the computation could take a very long time to complete It is recommended that the user first test the model using one or two risk element files in order to get an idea of optimal output cell size run time required and hard disk space requirement
7. 285925367842 8 Cost 1075 0 PUs 71 Boundary 216 8 Missing 19 Shortfall 3631 522 65 Penalty 285925361367 792175 TNC Protected Area Tools PAT Version 3 0 70 The Nature Conservancy August 2009 3 4 Joining and Displaying Marxan Output 3 4 2 Joining Marxan Output Files gt Tydixton_Park mxd ArcMap Arcinfo File Edit View Insert Selection Tools Window Help Now let s view the results using ArcMap by joining D Hg Ea m h 66 99 the new output Marxan me run_name_best txt te EERE ETE and run_name_ssoln txt with the planning units tec EEM ID The planning unit ID acts as the common key to join these text files To do this click on the Join and Display Marxan Output menu item This will bring up a new dialog box and you must specify the Planning Unit feature class the Planning Unit ID field the Marxan output file you wish to join and the name of the join field and the new output field JOIN AND DISPLAY MARYAN OUTPUT which will store the new information You will have to run this routine twice once for the run_name_best txt Field Name should be SOLUTION and another time for the run_name_ ssoln txt Field Name should be NUMBER The SOLUTION refers to which planning units actually made it into the final portfolio Planning units assigned the number 1 are included those assigned a O are excluded The NUMBER refers to how many times the planning unit was chosen based on the total numbers of runs th
8. Marxan Input File Preparation Suggested steps to follow when conducting a Marxan analysis are diagramed in the figure on the next page In order to run the Marxan Tools the user will need to prepare four basic data layers These layers include 1 Conservation Targets These are the habitats or species in which conservation goals are set and can be represented as points lines or polygons These features should be previously screened as potential candidate sites for meeting conservation goals that are expressed in number of occurrences points area polygons or length lines in map units i e hectares If you are using a block definition file these goals can be expressed as percentages of the target s total units Species penalty factors can be assigned to each target depending on how important it is for each one to reach the conservation goal It is recommended to use the Target Prep tool when preparing your targets for the Marxan Input TNC Protected Area Tools PAT Version 3 0 AQ The Nature Conservancy August 2009 3 4 Generator This tool creates all the necessary fields and dissolves each target layer so there is one table listing for each unique target type Cost Surface This is also an optional layer but required if the user is going to include a Unit Cost measure to each planning unit as indicated in the Marxan algorithm Any number of measures may be used such as threat or suitability for conservation strategi
9. The Nature Conservancy 2003 Alaska Yukon Arctic Ecoregional Assessment Zenny N 2006 Technical Summary of the Jamaica Ecoregional Planning JERP Marine Analysis The Nature Conservancy Kingston Jamaica 16 pages TNC Protected Area Tools PAT Version 3 0 75 The Nature Conservancy August 2009
10. This can be useful if the goals are high and the cost to meet the last small part of the goal would be very expensive Load Save Saves Deworkspace marxantinput dat We Save Summary J Save Log File Save each n Steps Save each n Changes Species missing if proportion of target lower than 1 Save File Name tydistor_run Output Directory D workspace marsan The text within the box Save File Name will prefix all the output text files Enter a descriptive name that will help you remember the specific run that the output files refer to e g tydixton__100runs In the Output Directory enter the same folder path where you input files exist It s best to keep all the files associated with the same run together TNC Protected Area Tools PAT Version 3 0 68 The Nature Conservancy August 2009 This is the folder where the output files will be written by Marxan Click the Save button to save the information to the input dat file 6 Click on the Cost Threshold tab on the Inedit screen This screen should be left with the default values and the Threshold Enabled ay Input File Editor for Marxan SEE Problem Aur Options Annealing Input Output Cost Threshold Misc box unchecked as shown 7 Click on the Misc tab on the Inedit screen This tab allows the user to specify a starting proportion of the planning units to be in the random starting portfolio Type 0 into this box and uncheck t
11. Zonal Statistics in Spatial Analyst can now be used to summarize the ERS surface statistics by planning unit hexagon or habitat polygon In doing so planning units can be assigned a mean cost value for use in Marxan or habitat polygons lines points can be ranked by the underlying ERS area weighted statistics In order to do this each planning TNC Protected Area Tools PAT Version 3 0 24 The Nature Conservancy August 2009 unit or feature i e polygon must have a unique ID field If you do not have a unique ID field present you must add a new integer field to the table and calculate the field to a unique value e g FID field In this example we will use the tydixton_planning_units shp file to run zonal statistics of the ERS grid This file was created using the HexGen tool listed under the Marxan Tools Add this shapefile to the view and go to Spatial Analyst gt Zonal Statistics Make sure the following fields have been defined before clicking OK Zone dataset tydixton_planning_units shp Zone field D Value raster Your ERS ouput grid Ignore NoData in calculation checked Join output table to zone layer unchecked Chart statistic unchecked Output table specify the directory and name of the table e g zstatl dbf Once you click on OK the surface univariate statistics of the ERS are computed within the boundaries of each unique planning unit hexagon The zstat table will appear which can now be used to join back to the pol
12. a comprehensive representation of biodiversity the ultimate question conservation planners want answered is Where do I get the best ecological return for my conservation dollar This question has driven the design of a systematic logical and repeatable toolkit that helps planners evaluate activities or events that may be threatening habitat health identify a comprehensive representation of biodiversity for protection and configure an optimal portfolio solution for meeting habitat conservation goals PAT consists of three conservation modules which operate within Environmental Systems Research Institute s ESRI ArcGIS 9 3 Geographic Information System GIS software 1 Environmental Risk Surface ERS 2 Relative Biodiversity Index RBI 3 Marxan Tools ArcGIS 9 3 software was chosen as the application for the tool since ESRI is a strong supporter of TNC s mission and provides a grant agreement in which conservation partners can freely obtain their software for conservation related work Each of the three modules was developed using Visual Basic NET ArcObjects PAT operates on three basic input data layers including a habitats species b risks elements to habitats species and c protected areas As this is an iterative process users are encouraged to continue to refine habitat species data goals and risk elements in order to reassess ecological gaps over time These tools permit countries to continue the refinement process in a sys
13. algorithm The E Hexcen program should run for less than 5 minutes i nay Mer MARXAN TARGET PREP using the tutorial data depending on the speed a g MARXAN INPUT GENERATOR and available resources of your computer O COMBINE MARXAN INPUT FILES F RUN CONVERT TO MATRIX FILE Error messages at the beginning showing a0 RUMINEDIT RUM MARKAM warnings about blockdefname and highdata are normal For the tutorial there should be 113 Soe eee eevee Se a en tae planning units 22 species targets 334 boundaries and 85 conservation features read by the algorithm The information screen will then print any further information This can help identify any problems with the input files A message will appear here if one or more targets are already adequately represented in a portfolio e g if locking in any planning units at the beginning of the run or if there are problems with the formatting of the dat files causing them to be unreadable If this occurs check the formatting including the uuu E placing of commas check all field Marine Reserve Design via Annealing headings are lowercase no capital letters Setn aE geen eee can appear in the headings Bhs Bonde ovens hposs ing zen uq edu au VARNING unable to find HIGHDATA default value will be used e o Entering in the data files When the program has finished running RES oere E anning Unit names read in 19 species read in press lt Enter gt to close the window Erta
14. and they use Target for what we refer to as the Goal Since the tutorial target data is already provided with the fields needed to extract and create the input files there is no need to run Marxan Target Prep on them If you would like to practice using this tool there is a copy of the sample targets without the last eight attributes listed in the above table located in the Tydixton_Park_Tutorial_Data Sample_Model MARXAN For_Target_Prep directory that can be run through Target Prep You can use the numbers listed in the table below to prepare these targets It is highly recommended that you use the Target Prep routine if you have new target features that need new Marxan input fields added and assigned values to the attribute table However if you are using new target data there are two fields that need to be manually defined before using Marxan Target Prep 1 TARGET_NAM A text name needs to be assigned to each point line or polygon that describes each unique conservation target class This can include spaces but all words must start with a letter e g Semi deciduous forest West Indian whistling duck etc When using your own data make sure any entry in the target name field does not contain any special characters e g fi 6 or the program may fail Try to limit the length of the target name to fewer than 50 characters 2 TARGET_ID A unique integer number must be assigned to each unique target class e g 1 2
15. if the user has specified roads with different levels of intensity the overlay function specified here will be used to calculate how to resolve areas where two roads of different intensities meet within the same risk element features Although SUM is the default there are instances where MAXIMUM may be a better option You may choose any of the overlay functions previously explained e g mean majority maximum median minimum minority range standard deviation and variety The Weight field is used to assign higher weight criteria to individual risk element features The default is set to 1 meaning all features are weighed equal in the computation of the final risk surface model The weight value behaves much like the intensity value so caution should be used when altering this value Now select the appropriate intensity influence distance decay type overlay and weight function values manually or by using the drop down menus For this exercise choose the Terr_Dista for influence distance and Terr_Inten for the intensity values for all input TNC Protected Area Tools PAT Version 3 0 23 The Nature Conservancy August 2009 layers risk element groups and leave the default values for the remainder of the input parameters If you want to see the commands as they are executed you need to open your Command Line Window by clicking on the Open Close Command Line Window button in the ArcGIS menu bar When ready click OK to
16. include conservation targets cost surface planning units and status layer 3 2 1 Marxan Input Files The Marxan Input Generator MIG can produce up to five input text files three required and two optional files that Marxan uses to run These files are automatically generated using the four data layers described above and are in a tabular matrix format a compatible input format for use with Marxan 1 8 10 and earlier versions A new version of Marxan 2 0 2 Marxan Optimised was released in 2007 and is designed for larger and more complex Marxan investigations This version is sensitive to the order of TNC Protected Area Tools PAT Version 3 0 51 The Nature Conservancy August 2009 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 a tabular matrix format Please consult the Marxan website to obtain a copy of the command line program convert_mtx exe which converts existing Marxan tabular matrix files into a sparse matrix format compatible with Marxan Optimised Since Marxan exercises may require several different runs involving the testing of multiple parameters good file management is necessary to maintain organization during the analysis A recommended Marxan working directory should be set up with two sub directories one containing the input files and another containing the output files Three files s
17. networks using a variety of tools available on the web i e ArcHydro AGREE Rivertools is an exceptional hydrology modeling software with powerful tools for creating stream networks and ordered watersheds with high precision ArcHydro http www crwr utexas edu giswr hydro index html AGREE http www ce utexas edu prof maidment gishyd97 terrain agree agree htm Rivertools Software http Awww rivix com TNC Protected Area Tools PAT Version 3 0 77 The Nature Conservancy August 2009 Flow Accumulation Network Flow Accumulation GRID Process for creating flow direction and flow accumulation Each cell can exit in one of eight directions The flow direction grid is computed by the slope of exiting adjacent cells Once the flow direction is established the weight grid i e intensity can be accumulated throughout the network TNC Protected Area Tools PAT Version 3 0 28 The Nature Conservancy August 2009 1 3 4 2 Marine ERS Models Developing ERS models for the marine realm is often the most difficult of the three realms due to the lack of data and the dynamic nature of the ocean an environment that is constantly moving Assigning risk boundaries to the ocean is a complicated and perplexing task Attempts to model coastal transport with ocean current data for assigning marine risk distributions has been attempted by Schill 2005 using the cell assigned velocity from the Hybrid Coordinate Ocean Model HYCOM data model The model oper
18. target sub groups The portfolio will be greatly influenced by the way the targets are defined For example if the portfolio is required to hold both upland and lowland portions of a specific target it must be defined in a way that includes this information Examples include stratification by elevation or bathymetry surface geology or by other geographic units that define biologically meaningful differences d Designing Planning Units Adapted from Game and Grantham 2008 and Pressey and Logan 1998 An essential pre processing step is to divide your planning region into a set of planning units Planning units are areas for which data on occurrence frequency and extent of the targets exists In their simplest form planning units may be defined by overlaying your planning region with a TNC Protected Area Tools PAT Version 3 0 46 The Nature Conservancy August 2009 grid of squares or lattice of hexagons They must capture all the areas that can possibly be selected as part of the reserve system and their size should be at a scale appropriate for both the ecological features you wish to capture and the size of the protected areas likely to be implemented In general they should be no finer in resolution than the data on conservation features and no coarser than is realistic for management decisions There is however no necessity to have uniformly shaped planning units Nor is it always true that smaller planning units are better In some c
19. targets than is expected for the planning unit size which may or may not justify conservation action N nRBI nRBIr N where set of targets T ti t2 ts tn N number of targets TNC Protected Area Tools PAT Version 3 0 32 The Nature Conservancy August 2009 RBI Aggregated Target Domains Can sum up individual target RBIs across a set of targets T tit t3 ty RBI RBI N T can be defined as e All targets e All forest matrix targets e All riparian targets N can be defined as e The count of targets in the set T e The count of targets in the set T that occur in that Query Domain Aggregated RBI Sum Value m of all individual y the total a f i n Normalized relative biodiversity index values can be summed across multiple targets at the landscape and planning unit level to calculate aggregate nRBI for terrestrial freshwater and marine realms The Relative Biodiversity Index calculated at the planning unit level can be combined with the results of Marxan and environmental risk surface ERS modeling This approach allows further more specific insight into potential conservation action such as setting priority sites that inform habitat specific strategies Moreover this combination can be used to predict maximal return on conservation investment towards long term habitat goals and systematically provide sequence information for building a representative network of conse
20. to keep your intensity values within a certain range for comparative purposes h Enter the Expand Extent By Value This value represents the distance that final extent will be extended beyond the maximum spatial extent of all the input layers This will prevent the output grid intensity values along the edges from being inadvertently cut off Commonly this is the maximum influence distance that is used on any one of the input risk elements For the tutorial example we will use the default of 1000m On some occasions it is desirable to enter a greater extent if further processing will be required using datasets outside the current extent Once you have all the input parameters entered click OK 1 3 2 Specify the Intensity Influence Distance Decay Type Overlay and Weight for each Risk Element TNC Protected Area Tools PAT Version 3 0 J9 The Nature Conservancy August 2009 Once you click OK in the previous menu a new dialog box will appear that allows the user to specify the values for Intensity Influence Distance Decay Type Rate Overlay and Weight for each input risk element feature The name of each selected risk element feature will appear on the left side of the dialog box The user has the option of typing these values in or clicking on the down arrow and choosing a field that contains the corresponding values If the user is going to type in the values the ERS risk matrix previously prepared should be opened so the correct v
21. uq edu au marxan You need around 2 MB of free disk space to install Marxan and the associated files When you download Marxan you will receive the following files a Marxan exe the Marxan program executable b Inedit exe a program that allows you to easily generate the Input Parameter File the file that controls how Marxan works c input dat an example Input Parameter File d A folder labeled Sample containing examples of the other input files used to run Marxan e The Marxan User Manual These files can be saved anywhere on the computer For simplicity when running Marxan the executable Marxan exe should be located in the same folder as the input files for that project Rather than continually moving files around Game and Grantham 2008 recommend simply copying the Marxan executable to each folder containing a Marxan project It is important to note that there are a number of Marxan variations with modified functionalities that have been developed over the years Game and Grantham 2008 There is a version that allows probabilistic information on threats or the presence of conservation features at sites to be included in the reserve design problem and Marxan with Zones which is being developed to handle multiple objective zoning The most widely used version is Marxan 1 8 10 which uses a traditional tabular matrix format Users should also be aware of an optimised version 2 0 2 which uses only uses a sparse matrix for
22. 3 etc Double check to make sure that you have not assigned the same ID to any of your target classes TNC Protected Area Tools PAT Version 3 0 58 The Nature Conservancy August 2009 An example of what an attribute table should look like prior to using the Marxan Target Prep tool r Attributes of new_polygon_habitats M fx FID Shape TARGET_NAM TARGET_ID 9 Pobgon Diy Aluvial Forest 5082 14 Polygon Dry Alluvial Forest 5082 15 Pobgon Dp Alluvial Forest 5082 E 2 B Pogon Bi Limestone Forest A112 a occas E Before executing the Marxan Target Prep tool it is a good idea to create a master table that lists all unique conservation target classes with each input field and corresponding value that will be assigned This can be done using Excel or another type of spreadsheet application An example of what this table should look like is found below These values could be assigned by experts who understand the conservation needs of each target Having this table will make it easier to use the Marxan Target Prep as you type in the field values for every target class The assignment of these values is very important because they will drive the results of your Marxan analysis and resulting conservation assessment Consequently these numbers should be reviewed by conservation experts who understand both how Marxan operates and the objectives of your conservation planning exercise An example of a conservation targe
23. 6 AND ore stats MEAN lt 12 55 low risk value Go to Selection gt Select by Attributes in Clear Verify Hep Load Save the main ArcGIS toolbar When the dialog box appears enter the following Apply Close formula your_output_name_RBI_SUMMARY RBNT1 gt 1 056 AND ers_stats MEAN lt 12 55 TNC Protected Area Tools PAT Version 3 0 40 The Nature Conservancy August 2009 This selection routine will choose the planning units highlighted in light blue that are above the mean RBI value and below the mean risk value indicating high conservation value with low risk based on model inputs as shown in the figure below This approach is an example of providing insight into potential conservation areas and setting priority sites based on target specific strategies for maximum return on conservation investment Similar analysis can be conducted using Marxan irreplaceability number values a Highest RBI Scores Sa a below Risk Mean An example of selecting planning units highlighted in light blue that are above the mean RBI value gt 1 056 and below the mean risk value lt 12 55 These planning units indicate areas of high conservation value within low risk areas based on model inputs TNC Protected Area Tools PAT Version 3 0 41 The Nature Conservancy August 2009 MODULE 3 Marxan Tools Marxan is a free software program that provides decision support to teams of conservation planners and local expe
24. ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE THE AUTHORS DO NOT WARRANT THAT THE OPERATION OF THESE SCRIPTS SHALL BE UNINTERRUPTED OR ERROR FREE THE USER BEARS ALL RISK AS TO THE QUALITY AND PERFORMANCE OF THESE SCRIPTS IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR COSTS OF PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES LOST PROFITS LOST SALES OR BUSINESS EXPENDITURES INVESTMENTS OR COMMITMENTS IN CONNECTION WITH ANY BUSINESS LOSS OF ANY GOODWILL OR FOR ANY INDIRECT SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THIS AGREEMENT OR USE OF THESE SCRIPTS HOWEVER CAUSED ON ANY THEORY OF LIABILITY AND WHETHER OR NOT THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE THESE LIMITATIONS SHALL APPLY NOTWITHSTANDING ANY FAILURE OF ESSENTIAL PURPOSE OF ANY LIMITED REMEDY TNC Protected Area Tools PAT Version 3 0 3 The Nature Conservancy August 2009 Introduction Many countries are seeking technical assistance to meet the requirements laid down in the Seventh Conference of the Parties COP 7 Global Program of Work PoW on Protected Areas PAs The PoW mandates an established global network of representative and effectively managed national and regional PAs on land by 2010 and at sea by 2012 CBD 2001 The Nature Conservancy TNC has a vested interest in helping countries develop science based PA networks and has pledged to build capacity through the development of country driven Nation
25. August 2009 3 3 Setting up the input dat file with Inedit and Executing Marxan 3 3 1 Running Inedit Tydixton_Park mxd ArcMap Arcinfo You are now ready to create the input dat file using the Inedit exe program the Input File Editor for Fle Est Mew Insert Selection Tools Window Help Marxan program created by Ian Ball The input dat Dee amp i K h file will be read into Marxan using the user defined E parameters This section was adapted from Huggins 2005 and will walk you through the process of creating the input dat file using the text files you just created with the MIG tool s FB MARXAN Tools Spatial Analyst fy Hexen amp Lay Me MARYAN TARGET PREP z z E gt MARSAN INPUT GENERATOR RUN CONVERT TO MATRIX FILE You have the option of running the Inedit exe and Le Marxan exe outside of ArcGIS or the Marxan ME RUN MARIAN Tools provide an option to specify the location of 40 JOIN AND DISPLAY MARXAN OUTPUT the executable files using the Run Inedit and Run Marxan options on the drop down menu If you have not already specified the location of these executable files the tool will prompt you to locate them You must do this for every new ArcGIS session It is useful to have the Inedit executable file located inside each Marxan directory you plan to use If you do not already have an input dat file in the same directory an error will appear Click OK and disregard the er
26. IODIVERSITY INDEX nRBI 0 03 0 0034 8 82 1 Target set is proportional to its area gt 1 Target set over represented in this query domain lt 1 Target set is under represented in this query domain occurrences presence absence Normalized Relative Biodiversity Index nRBI is calculated using an area weighted function When using polygon targets values greater than 1 indicate a high level of habitat uniqueness when considering the overall landscape The range and scale of RBI values will be different depending on what features are used as input e g line point This index computes relative abundance so the abundance can be any metric such as hectares of target habitat number of occurrences length of stream etc Itis important to note that the relative abundance calculations are different depending on the feature type of the target For polygon targets which use area values for nRBI greater than 1 indicate proportionately more target abundance in a planning unit than is expected for the planning unit size Line targets use linear length and point targets have no area so these features result in much lower values compared to polygon targets Normalized relative biodiversity index values can be summed across multiple targets to calculate aggregate nRBI for terrestrial freshwater and marine realms see figure below A higher RBI sum score gt 1 for polygon features implies that there is a greater representation or extent of the
27. LTARGET D Dry_Limestone_Forest Endemic_Fish Endemic_Turtle Huitas Query Builder Karstic_Streams Medium_River_Non_Karstic Small_Rivers_Non_Karstic IQ nrin ea Get Unique Values SELECT FROM tydixton_RBI_ALL_TARGETS WHERE RBI_TARGET Medium_River_Non_Karstic OK Cancel Once this step is performed you can symbolize this layer using the symbology tab in the layer properties Tydixton_Park mxd ArcMap ArcInfo DE File Edit View Insert Selection Tools Window Help SES Sex o spes mesno Ers Rer marxaw Tools spatialanayst se TTA a tor gt QANAPI PIROALS 7 Tasi New Feature Target amp Layers a tydixton_park_rbi_RBI_ALL_ RBN Ml 0 014233 0 747588 Wl 0 747589 1 868008 E 1 868009 4 201849 E 4 201850 8 393299 E 8 393300 13 313526 E tydixton_park_rbi_RBI_SUM b RBNT1 E 0 2 56168021392 MB 2 56168021392 5 1233 E 5 12336042784 7 6850 E 7 68504064176 10 246 O target_point_species zl E 10 24672085568 12 80 O target_line_habitats O tydixton_park_rbi_RBI_ALL_ e O target_polygon_habitats E O tydixton_planning_units tydixton_watershed 721470 412 656812 421 Meters Classified RBI values based solely on the Medium_River_Non_Karstic streams target TNC Protected Area Tools PAT Version 3 0 39 The Nature Conservancy August 2009 We are now
28. The Nature Ci Conservancy A Protecting nature ene life Southern Miss Lab ee h l gt Inter American Biodiversity Information Network THE WORLD BANE Protected Area Tools PAT for ArcGIS 9 3 Version 3 0 USER MANUAL and TUTORIAL Written by Steve Schill and George Raber Funded by The Inter American Biodiversity Information Network IABIN and The World Bank Development Grant Facility DGF August 2009 Table of Contents JNCKMOW IEC SEMIC IIIS 5 cacy sticuivs Gecsmasdadsiiguusandsa E EE 3 LABURREI LEKEI t EARTE EE E latest beaneieertinhatea E E E 4 Mandatory Requirements Needed to Run the Protected Area Tools eeeeeeeeeeees 5 Installing the Protected Area Tools PAT V 3 ssssseessssssssssensssssssssserrsssssssscerrrssssssseeeeees 7 The Protected Area GAP Assessment Process tas rscesgeceesicieiihaneedaatniedeliniend andes 7 MODULE 1 Environmental Risk Surface ERS cecceecceecceseseesseensseeeseeaes 10 MA ol DU SST V A ahaebace sa lacerate tears tein accion cede E em atcceoies 12 V02 Ent MEN Ces IS an sc cascus niche nsaccteseewetctewiareta nen anaadasenad ep etaeadncrsiems eeeaan nena eons 12 NEO DISTANCE Decay UVC varsity a E eet t ome haueaianbnet esate 12 EXERCISE 1 Building an Environmental Risk Surface 20 0 0 ccceeesseeeeeseeeeeeeeeeeeeeees 14 Sample Data Tydixton Park Watershed Jamaica ccecccccccccecceeeeeeeeeeeeseeeeeeeenees 14 1 1 Sets Up The ERS TaDle cernerent n a
29. The output grid name cannot contain spaces Underscores are permitted e The output grid name cannot contain special characters for example The output grid name cannot begin with numbers You may also specify a raster catalog location to save your output to If you specify a raster catalog output you must specify the name for the raster catalog item in the Raster Catalog Item box described below This box will be grayed out unless you have specified a raster catalog output When specifying a raster catalog location for output your final result will not be added to the map You will need to manually load the data into ArcMap If you have specified your output as Raster Catalog specify a name for the Raster Catalog Item that will be created Enter the Intensity Scale Max field This represents the theoretical maximum value for intensity It represents the maximum value in the scale of all your intensity values In other words if you have established your intensity values on a scale from 0 0 1 0 enter a value of 1 in the Intensity Scale Max field The tool does not support using a value other than 0 as the minimum scale value You may or may not actually have any intensity values assigned to the value you enter here For the tutorial data we will use a scale of 0 100 so enter the value of 100 as the maximum intensity value Enter the Output Cell Size This is the desired cell size of the final output grid The default value i
30. Tools Spatial Analyst D Hexen Lay Me MARXAN TARGET PREP z E 3 z R gt MARXAN INPUT GENERATOR COMBINE MARYAN INPUT FILES F RUN CONVERT TO MATRIX FILE TRUM INEDIT MF RUN MARZAN 42 JOIN AND DISPLAY MARYAN OUTPUT E O O O O O Output File D Mworkspace maranipuvspr_combined dat al Ok Cancel 3 2 5 Run Convert to Matrix File For those using Marxan 2 0 2 and above Marxan Tydixton_Park mxd ArcMap Arcinfo Optimised you must obtain a copy of the File Edit View Insert Selection Tools Window Help convert_mtx exe executable available on the Marxan O a lel amp i Ky i website in order to converts existing Marxan matrix Eke Re MARxAN Toos Spatial Analyst files into a format compatible with Marxan Optimised Hexcen These versions of Marxan are sensitive to the order of Z planning unit identifiers in the Marxan planning unit by a g gt MARSAN INPUT GENERATOR species sparse or relational matrix and can only use a F E COMBINE MARXAN INPUT FILES HIN COVER O MATRIS sparse matrix which is not compatible with a tabular ao ee RUM INEDIT matrix Once the executable is available on a local hard ao Pe drive users can use this tool to point to the executable pe GPT E Terre ee and convert the tabular horizontal matrix into a sparse relational or vertical matrix TNC Protected Area Tools PAT Version 3 0 65 The Nature Conservancy
31. al Implementation Support Programs NISPs a program that supports the Convention on Biological Diversity One way to help overcome the technical challenges of the daunting process of evaluating and filling protected area gaps is the development and use of GIS based user friendly tools that support the protected area gap process The development of a Protected Area Gap Decision Support System DSS was conceived as part of an ongoing process to help fill the technical void that exists in many countries The development of these tools was funded by the Interamerican Biodiversity Information Network IABIN and The World Bank Development Grant Facility DGF It is part of a process to further support I ABIN s objectives and help conservation planners throughout Mesoamerica and the Caribbean assess current PA status and establish priorities for future conservation management Version 1 0 of these tools was completed in September 2006 and works in ArcGIS 9 1 The new version 3 0 was completed in August 2009 renamed to the Protected Area Tools PAT and is now compatible with ArcGIS 9 3 This version includes many new features requested from our users It is hoped that PAT will continue to evolve and provide utility for evaluating land purchase acquisition for achieving maximum return on investment in terms of overall contribution to a country s conservation goals In addition to questions that may be asked about the best remaining core habitat or covering
32. alues for each element can be typed in Environmental Risk Surface Generator Selected Layer Intensity Influence Distance Decay Type Overlay Weight isk_ag_smallscale Tern_Inten Ten_Dista Linea tow frisk_ag_sugarcane Ten_Inten Ten_Dista Linea A frisk_bausite_mines Tern_Inten Ten_Dista Linea A E E E ITisk_quarties IT erm_Inten ka IT em _Dista kd Linear isk_roads IT en_Inten IT em_Dista r Linear x isk_utban_areas T ern_Inten ka IT em _Dista kd Linear For this exercise we are going to use the influence distance and intensity values that have been previously assigned in the shapefile attribute fields Since we are computing an ERS model for a terrestrial example the fields have been defined as Terr_Inten for intensity and Terr_Dista for the influence distance If the user needs to generate a variety of ERS scenarios for modeling risks for an array of species or ecosystems several different fields could be created that represent the intensity and influence distance values for each corresponding species or ecosystem As previously explained the Decay Type refers to the spatial function that will be applied to the intensity values as distance away from the risk element increases 1 e LINEAR CONCAVE CONVEX and CONSTANT functions The Overlap function on this screen allows users to choose how to combine individual risk elements contained in each layer For example
33. an be defined as anything identified by experts as having a negative influence on the health of a critical habitat or key species One can also refer to risk elements as a threat The ERS measures cumulative levels of risk impacts across the landscape and can be used to focus conservation site selection by steering habitat selection away from high risk areas where the abatement of pressures on biodiversity seems less likely The composite surfaces or disaggregated individual surfaces can be used to get a better idea of the specific environmental risks on the landscape that may be degrading the viability of certain conservation habitats species i e targets ERS model output can also be used to assist in the fi screening of habitats and creating cost re MARINE surfaces for Marxan runs FRESHWATER Examples of customized Environmental Risk Surfaces ERS models for Jamaica s terrestrial freshwater and marine realms Red areas indicate Cr eating an ERS model first r Cquires higher risk to habitats based on the aggregation of intensities of assembling a suite of the best available GIS underlying risk elements McPherson et al 2008 data to spatially represent the specific risk elements e g human activities most likely to impact critical habitats or key species This means all risk element features must be spatially mapped on the landscape with precise location and boundaries when possible using expert opinion or obtain
34. ance to arrive at an optimal portfolio so the user has to decide how much influence they would like each factor to have Some planning situations require the cost surface to have a larger or smaller effect and the same can be said about the amount of clustering needed The amount of experimentation on the cost range with the BLM depends on the magnitude of the boundary in comparison with the importance of each target meeting its goal There are three suggested scenarios users should try pertaining to cost range Huggins 2006 1 Seta flat cost of all units set to the area of the planning unit e g 260 2 Seta range of cost values with 260 as base then going higher with the cost factors i e 5 base cost so you end up with a fairly tight range e g 260 1300 3 Set cost where managed protected areas e g MPAs offset the cost so that the cost in these areas is reduced by a factor e g 0 33 In this case if you have a planning unit where trawling activities drive the cost up the managed protected areas will have a lower unit cost That way there is a quantitative difference between trawling in and out of a managed area This should produce better results than locking in managed protected areas as a scenario f Boundary Length Modifier BLM Experimentation The BLM is specified in the input parameter file using Inedit exe Before the boundary length of a portfolio is added to the Marxan cost function as the boundary cost i
35. as sewage outfall locations dams water abstraction and invasive species Marine habitats may be impacted by fishing pressures practices ports marinas and land and marine based pollution 1 3 4 1 Freshwater ERS Models A flow accumulation model can be used to measure the impact of defined risk elements on freshwater biodiversity by creating a grid of accumulated risk intensities that flow into each cell of a watershed To do this the user must first create an ERS model using expert defined freshwater risk element features as described above and then specify the output grid model as the input source grid for the flow accumulation function See FLOWACCUMULATION grid function in ArcGIS Help This function requires the user to specify a flow direction grid which indicates the direction water flows Flow Accumulanion on a cell by cell basis starting at ms vaLue niii aa EZ EH i E r i i LEH GL Te The Nature Conservancy August 2009 higher elevations and ridges moving downward much like water moves across a sloped surface In order to define a drainage network the steepest down slope flow path between each cell is identified between its eight neighbor cells Once the flow direction is established the intensity values of the combined freshwater risk elements e g agriculture urban areas and sewage outfalls can be accumulated as the model runs from the top ridges to the bottom outlet of each watersh
36. ases it will make more sense to have planning units that are informed by natural ecological divisions such as hydrological units or even by political governmental divisions such as cadastral parcels For other uses a uniform planning unit will provide more useful results The choice of planning units has important implications for the process of portfolio selection as well as implementation of its results The choice of planning unit size and configuration for both wide and local scale analysis must be made with many factors in mind These include e The size of the planning unit relative to the scale of the underlying features e g planning units that are much larger than underlying fragments of vegetation can mask the size shape and extent of fragmentation planning units that are very small relative to the vegetation types will mostly be homogeneous ie small and large patches of habitat will be indistinguishable e The number of planning units that can be handled by the analysis computer in a time that is reasonable for the intended process e g calculation of target area within planning units clustering test There is a limit on the number of planning units that Marxan 1 8 1 can handle This is not however a fixed number as it depends also on the number of conservation features you wish to plan for and even to some extent on the power of your computer Marxan 2 0 2 can handle very large marxan projects gt 20 000 planning units and
37. at were specified For example if you entered 200 runs and a planning unit s NUMBER field is assigned 153 then that planning unit was chosen 153 times out of the 200 runs The NUMBER is also often referred to as a level of irreplaceability amp Lay Mer MARMAN TARGET PREP 4 gt MARSAN INPUT GENERATOR a0 COMBINE MARMAN INPUT FILES O SE pun CONVERT TO MATRIX FILE O TE RUN INEDIT ME RUN MARYAN MARXAN OUTPUT JOIN AND DISPLAY Planning Unit tydixton_planning_units When you join the planning unit ID field with the text files a new field is created in the planning unit feature class and the results are MARAN File D workspace marsan tydiston_ eel displayed in the map view Planning units Planning Unit Field 1O MAXAN PU Field planningunit with a value of zero 0 are excluded from the o classification You may want to make a copy MAXAN Join Field solair E of the planning unit file for each scenario that Dutput FieldName solution was executed e g cost_palock cost_nopalock nocost_palock OK Cancel nocost_nopalock TNC Protected Area Tools PAT Version 3 0 71 The Nature Conservancy August 2009 3 4 2 Displaying and Analyzing Marxan Results You can now analyze each of the six types of output files that Marxan has produced during the run Ball amp Possingham 2000 1 Solutions for each run e g tydixton_run _best txt A file is produced for each run of the algorithm containing th
38. atabases and shapefiles Unlike the other modules the ERS module works with grids and other raster formats supported by ArcGIS TNC Protected Area Tools PAT Version 3 0 5 The Nature Conservancy August 2009 5 All input features must have the projection defined and all input features must be in the same projection Since ArcGIS does projections on the fly layers may appear in the same projection but in reality they are not You can check the defined projection information by right clicking on the data layer and going to Properties gt Source Data Source Remember that you will not be able to calculate correct areas or lengths if you files are in Geographic projection e g decimal degrees You need to use a projection that uses units such as meters or feet e g UTM State Plane 6 For optimal performance your machine should have at least a 1 0 GHz processor or higher and have at least 1GB of memory RAM It is also recommended you have at least 5 10 GB of open hard drive space It is recommended to operate this program using Windows XP as problems may be encountered using Windows 2000 or Vista 7 Many of the tools available in PAT require a significant number of processing steps You must specify a location on the local hard drive that has write access and sufficient storage space Please use the Options gt Settings drop down menu to specify the location of the scratch folder on your machine e g C temp This directory wi
39. ates using eastward and northward velocities on a cell by cell basis to compute a travel cost surface which represents the number of seconds it takes to cross a cell Additional investigations are currently being conducting using the new network data model in ArcGIS Network Analyst As with the other ERS models marine experts must first identify the risk elements to the marine habitats Human activities that are risk Lagan elements can be divided into four categories based on their marine impact direct impacts e g population density contamination e g coastal industry ports marinas extraction e g fishing and harvesting practices and watershed based CONTAMINATION FLOW ACCUMULATION Eide deed Pu sedimentation run off land and marine based pollution This process ue was followed for the marine ERS a a a models that were developed for the a ik ea sone af fier aed ne and hype of Goal Jamaica Ecoregional Planning Marine Analysis Zenny 2006 Each risk element that was identified and mapped by experts was assigned an intensity value an influence distance then combined to create an overall risk surface One idea for modeling potential upland sedimentation on coastal environments is to use the flow accumulation of the freshwater ERS model to gauge risk intensity at coastal outlets As discussed in the previous section the flow accumulation function aggregates and The creation of the Jama
40. be able to processes from within ArcGIS You may obtain these executables freely from their source at http www ug edu au marxan This ensures that these tools are execute these processes within ArcGIS obisined licensed and cited properly You may obtain these executables freely Maman Executable E Maman Mananese l from their source at MEd Executable C Mansan inedit exe ea Convert2Matrix Executable C Marxan convert_mtx exe E http www uq edu au marxan This ensures that these tools are obtained _ 0K Cancel licensed and cited properly TNC Protected Area Tools PAT Version 3 0 6 The Nature Conservancy August 2009 Installing the Protected Area Tools PAT v 2 MAKE SURE YOU HAVE Microsoft NET Framework 2 0 installed AND the NET Support enabled in ArcGIS prior to installing PAT Failure to do so will prevent the tools from working properly This functionality ts NOT installed in the default setup of ArcGIS For more information see number 2 above Download the zip file patv2 zip from http www gispatools org This file contains the setup exe executable file that installs the tool in your ArcGIS bin directory and makes the tool available in your View gt Toolbars menu Remember that version 3 0 of the program only works with ArcGIS 9 3 For those using ArcGIS 9 1 or 9 2 an older and less functional version 1 0 of the tool is available at http www gispatools org Please note that version
41. bjective cost function and is made up of three user defined costs Total Cost X Unit Cost gt Species Penalties Boundary Length where Total Cost is the objective to be minimized Unit Cost 1s a cost assigned to each planning unit Species Penalties are costs imposed for failing to meet biodiversity target goals and Boundary Length is a cost determined by the total outer boundary length of the portfolio Attempts are made to minimize the total portfolio cost by selecting the fewest planning units with the lowest total unit cost needed to TNC Protected Area Tools PAT Version 3 0 43 The Nature Conservancy August 2009 meet all biodiversity goals and by selecting planning units that are clustered together rather than dispersed thus reducing outer boundary length This task 1s accomplished by changing the planning units selected and re evaluating the cost function through multiple iterations Alternative scenarios can be evaluated by varying the inputs to the total cost function The boundary length cost factor for example can be increased or decreased depending on the assumed importance of a spatially cohesive portfolio of sites TNC 2005 Conservation portfolios can be identified that met stated goals for representation of the biodiversity targets The ultimate objective is to find a portfolio that meets stated conservation goals for all target groups in an efficient manner while also
42. centroid of Dior out of the system pu pu pu DEFAULT 0 CRITICAL for Separation CRITICAL for Separation CRITICAL The values are separated by commas The file format looks like id cost status 1 2 3 0 2 4 5 0 The status of each planning unit can take one of 4 values Default 0 Status Meaning The PU is not guaranteed to be in the initial or seed reserve However it still may be Its chance of being included in the initial reserve is exactly the starting proportion from the parameter input file The PU will be included in the seed reserve or the initial reserve It may or may not be in the final reserve The PU 1s fixed in the reserve It starts in the initial reserve and cannot be removed locked in The PU 1s fixed outside of the reserve It 1s not included in the initial reserve and 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 planning units It is sometimes called the abundance file The contents of this file are Species pm amount Conservation target id must Planning unit id Number area or length of be a number nee a conservation target CRITICAL CRITICAL The values are separated by commas The file format looks like species pu amount 26 263 535739 34 27 271 228479 37 TNC Protected Area Tools PAT Version 3 0 53 The Nature Conservancy August 2009 4 Blo
43. ck Definition File block dat OPTIONAL This optional file can be used to group targets together or to use the facility that allows the goal to be set as a proportion without calculating the actual amount in area length or number of occurrences When using this file the type of each target must be set in the spec dat file If no grouping is necessary the type names can remain the same as the target id If you are using a block definition file it is highly recommended that you read Game and Grantham 2008 to gain a better understanding of how this file works The contents of this file are the type The Minimum The number Target Minimum An The for which goal clump of number distance at alternative penalty the other forthe size Ifa occurrences of which to target factor attributes target clump ofa of the target mutually planning This is the for that are of the number of required separated units proportion target defined given planning Thiscanbe planning holding the of the ee type units with used in units in target are total wy the given conjunction valid considered amount of target is with or clumps to be the target below this instead of PEFAULTCD separated which size then it target ail must be does not PEAT D preserved count N A toward the goal DEFAULT 1 The values are separated by commas The file structure looks like type target targ
44. d Grantham 2008 Ball amp Possingham 2000 and Possingham et al 2000 The Marxan Target Prep routine generates all the fields listed below the Target_Nam and Target_ID fields Once populated these fields can then be used in the Marxan Input Generator MIG FIELD TYPE DESCRIPTION Target Name The name of the conservation target This field can include spaces but all words must start with a TARGET _NAM TEXT letter Try to limit the length of the target name to fewer than 50 characters A duplicate of this field will be created by the Target Prep tool and named TNAME Target ID The unique ID assigned to each conservation target The ID should be limited to no greater than 16 TAROT ANEGRE A eran each A uoe o nig Held willbe created by the Target Prep tool and named TID Target Goal The conservation goal for each target stated in number of occurrences points length lines or area polygons An alternative of defining the goal is to use the PROP field Proportion in the Block Definition file TOR ae Do not use both methods choose one or the other Make sure the units are consistent with what is specified in the MIG conversion window default hectares and kilometers Total field length is 15 numbers Target Type This is a user defined number used in the TYPE INTEGER block definition file Could be the same as the Target_ID Total field length is 16 numbers Species Penalty Factor Higher numbers e g 100 000 en
45. d with Marxan output to guide prioritization of conservation areas Areas are ranked from highest to lowest priority High risk high RBI areas may be more expensive to acquire but these habitats may be irreversibly lost if immediate action is not taken TNC Protected Area Tools PAT Version 3 0 34 The Nature Conservancy August 2009 EXERCISE 2 Calculating the Relative Biodiversity Index RBI REMEMBER e All layers used in the analysis must be in the same projection and VN have the projection information defined Do not use Geographic projection e g decimal degrees since unit areas or lengths will be calculated incorrectly e The RBI Module does NOT require an ArcGIS ArcInfo Level e The Universe Domain is the total study area or landscape i e large watershed political boundary e The Query Domain is the analysis unit or planning unit layer i e hexagons or sub catchment watersheds and must have an ID field with a unique number assigned to each unit A hexagon layer can be generated using HexGen in the Marxan Tools e The word Target refers to a conservation habitat or species and can be represented as a point line or polygon When using your own data make sure any entry in the target name field does not contain any special characters e g 6 or the program may fail e The target layer must have a unique name or ID field that represents each unique target class or type e g forest type stream type speci
46. dy to start in order to create the input files that Marxan will use 3 2 3 Marxan Input Generator MIG Tydixton_Park mxd ArcMap ArcInfo Now that the target layers have the required fields and corresponding values assigned you are ready to use File Edit View Insert Selection Tools Window Help the Marxan Input Generator MIG to create the input O gt H amp BX oo e ie files that Marxan will use Make sure the following Es er MaRxAN Toos Spatial Analyst data layers are in your map view s table of contents Q Hexen before proceeding with MIG both the status and cost i i Hier MARZAN TARGET PREP layers are optional for running Marxan e e Gea O Hj COMBINE MARAM INPUT FILES O SE RUN CONVERT TO MATRIX FILE 1 Planning Units a polygon feature e g n hexagons with unique ID assigned 12 BUREREEGI 2 Target Layers these must be previously run 4 JOIN AND DISPLAY MARXAN OUTPUT through the Target Prep tool or have all required fields with user defined values Targets must also be dissolved so there is one record per unique target class Target Prep does this for you If they are not dissolved you will have repeating targets listed in the spec dat and block dat files 3 Status Layer this is an optional layer but needed if you plan on using a protected area layer or other special interest areas to lock in planning units The user also has the option of locking in planning units by sp
47. e planning units which constitute the final solution produced by that algorithm The file consists of a list of planning unit ids which constitute the portfolio 2 Missing value information for each run e g tydixton_run1l_mvbest txt This file contains information on how well the final portfolio from each run and also the best run did with regard to meeting the conservation target s goal The final column is the actual amount of that target which appears in the portfolio A sample listing is shown in Table 3 3 Best solutions of all runs e g tydixton_run _best txt It contains the best solution from a set of runs The file consists of a list of planning unit ids which constitute the portfolio 4 Summary information e g tydixton_run l_sum txt It contains summary information on each run with a header line which describes what 1s in each line 5 Scenario details e g tydixton_runl_sen dat It contains a documented list of the options that made up that scenario 6 Summed solutions over all runs e g tydixton_runIl_ssoln txt Each line has the id number of a planning unit and the number of times that that planning unit was involved in a solution Now let s examine a few of these new Marxan output files Double click on tydixton_100runs_mvbest txt or whatever file name it was given in windows explorer to open it within Notepad choose Notepad from the list of programs if it does not open automatically It may be easier to view t
48. eas but with insufficient quality or quantity to provide long term protection while management gaps refer to situations where protected areas exist but are failing to provide adequate protection either because they have the wrong management objectives or because they are managed poorly Employ a participatory approach collaborating with key experts and stakeholders in making decisions about protected areas Make protected areas system design an iterative process in which the gap analysis is documented reviewed and improved as knowledge grows and environmental conditions change Assemble Team UOT CANE Reassess Once New _ Data Becomes ee ond Engage Available Je iders antify ation ets Threats ervation gets fy PA aries and agement actices i d zigis e Set Ge atial Data Based on Exper Review TNC Protected Area Tools PAT Version 3 0 g The Nature Conservancy August 2009 The majority of the work that goes into a protected area gap assessment involves the spatial delineation and critical evaluation of habitats species protected areas and risks to focal habitats The Protected Area Tools are ready to be used only after users have obtained the highest quality data available conducted an ecological inventory and assessment of these data layers through expert review and carefully considered all model scenario settings Three modules presented in this tutorial will guide users through the pr
49. ecifying a pre assigned planning unit field value 0 1 2 3 that is extracted and written to the pu dat file 4 Cost Layer also an optional layer but needed if you are using planning unit cost values in your Marxan analysis For defining cost the user has the following options to choose from a choosing a grid e g ERS model whose planning unit mean value will be extracted and written to the pu dat file b selecting a pre defined cost field that already exists in the planning unit layer c using the area of the planning unit as cost or d typing in a flat cost that will be assigned to every planning unit Before executing MIG remember that all input layers must be in the same projection and have the projection defined You must also make sure you have an ArcGIS ArcInfo Level license with ArcInfo Workstation installed ArcMap ArcInfo should appear in the title bar of your ArcGIS program Also check your ArcGIS Start Up menu to see if ArcInfo Workstation is listed which indicates it has been installed The Spatial Analyst extension must also be turned on Tools gt Extensions Once you verify these requirements you are now ready to launch MIG For this exercise we will use the planning units tydixton_planning_units shp all the target input files target_point_species shp target_line_habitats shp target_polygon_ habitat shp the protected areas tydixton_protected_areas shp and the sample ERS model grid tydixt
50. ed The final accumulated grid surface calculates accumulated risk in intensity values upstream from any point cell in the watershed Output cells with a high flow accumulation are areas of concentrated flow and may be used to identify stream channels and high risk areas Output cells with a flow accumulation of zero are local topographic highs and may be used to identify ridges This method also permits users to calculate the total risk intensity by watershed thus quantifying the risk on a watershed level If freshwater experts think that the high accumulated values are too high for large rivers the effect can be lessened by subtracting a dilution factor to parts of the watershed A zonal max function can be applied to locate the maximum flow accumulation value for each planning unit or unique watershed thus quantifying the maximum flow accumulation value on a per unit basis MODEL VERFICATION AND a ADJUSTMENTS CREATE FLOW DEM gt DIRECTION CREATE FLOW SUMMARIZE ACCUMULATION ZONES DEVELOP RISK p ERS FRESHWATER ELEMENTS MODEL PLANNING UNIT WITH AVERAGE ACCUMULATION VALUE Step flow process that uses a Digital Elevation Model DEM and Environmental Risk Surface ERS as a weight grid for accumulating intensity values when assessing risk to freshwater and marine habitats In areas of low or zero slope creating a suitable flow direction grid may be a challenge Users may want to preprocess the DEM by burning in stream
51. ed Area Tools PAT Version 3 0 30 The Nature Conservancy August 2009 MODULE 2 Relative Biodiversity Index RBI Calculator Although Marxan can identify an efficient portfolio that meets conservation goals for multiple conservation targets in many cases more target specific information is needed for management decisions Marxan identifies the optimal solution based on representation of multiple conservation targets This optimal solution is often counter intuitive and difficult to interpret and explain to managers and stakeholders One of the reasons for this phenomenon is that Marxan is finding solutions for representation of all elements and Marxan solutions represent a compromise between all the best areas for each target Marxan solutions often exclude some of the best remaining areas for single targets and focus on areas that contain multiple targets Many times areas that are excluded from optimal solutions are intuitively important to protect As a complementary analysis to Marxan a normalized relative bio diversity index nRBI can be computed which quantifies the area weighted relative contribution of each planning unit compared to the total distribution of each conservation target In other words the nRBI for each planning unit is directly proportional to the amount of conservation target present in the planning unit e g hectares of habitat length of stream or number of occurrences The index can be summed f
52. ed an intensity value of 40 compared to river aggregate which is assigned 30 Likewise the file risk_roads shp has four road class types and corresponding intensity values have been assigned based on expert opinion of the degree of potential risk to critical habitats TERRESTRIAL FRESHWATER TERRESTRIAL INFLUENCE FRESHWATER INFLUENCE ae ios ELEMENT CLASS ns a ar ae risk _ag_small_scale risk_ag_small_scale sh p o 3000 risk bauxite_ mines aie 1000 8000 caran a risk_quarries shp Aggregate 500 10 1000 Limestone 1000 risk_roads shp TRACK S o G D E e CLASS B o s a0 0 o 20 It is important to remember that when assigning intensity values and influence distances you are using a relative scale not a representation of the absolute measure of the impact of activities on biodiversity These values should be a relative degree to which biodiversity is more likely to survive in one place over another based on the presence of a given activity in comparison to the other risk elements For this exercise we use a scale of 0 100 with 100 being the highest degree of risk to a habitat It is up to the user to define the scale but the user should use whole numbers integers for computational reasons The influence distance should be in whatever units your input data is in i e projection information In the sample data the units are in meters As with intensity TNC Protected Area Tools PAT Version 3 0 15 The Natu
53. efile ES tydixton_protected_sress shp Shapefile Eo tydixton_vatershed chp Shapefile Tydixton Park Watershed JAMAICA TNC Protected Area Tools PAT Version 3 0 The Nature Conservancy August 2009 14 1 1 Setting up the ERS Table Successful conservation planning involves risk management ERS models are about categorizing and ranking potential risks to habitats or features on concern The first step in creating an Environmental Risk Surface is to create an intensity value and influence distance table for all identified risk elements and associated classes These values can be customized specifically for the creation of ERS models for terrestrial freshwater or marine realms Remember that each risk element has to be thought of in terms of its impact on the habitats or species in the focal realm i e terrestrial freshwater and marine A sample Excel spreadsheet risk matrix table is provided with the tutorial data named Sample_Intensity_Table xls Open this risk matrix table and you will see six columns that represent the risk element the associated class for each risk element followed by the terrestrial and freshwater intensity value and influence distance columns For instance the file risk_quarries shp contains two classes River Aggregate and Limestone According to the experts mining for limestone is more damaging to terrestrial systems than river aggregate mining Consequently limestone mining is assign
54. efined Remember you can use either the GOAL field to define the goals in specific units number of occurrences length or area or you can use the PROP field to set up proportions percentages If you use the PROP field Marxan will calculate the appropriate target amount based on the proportion specified using a block definition file If GOAL and PROP are both set then the PROP variable will take precedence and the GOAL variable will be ignored in the block definition Also note that the proportion is based on the total amount defined in the puvspr dat file Before moving on to the next step you are also going to need your planning units with unique IDs the optional status layer e g protected areas if using a status flag for locking in areas and a method for extracting the optional cost parameter e g ERS model MARXAN PREP FORM Once you click on Marxan Target Prep a dialog box appears that asks you to select the Target TagetLayerto Prepare forest_types Layer to Prepare and corresponding Target Target Name Field TARGET NAM Name and ID Fields You must also specify an Target ID Field TARGETID output feature class e g shapefile A new Output Location D workspace forest_types_p feature class will be created so make sure you OF Cancel give it a descriptive name and have it written a ee out to your Marxan working directory When you are ready click OK and the new feature class will be created containing al
55. ension and it should be turned on Tools gt Extension 4 The user should have all geometry checked repaired for each input feature file If problems persist after repairing geometry converting shapefiles into coverage format then back to shapefile format will often solve the problem The Marxan Tools will process geodatabases and shapefiles but NOT grids 5 It is highly recommended to use the Target Prep tool since it creates all the necessary fields used in the Marxan Input Generator and dissolves each target i e there is one table listing for each unique target type TNC Protected Area Tools PAT Version 3 0 44 The Nature Conservancy August 2009 6 10 11 All input features must have the projection defined and all input features must be in the same projection Do not use Geographic projection e g decimal degrees since unit areas or lengths will be calculated incorrectly Remember that depending on the size and level of detail requested by the user the Marxan Tools may require large amounts of disk space to operate and may take a considerable amount of time to run You may want to temporarily disable any Virus Checkers since the program will be accessing and deploying executable files When using your own data make sure any entry in the target name field does not contain any special characters e g 6 or the program may fail If you have not already users should register and download Marxan from http www
56. erdana 2006 Please consult Game and Grantham 2008 for an excellent description on how BLM should be employed g Flexible Low Irreplaceability Units Areas that are not being indicated as highly irreplaceable are not unimportant for conservation they are more flexible as there are other planning units that contain similar biodiversity A highly irreplaceable area may not be known locally for its biodiversity value but may for example contain 100 of the occurrences of a particular target and is therefore irreplaceable for meeting the representation goal for that target Marxan is also useful for highlighting areas that have previously been overlooked for example where goals for many targets can be met in a spatially cohesive manner that increases the likelihood of strategy effectiveness h Unexpected Results Targets goals and cost surface are all crucial to creating the best portfolios If areas that are known to be important are not being reflected in the portfolio it may be because the targets or the cost surface are not defined in a way that distinguishes those areas as different from others For example if no highland targets are represented in the portfolios it may be because the targets have not been stratified by elevation so those highland parts cannot be distinguished as needing representation separate from the lowland areas The goal representation for that target will be met but it could be all within lowland areas 3 2
57. ersion 3 0 36 The Nature Conservancy August 2009 the targets polygons with lots of vertices It is best not to work on the computer or click on ArcMap while the model is executing Once the model 1s completed a text box stating Processing Complete will appear and the results will be loaded into the map view 2 2 Interpreting RBI Results When processing has completed the your_output_name_RBI_LSUMMARY feature class will appear in the map view s Table of Contents The output is color ramped and displayed in an equal interval classification using the RBNTI field which is the aggregated Normalized RBI values summed across the total number of targets found within the Universe Domain or total landscape extent In this case it is the Tydixton Park watershed boundary The RBNT2 field is the aggregated Normalized RBI values summed across the total number of targets found within the Query Domain or hexagon planning unit As previously explained when using polygon targets higher RBI sum scores gt 1 implies there is a greater abundance or extent of the targets than is expected for the analysis unit size in comparison to the rest of the landscape The range and values of the RBI scores will be different depending on the combination and number of feature types you use Open the Attribute Table by right clicking on the your_output_name_RBI_LSUMMARY layer and you will see a series of RBI columns FIELD DESCRIPTION RBIT1 Non normalized RBI
58. es 2 1 Running the RBI Module The RBI tool requires three input data layers to operate on The first layer is the target Tydixton_Park mxd ArcMap ArcInfo layer or the layer that represents the conservation targets These can be points lines or polygons The second required layer is the universe domain a polygon ER feature that represents the total analysis File Edit View Insert Selection Tools Window Help ie amp A K SARXAN Tools Spatial Analyst x extent to be considered This could be a Layers t t_point i country boundary or a watershed The final sp a als O target_line habitats layer needed is the query domain also a O target_polygon_habitats polygon feature that represents the analysis E L tydixton_planning_units O tydixton watershed or planning unit layer and the basic unit that receives the RBI calculation This could be hexagons or other polygon features such as watersheds Prior to clicking on the RBI button make sure you have the input files that will be used loading into the view For this exercise this includes the target shapefiles target_point_species shp target_line_habitats shp and target_polygon_habitats shp the Tydixton Park watershed boundary tydixton_watershed shp and the analysis unit hexagons tydixton_planning_units shp Remember that the analysis extent is also TNC Protected Area Tools PAT Version 3 0 35 The Nature Conservancy August 2009 refer
59. es or a surrogate for actual cost such as area The Environmental Risk Surface ERS module can be used to create customized grids which can be summarized at the planning unit and used as a cost measure Marxan attempts to minimize the total portfolio cost by selecting the fewest planning units with the lowest total unit cost needed to meet all biodiversity goals The Marxan Input Generator allows users to assign cost to each planning unit by extracting values from a grid using an existing planning unit field taking the area of the planning unit or typing in a flat cost that is assigned uniformly to all planning units Planning Units These are the units that house all the necessary information for Marxan to run and allow comparison and selection between candidate areas Planning units can be systematic units such as hexagons or unsystematic sub divisions of the landscape such as watersheds or administrative boundaries The size of the units should be representative of the scale of analysis and input data resolution For users who would like to use hexagons as planning units the HexGen tool is available in the Marxan Tools drop down menu Protected Areas or Special Interest Areas This is an optional layer used in Marxan for what is called the Status Layer or Status Identifier This layer must be a polygon feature class and is required if the user plans to run a scenario where the planning units that overlap declared protected areas
60. es of roads For the tutorial example we will use the default SUM function which is the more commonly used function since it aggregates all risk element intensity values MAXIMUM Takes the maximum grid value for each cell in all computed intensity layers For example if cell values between j 78 layers are 35 78 and 21 the final cell number would be 78 24 OUTPUT 78 SUM Takes the sum of the grid values for each cell in all i computed intensity layers For example if cell values between 78 layers are 35 78 and 21 the final cell number would be 134 OUTPUT 134 Other less used overlay functions available for use include MEAN Takes the arithmetic average of the values between input rasters on a cell by cell basis The mean provides a measure of the center of the distribution of the values MINIMUM Takes the minimum grid value for each cell in all computed intensity layers For example if cell values between layers are 35 78 and 21 the final cell number would be 21 This is not a common option to choose since a value of 0 no risk in any location in any risk element input will produce a value of O in that location in the final output grid regardless of any of the other input values In other words in areas of no overlap between risk elements the risk assigned will be 0 TNC Protected Area Tools PAT Version 3 0 21 The Nature Conservancy August 2009 MAJORITY Takes the majority value or the value that appea
61. es that support all elements of biodiversity One of the key aspects of this approach is minimizing environmental risk to critical habitats and key species Although not all human activities can be considered risks to biodiversity direct or indirect human impacts are ultimately responsible for most alterations of the ecological processes that sustain biodiversity In addition there are other events that pose significant risk to habitats and species e g hurricane volcanic activity climate change Consequently understanding the spatial relationship between these risk elements and ecological health within focal conservation sites provides valuable insight into conservation management However assessing and predicting risks to habitats represents one of the most challenging dimensions of conservation planning due to the unpredictability wide variation and lack of existing information regarding the functional relationships of ecological processes to impacts in terrestrial freshwater and marine realms Standardized and widely accepted methods for quantifying the relative degree of impacts and utilizing risk measures to prioritize areas for conservation is in its infancy and will surely be more fully developed in the coming years An Environmental Risk Surface ERS is a modeled surface developed using mapped risk elements e g socioeconomic information to explore the overlap between these risk elements and biodiversity features A risk element c
62. essary to run this step with the tutorial data provided since these target files have already been prepared meaning they have already been dissolved and have the required fields added and corresponding values calculated This step is only for users who need to create Marxan files using new target data that does not already have the required fields added and values calculated HEEE h OOOOOOSs In the PAT toolbar you will see the Marxan Tools drop down menu Marxan Target Prep is the second tool in the menu Before launching this tool make sure that your TNC Protected Area Tools PAT Version 3 0 56 The Nature Conservancy August 2009 conservation target files are already loaded into the map view To get an idea of what the Target Prep tool does you can load any of the sample target shapefiles into the view target_point_species shp target_line_ habitats shp or target_polygon_habitats shp Now open up the attribute tables of one of the sample target shapefiles by right clicking on the layer and choosing Open Attribute Table You will see that in addition to the TARGET NAM and TARGET_ID fields there are additional fields that are described in the table below These additional fields are created using the Target Prep tool and will be used in the next step Marxan Input Generator MIG to extract the field information and create the Marxan input files More information about each of these parameters can be found in Game an
63. et2 targetocc sepnum sepdistance prop spf 1 1 1 1 1 1 0 25 10000 2 1 1 1 1 1 0 30 10000 5 Boundary Length File bound dat OPTIONAL The boundary length file contains information on the boundary costs of adjacent planning units Although this is an optional file it is highly recommended to use since it helps set the level of fragmentation in the solution Whereas this cost is typically the actual length of the boundary it can be modified to a cost or effective length value to take into account boundaries that are particularly desirable or undesirable Bound dat can be created automatically using the Marxan Input Generator This table can have tabs or commas between the columns If you see repeating PU ids in the bound file these are edge planning units and repeating them in the bound dat file helps to avoid bias in the BLM because they have shorter shared boundaries It is not necessary to specify boundary lengths for all planning units where they are not specified Marxan will assume there is no boundary between planning units However any missing values within the file will prevent Marxan from running for instance if idl and TNC Protected Area Tools PAT Version 3 0 54 The Nature Conservancy August 2009 id are set but no value for boundary is entered Game and Grantham 2008 The contents of the bound dat file are planning unit id neighboring planning the boundary length ote uni
64. etween a grassland and fire that has to be identified and modeled TNC 2006 Prior to modeling an ERS experts must identify how risk in each element decays over distance or if there is a decay factor at all PAT provides four decay types for expressing the function of distance decay These include a linear b concave c convex and d constant and are represented in the figure below The default function is a linear decay type where the rate of intensity decay is constant until the maximum distance is reached and the intensity becomes zero A concave decay has an initial rapid decrease in intensity while a convex has the opposite effect a gradual intensity decay followed by a steep decay as maximum distance is reached A constant decay has no change in intensity value until the maximum distance is reached ending in an abrupt zero Users should consult with ecological experts who have reviewed each risk element and defined the types of decays that are appropriate to apply based on the ecosystem in question a z 3 U A U A gt z g z 2 lt Z lt lt DISTANCE DISTANCE DISTANCE DISTANCE TYPE LINEAR TYPE CONCAVE TYPE CONVEX TYPE CONSTANT a RATE 1 b RATE 3 C RATE 3 d RATE 1 influence Distance 1000m Influence Distance 1000m Influence Distance 1000m Influence Distance 1000m tenem as intensity 100 intensity 100 Intensity 100 Decay Function Linear Decay Function Concave Decay Function Convex Decay Function Co
65. execute the model You will notice in the lower left hand corner of ArcMap the risk element layer number that is being processed As the processing consumes much of the computer s resources it is best not to work on the computer or click on ArcMap while the model is executing Once the model is finished a text box stating Processing Complete will appear and the results will be loaded into the map view 1 3 3 Viewing the ERS Results and Summarizing Spatial Statistics When the ERS model has finished processing the final grid will appear in your map view and have the spatial extent of the boundaries of all specified input layers The output grid is displayed in the view with the background values set to zero but the user can modify this and other display parameters using Layer Properties gt Symbology All of the intermediate processing steps are saved into the specified PAT scratch directory This directory is deleted every time ArcMap is started _ Tydixton_Park mxd ArcMap Arcinfo File Edit view Insert Selection Tools Window Help D gg BX a g fi 171 336 J L ESON QQuUuMr ens Gok ome S ERs RB MARXAN Tools Spatial Analyst Layer ers 4 ih Editor hz 7 2 Layers ers Value p 204 Low 0 O risk_ag_small_scale O tisk_ag_sugarcane O tisk_bauxite_mines O risk_quarries O tisk_roads O trisk_urban_areas Display Source Selection 725761 037 663360 549 Meters
66. h risk element can be defined using information from existing literature and or expert opinion regarding the impacts of these activities or features on ecosystems Separate intensity values can be assigned relative to their impact on terrestrial freshwater or marine biodiversity The intensities should be normalized based on a relative scale e g 0 0 1 0 or O 100 so that they are comparable across all risk elements and classes i e different types of roads The normalized intensity scores are not a representation of the absolute measure of the impact of activities on biodiversity Rather these normalized values should be a relative degree to which biodiversity is more likely to survive in one place over another based on the presence of a given activity in comparison to another activity Examples of intensity values used in a conservation assessment for Jamaica can be found in McPherson et al 2008 1 0 2 Influence Distance After the intensity values have been assigned the next step is to determine the influence distance of each risk element The influence distance is the spatial extent or footprint of the activity and represents the maximum distance the feature has a negative impact on a biodiversity In other words as the distance of the buffer increases away from the center point line or polygon where the activity is taking place the intensity values of the cells within the buffers diminish progressively distance decay and the r
67. he Specify Random Seed box The Clumping Rule and the Best Score Speed Up option will not be in use so they can be left unchecked as shown in the graphic Click on the Save button to update and save the input dat file This is the file that the Marxan exe file will read Exit the Inedit program by clicking on the Exit button Now you are ready to run Marxan Cost Threshold Threshold Penalty Factor 4 exp Bt 4 tanes from 0 to 1 Penalty Factor 4 Penalty Factor B Load cave De workspace marxantinput dat Save As Exit Bee Problem Run Options Annealing Input Output Cost Threshold Misc a Input File Editor for Marxan Advanced Options Starting Prop o Random Seed Clumping Rule Partial clumps do not count Out dated Options Best Score Speedup Load Ceworkspacelmarxan input dat Save Save As Exit TNC Protected Area Tools PAT Version 3 0 69 The Nature Conservancy August 2009 3 3 2 Running Marxan The Marxan exe should be located in the same g directory as your input dat file You can launch Peski S Is Tre hee tee bility the Marxan exe either through the Marxan Tools f Fie Edit view Insert Selection Tools Window Help drop down menu specifying its location or reas a f double clicking on the Marxan exe from within windows explorer A screen will appear to Eks Ry MARKMAN Tools Spatial Analyst show the progress of the
68. he data in columns by importing the output text files as comma delimited in Excel Check to see if each target met its goal remember that the goal is called target by Marxan by looking at the last column in the mvbest file An example of the mvbest sample output is found in Table 3 In this table the target Wet_Alluvial_Forest did not meet the goal You can determine how much more is needed by looking at the Amount Held field and comparing it to the Target field which is the Goal A high Species Penalty Factors SPF value e g 100000 penalty for not representing targets to the set goals for all targets will raise the relative importance of the target representation in comparison to overall portfolio cost a combination of boundary length and modifier cost per planning unit and SPF thereby forcing the representation goals to be met Huggins 2005 Also check tydixton_100runs_sum txt to view the score of each run TNC Protected Area Tools PAT Version 3 0 72 The Nature Conservancy August 2009 tydixton_100runs tydixton_100runs NUMBER SOLUTION 0 3 ot a 4 31 g 32 48 I 49 58 E 59 75 MM 76 100 Figure 12 Results of joining the tydixton_100runs_best txt Solution field and tydixton_100runs_ssoln txt Number field with the planning unit ID field These are the planning units that constitute the portfolio Solution that meet all the goals and the number of times that
69. he watershed Similarly you will notice that Dry Alluvial Forest is a very rare habitat type and it occurs only in small amounts within the watershed total of 38 8 hectares If you look at planning unit 65 you will notice that a large majority of what does exist for this habitat is located in that unit approximately 28 79 hectares This was the highest individual RBN score in the entire watershed 73 87 Similar conclusions can be made for planning unit 65 where Wet_Alluvial_Forest and Small_Rivers_Non_Karstic also scored relatively high RBN values 34 06 and 21 64 respectively Please note that if you are only using point feature class targets your RBI scores will be significantly lower given the fact that there is no area to calculate for points You can choose to symbolize the RBI values for a single Target using the your_output_name_RBI_ALL_TARGETS feature class To do this go to the layer s properties dialog and select the Definition Query tab Then use the query builder to create a query that will only display the information for the target you are interested 1n See the example below TNC Protected Area Tools PAT Version 3 0 3g The Nature Conservancy August 2009 Layer Properties General Source Selection Display Symbology Fields Definition Query Labels Joins amp Relates Definition Query RBITARGET Medium_River_Non_Karstic Query Builder FI D TCOUNT RB RB N RBI
70. hould 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 Marxan program executable see Game and Grantham 2008 Before we begin discussing how to use the tool to prepare the features and create these files the user should understand the purpose and contents of each of these files They are described by Huggins 2005 1 Conservation Feature File spec dat This file holds information about each target including the goals and names Only id type and target are essential all other variables are optional although assigning a high e g 10000 Species Penalty Factor spf will help ensure that your goals are met If a column is missing the default values will be used For some columns a value of 1 indicates either that the default is to be used or that value is given in the block definition file The name column can contain spaces or other word separators but any separator will be replaced by a single space If there are any duplicate definitions all but the last one will be ignored The contents of this file are id Type _ target spf target2 Id of Looks for Goal Species Minimum Minimum target block representation penalty clump size separation USE F definitions of the target factor for optional distance correspon DEFAULT
71. ican marine cost surface used in the MARXAN model included the combining of four risk categories contamination direct impacts flow accumulation and extraction JAMAICA MARINE COST SURFACE routes risk intensities to watershed outlets which often empty into the TNC Protected Area Tools PAT Version 3 0 29 The Nature Conservancy August 2009 ocean GIS point features representing coastal outlets can be created at the end of the freshwater flow accumulated routes and the intensity values can be extracted and transferred to the point attribute table The intensity values attached to these coastal points can then be assigned an influence distance and used as a part in the process of creating a comprehensive marine risk surfaces The following ArcView 3 x tools were designed to extract a grid value to a point feature A later version of the ERS module will include this functionality Get Grid Value Extension 2 Attp arcscripts esri com details asp dbid 10200 Grid Pig v2 6 http arcscripts esri com details asp dbid 11872 RISK an fre a DS 4 A EA gt F Ae a SA ft As fy ri U a we Mint V of La _ As gt AAS r gt FLOW ACCUMULATION SURFACE P ade a ee i A gt y d n E AE b iFa F MARINE RISK SURFACE Using flow accumulation of land based risk surfaces to estimate coastal outlet risk intensity on the marine environment in the Dominican Republic TNC Protect
72. ick again to unselect All layers in the current map view will appear here You cannot use layers with the same name Click this box is you would like to create a boundary file bound dat You will need this file if you are going to specify a boundary length modifier BLM parameter in your Marxan runs Click this box if you would like to create a Block Definition file block dat If choosing this option you need to have the following fields assigned in your target files Type TYPE Species Penalty Factor SPF Target 62 The Nature Conservancy August 2009 Area Length Conversions Status Options Occurrence OCC Minimum Clump CLUMP Separation Number SEPNUM Separation Distance SEPDIS and Proportion PROP The default units are specified in hectares area and kilometers length If using the area of the planning unit as cost the cost will be reported in hectares You should only change the default numbers if you are using units other than hectares 10000 sq m for polygons and kilometers 1000 m for length e g feet The user should also make sure that the specified goal units are the same as the calculated units Status is optional but needed if you plan on using a protected area layer or other special interest areas to lock in planning units Click the Use Layer option for specifying a protected area polygon feature class or special interest areas Click the Use PU Field is you have al
73. ing or creating through on screen digitization the most accurate GIS layers available Human activities are often the most common risk element features used to create ERS models Activities such as agriculture urbanization tourism zones and hotels roads industry and population density are examples of risk elements that can be used in the creation of an ERS These models can be developed specifically for terrestrial freshwater and marine realms based on available input data and expert assessments for each risk element Once all input data are gathered experts must then review and rank each risk element to the degree that it is a threat to the habitat species in question This is done by assigning three variables to each point line or polygon feature that represents the corresponding risk element The three variables assigned are intensity value influence distance and distance decay function These values can be derived through expert evaluation of the extent severity and reversibility of each risk element in relation to the conservation target s In addition to socio economic data natural event data for events such as hurricanes volcanic activity and climate change may also be used in the creation of an ERS although it may be difficult to rank and assign these values due to the extreme unpredictability and complexity of these events The figure below shows examples of polygon line and point risk elements that represent modeled risk su
74. is really only limited by available memory e The size of planning units in relation to the reliability of mapping e g larger planning units could be needed where the locations of the targets to be represented are imprecise or where the boundaries of planning units are known to be inaccurate e The ability of regular grids or hexagons to show per unit area values for criteria such as richness of unprotected targets e Equality of the sizes of planning units over large geographic areas when factors such as map projections are an issue e Convenience of conversion of planning units to management units on the ground when analyzing at the fine scale e Appropriateness of boundaries for conservation management when analyzing at the fine scale TNC Protected Area Tools PAT Version 3 0 AT The Nature Conservancy August 2009 e Planning Unit Cost Range The range of cost values must allow the desired influence on the selection of planning units This must be considered with relation to boundary length as the objective function is a combination of boundary length boundary length modifier BLM and cost The effect of the BLM will also be affected by changes in cost If a range of costs is to be used the BLM value should be tested with the costs in place The Species Penalty Factor SPF is the importance a user puts on each target meeting its goal and also influences the selection of planning units All of these factors have to be in correct bal
75. isk to the habitat is lessened Some features may have high risk activities that extend a long distance from the center while others have a lower risk with more constricted boundaries It is best to set up a risk element table that indicates the _ intensity and influence distance of Value each risk element This will be 7 High explained in more detail in the next section Low 1 0 3 Distance Decay Types Ecologists have documented that depending on the ecosystem some risk elements may have a different impact than on other risk elements Ervin and Parish 2006 Theobald TNC Protected Area Tools PAT Version 3 0 12 The Nature Conservancy August 2009 2003 Araujo et al 2002 In some cases there may be a direct linear relationship between a risk element and an ecosystem s response to the threat Often times the greater the expression of a risk element the larger that threat may have upon an ecosystem However this is not always the case because some ecosystems have different characteristics that govern the way they might respond to a given threat For example fire in certain ecosystems can be a disaster and immediately destroy or highly degrade an ecosystem such as rainforests in the Amazon But in grasslands such as in the Orinoco Basin it is necessary to have fire in certain intensities and frequencies To little fire is bad for that ecosystem and too much fire is equally bad There is a non linear response relationship b
76. ive Heuristic Improvement Click on the Save button at the heise O M bottom of the Inedit screen W lterative Improvement Normal Iterative Improvement Save As Exit Dworkspace marzan input dat 3 Click on the Annealing tab positioned third P a tac KE from the left at the top of the Inedit screen The f Problem Run Options Annealing Input Output Cost Threshold Misc default value for the annealing controls should be Annealing Controle used These are 1000000 six zeros Iterations of eaea o the algorithm with 10000 four zeros eee ooo Temperature Decreases used with Adaptive e W Adaptive Annealing Annealing Initial Temperature Cooling Factor Final Temperature adaptive annealing re Save as Exit Deworkspacelmarxantinpuk dat TNC Protected Area Tools PAT Version 3 0 67 The Nature Conservancy August 2009 4 Click on the Input tab of the Inedit screen The input folder must be set first before navigating to POPA the input files Click on the input directory browse Problem Run Options Annealing Input Qutput Cost Threshold Misc button towards the bottom of the screen and navigate to the output folder where your new input Necessary Input Files Species FileName spec dat Browse files are located Planning Unit FileName pudat Browse Planning Unit versus Species puvsprdat Browse The input dat files can then be specified by clicking on the browse button
77. l the additional fields and a new dialog box will appear listing each unique target on the left side and the fields to be populated along the top The user can now enter the values of each field using the table previously prepared Each field has the default value already assigned but these numbers can be changed according to the conservation scenario that has been set up in the data prep table If you have many targets that need to be assigned the same value you can use the Fill Down First Row to automate the calculation of the fields using whatever values you enter in the first row These values will be duplicated to all other rows MARXAN TARGET PREP Penalty Clump Sep Sep Factor a Size Number Distance Prop Medium_River_N on_Karstic 710 11270 70 mall_Rivers_Non_Karstic 720 8442 21 Fill Down First Row Cancel When you are finished entering in all the values recheck the numbers and press OK Now add the new feature class to the map view and open the attribute table in order to make sure that the fields have been created and they have been populated with the correct TNC Protected Area Tools PAT Version 3 0 60 The Nature Conservancy August 2009 values These values will be used in generate the input files that Marxan will use You may notice that additional fields TNAME and TID were created These are created for consistent naming conventions when using the Marxan Input Generator which you are now rea
78. ll serve as your PAT_SCRATCH folder were temporary files will be written WARNING The entire contents of the directory that you specify will be periodically deleted so do not store other vital information in this directory or choose an existing directory on the disk that contains important information Remember that depending on the size and level of detail requested by the user these programs may require large amounts of free disk space to operate Be sure to check how much space you have on your operating hard drive the program will crash if you don t have enough space This can especially happen when executing the ERS module which can create very large multiple output grids ERs Per MARXAN Tools Options ET Settings Settings 8 You may also specify the location of the Marxan InEdit and Convert to Matrix seps You must specty a locaton on the local hard arive that has wite access e e and sufficient storage space WARNING The entire contents of the directory you executables using the Options gt specify will be deleted periodically so do not choose existing directory on disk that P contains important information Settings dr op down menu If you do not Scratch Directory C temp PAT_SCRATCH cal Sp ecify wher e these files r eside on your You may specify the location of the MARKAN InEdit and convert to matrix executables If you do not specify these you will not be able to execute these computer gt you will not
79. lso a number of ways solutions can be tested and found using the heuristics or the annealing algorithm In addition to setting the conservation scenarios there are several project considerations to be made before finalizing the conservation targets planning units protected areas and cost surface Ideally these considerations should be made through consultation with conservation experts and some can be determined through experimental model runs The following are suggestions from Huggins 2005 a Analysis Extent The areas of interest should be defined based on the extent of all target and socio economic data that have been gathered and assessed The extent should be defined by a polygon so that all features to be used in the model are clipped to the extent of the analysis area b Target Screening All target distributions to be entered into the analysis should be considered viable occurrences that are robust enough to influence the portfolio selection Screening biodiversity distribution maps should be considered to improve the likelihood of only including viable occurrences Methods previously used include screening vegetation by expert opinion removing all patches below a threshold size and screening using threat factors such as an Environmental Risk Surface ERS or freshwater flow accumulation models c Target Stratification Targets can be stratified to allow a geographic spread of representation or to represent biologically distinct
80. mat and was redesigned to handle very large and complex problems involving greater than 20 000 planning units This version is sensitive to the order of planning unit identifiers in the planning unit by species sparse or relational matrix and is not compatible with the traditional tabular matrix format Please consult the Marxan website http www uq edu au marxan to obtain a copy of the command line program convert_mtx exe which converts existing Marxan tabular matrix files into a format compatible with Marxan Optimised TNC Protected Area Tools PAT Version 3 0 45 The Nature Conservancy August 2009 3 1 Setting the Scenario and Marxan Project Considerations Before executing a Marxan model conservation experts should decide on scenario settings which may include a the set of data to be used and b the conditions applied to the objective function for Marxan to use Ball and Possingham 2000 Users must feel comfortable about the data that is going into the model and the conservation goals that have been assigned It is a difficult and often abstract task to set goals decide on cost measures planning units etc but these are essential decisions that must be made Remember that Marxan produces flexible solutions that meet specific quantitative representation goals in addition to minimizing threats constraints As this is an iterative process a number of conservation scenarios can be formulated and explored using Marxan There are a
81. meeting 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 be found 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 University of Queensland have written an enhanced user manual for Marxan that was released in February 2008 Game and Grantham 2008 Previous documentation was a mixture of mathematical theory and technical input data requirements and did not fully meet the needs of all tool users It is highly recommended that all Marxan users download this manual from _http www ug edu au marxan index html page 77823 amp p 1 1 4 2 and review with detail since it greatly facilitates understanding of the core software well beyond what this tutorial is designed for EXERCISE 3 Running a Sample Marxan Analysis REMEMBER 1 The user needs to have installed ArcGIS 9 3 ArcMap 9 0 9 1 or 9 2 may not 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 you also need to have ArcInfo Workstation installed and make sure the Coverage Tools Toolbox is loaded this is the default This toolbox is usually found in C arcgis arcexe9x Toolboxes If the user has installed it to the default location 3 The user must have the Spatial Analyst Ext
82. next to each input file name nr tss and navigating to the corresponding file The Block Definitions Browse necessary files are as follows Species File Name Boulos ME ui spec dat Planning Unit File Name pu dat and the Planning Unit versus Species puvspr dat We ret Diectow D workspace marsan will not run a block definition this time so un check the Block Definitions file locator under the Optional Input Files Click on the box to check Load save Savenc the boundary length file option and browse to the psworkspaceimarxantinput dat bound dat file Click on the Save button to save the information to the input dat file 5 Click on the Output tab of the Inedit screen REFIT DEAR This screen allows the user to specify the output Problem Fun Options Annealing Input Output Cost Threshold Misc files required to analyze the results Screen Ea Output General Progress gives a good idea ee Belia how the algorithm is running Click on the Eo rE i i lw Save Overall Best W Save Summed Solution output files shown in the graphic to the right Saving each run has minimal use and produces ah ae large amount of text files The most important F Save Missing Values Info files are the Overall Best the Summary and the Summed Solution Type 1 in the Species missing if proportion of target lower than box This option is to allow Marxan to consider a target to have met its goal if it is very close
83. nstant Rate 1 Rate 3 Rate 3 Rate 1 Examples of distance decay functions and the resulting output based on a single point occurrence and a 1000m influence distance Red and orange hues indicate higher intensity values while green and blue hues represent lower intensity values TNC Protected Area Tools PAT Version 3 0 13 The Nature Conservancy August 2009 EXERCISE 1 Building an Environmental Risk Surface YN REMEMBER Every intensity field must be a whole integer number NOT floating point with decimals The program creates an output grid for each unique intensity value thus it could take a LONG time run if you have hundreds of unique floating point combinations If you have floating point intensity values please rescale to integers with an appropriate number of unique values depending of computer hard drive free space and processing power All influence distances under the user specified cell size will automatically default to the user specified cell size Remember to enter an output cell size that appropriately fits your defined influence Check how much available hard drive space you have on your computer The program will crash if you don t have enough operating space e g 2 3 GB of space depending on scale resolution and distances complexity of your input features All risk element features shapefiles geodatabases and grids must be in the same projection and have the same projection information
84. ocess of 1 Developing a customized Environmental Risk Surface ERS based on mapped risk elements i e socio economic activities that have been identified through expert review as having negative impacts on the health of targeted habitats species or ecological systems 2 Calculating a landscape s Relative Biodiversity Index RBI which measures relative rareness or uniqueness measured in terms of biodiversity feature abundance in comparison to the overall study area Individual scores for each biodiversity occurrence can be used as a stand alone assessment for each planning unit or subsets of units e g hexagons watersheds 3 Creating input files and viewing model results for Marxan powerful software which provides users an easy way to manipulate input parameters and test review various conservation scenarios in order to achieve an optimal configuration of protected areas that meet user defined conservation goals This tutorial is not meant in any way to cover all facets of protected area gap assessments For a complete review of this process and for additional recommendations and guidelines on conducting a protected area gap assessment please refer to Dudley and Parrish 2004 TNC Protected Area Tools PAT Version 3 0 9 The Nature Conservancy August 2009 MODULE 1 Environmental Risk Surface ERS One of the primary goals of many conservation portfolio selection approaches is to create a functional landscape or network of sit
85. olygon 33 333333 44202923 Bat Phyllomycter 73 399339 50 000000 66 313385 Bat_Pteronotus 76 75309539 4347836 5 766381 Cave 76 75399539 8 400445 11 141238 Karstic_Streams 75 399559 0 113298 0150263 Medium River Non Karstic 75309559 25770366 34 172404 Dry Alluvial Forest 75 75399559 22896901 30 36742 Dry Limestone Forest 75399559 Al Polygon 54 Polygon 42 Polygon C C 35 Polygon _ 4 Polygon d Folygorn l 59 Polygon 64 Folygorn E 28 Polygon E 4 53 Polygon 123 Polygon e ee ee 4 Folygorn 131 Polygon Can Ta aa 4 APPS SSS Pte Sun eee 4 ee A 69 Folygor 73 Polygon Record Ki Ki 0 fal Show All Selected Records 6 out of 205 13 Polygon Ee 56 Polygon 36 L dd6d 12 184833 2 15475 16 160627 25 Polygon 25 1356442 5 866546 2 074904 7 780891 Ww Record Ki 0 fh Show All Selected Records 1 out of 113 Selected Options Based on the model results we see that almost all the RBN scores for this planning unit were calculated above 1 This indicates there is a high abundance of unique target occurrences areas contained within this planning unit compared to the same target s occurring in the rest of the Tydixton Park watershed Remember that these scores are relative and their range of values can vary widely depending on the input data that is used The highest two scores were for two rare bat species where there are very few occurrences throughout t
86. on_ers When the MIG dialog box appears you will be prompted to TNC Protected Area Tools PAT Version 3 0 61 The Nature Conservancy August 2009 enter in several fields and choose between many options that tell the program where to extract the values that it will use to create the input text files for Marxan MARXAN INPUT GENERATOR Analysis Unit tydivton_planning_units X ID Analysis ID Field Inputa tanget_point_ species tanget_line_habitats tanget_polgon habitats tidixton protected _ areas tidixton planning units W Create Bound File Area Conversion Factor Length Conversion Factor Statue Options Use Layer Use PU Field tidixton protected areas Status Value Status E Status Overlap Threshold 50 oe r Cost Options tydiston_ers Method fe cum o Mean blas Cost Surtace Field O E 10000 Output Directory 1000 D MAworkspace UK Cancel Create Block Def File Each of the items in the Marxan Input Generator menu will now be explained Planning Unit Planning ID Field Target Inputs Create Bound File Create Block Definition File TNC Protected Area Tools PAT Version 3 0 Specify the planning unit feature class polygon Specify the field that contains the unique ID for each planning unit Choose all the target layers points lines or polygons that will be used to create the Marxan input files Click on the layer to select it and cl
87. onservation Assessment of the Insular Caribbean Using the Caribbean Decision Support System Technical Report The Nature Conservancy Pressey R L amp Logan V S 1998 Size of selection units for future reserves and its influence on actual vs targeted representation of features a case study in Western New south Wales Biological Conservation 85 305 319 TNC Protected Area Tools PAT Version 3 0 74 The Nature Conservancy August 2009 McPherson M S Schill G Raber K John N Zenny K Thurlow and A Sutton 2008 GIS Based Modeling of Environmental Risk Surfaces ERS for Conservation Planning in Jamaica Journal of Conservation Planning Vol 4 60 89 Possingham H P I R Ball and S Andelman 2000 Mathematical methods for identifying representative reserve networks In S Ferson and M Burgman eds Quantitative methods for conservation biology Springer Verlag New York pp 291 305 Schill S 2005 Coastal Transport Modeling Using HYCOM Data Proceedings of the gin International Conference on Remote Sensing for Marine and Coastal Environments May 17 19 Halifax Nova Scotia Theobald D M 2003 Targeting conservation action through assessment of protection and exurban threats Conservation Biology 17 1624 1637 The Nature Conservancy 2006 South America Threat Assessment Arlington VA The Nature Conservancy 2005 A Regional Conservation Assessment for the Greater Caribbean Basin Arlington VA
88. or multiple targets to create an aggregate nRBI The advantage of this approach is that it can be used to identify the best remaining areas in terms of target abundance for each target or set of targets at the planning unit query domain or the landscape universe domain scale as shown in the figure below TNC 2005 In other words you are calculating the relative uniqueness or rareness of a habitat or species across the landscape nRBI RAI where RBI abundance planning unit abundance study area RAT area planning unit area study area EPERRA E TNC Protected Area Tools PAT Version 3 0 31 The Nature Conservancy August 2009 Location 608970 789808 685487 758391 Field Value oo Query Domain Hexagon FID 153 Shape Polygon Target Abundance 22 47 ha Arta 2538 PERIMETER 6 i JA_UNITSIK 2897 Universe Domain Area JAUNITS_1 2824 Total Area 76 388 ha Fw STRAT 1 MAR_STRAT 2 NULL_STRAT 0 RELATIVE BIODIVERSITY INDEX RBI ae 2590221 0164 22 47 76 388 100 0 03 aeo RBI_1 RBI_2 RBI_3 RBI_4 RBI_5 RBI_6 0 0 0 0 0 0 0 Query Domain Hexagon Bol 0 17329 Total Area 260 ha RLS z 2 RBI_11 0 Universe Domain Area RBL12 0 Total Area 76 388 ha RBA 0 ee s RBIL15 0 rget 19 RBI_16 0 Swamp ae RELATIVE AREA INDEX RAI Re 17 0 260 76 388 0 0034 pals 22 4699 RBIT_2 11 3213 Acres 642 034593 l Hectares 259 822182 NORMALIZED RELATIVE B
89. or special interest areas are to be locked in or fixed in the reserve thus always included in the solution These planning units are first considered when Marxan attempts to meet the conservation goals If goals are met within these areas no additional planning units are selected for that particular target goal The Marxan Input Generator permits users to specify a status layer to use when assigning the identifier Users can also specify a field in an existing planning unit attribute table TNC Protected Area Tools PAT Version 3 0 50 The Nature Conservancy August 2009 Define Study Area Extent t Identify Strata a Areas of unique biological significance b Selection of areas should also be based on habitat goal setting needs E Define Risk Elements Define Targets a Based on expert review a Expert review to screen both coarse b Each risk element should be assigned and fine filter 1 INTENSITYand b Each target class should be assigned 2 INFLUENCE DISTANCE 1 UNIQUE ID number 2 TARGET NAME text Y 3 Develop Cost Surface Set Target Goals a i 2 methods 1 actual area length or RCS ON APPO COS Tanga number or 2 percentages proportion e t Design Planning Units Each planning unit should have UNIQUE ID t Define Status Layer Protected areas or areas of special interest Run Marxan Suggested steps for preparing input data and conducting a Marxan analysis The four basic data layers
90. ork 2 0 be installed on your computer If you do not have Microsoft NET Framework 2 0 installed you should follow these steps a Download the Microsoft NET Framework 2 0 from http www microsoft com downloads details aspx familyid 0856 eacb 4362 4b0d 8edd aab 1 5cS5e04f5 amp displaylang en b Install ArcGIS 9 3 with Net support This only shows up after you do step a If you have already installed ArcGIS 9 3 input the DVD setup disk in your DVD drive and go to Start gt Control Panel gt Add or Remove Programs Scroll down to ArcGIS Desktop and click on the Change button Once the change Menu appears click on Modify and then install the NET Framework Support This option is only available once you install the Microsoft NET Framework 2 0 in step a Once you have added this support function you are now ready to install the Protected Area Tools The user must have installed the Spatial Analyst Extension and it should be turned on e Check to see if it is available and turned on under Tools gt Extensions Make sure you your input features are topologically correct by running geometry checked repaired for each input feature These tools can be found in ArcToolbox under Data Management Tools gt Features gt Check and Repair Geometry If problems persist after repairing geometry converting shapefiles into coverage format then back to shapefile format will often solve the problem PAT will process feature classes from geod
91. ote sustainable development and the conservation and sustainable use of biological diversity in the Americas through better management of biological information This project has established partnerships with organizations or programs in the region with similar goals and which have provided co financing to meet the specific objectives of the Connectivity Program In particular we would like to acknowledge Vince Abreu Douglas Graham Ivan Valdespino Boris Ramirez Rodrigo Tarte and Sandra Ann Icaza for their help and support offered over the course of this project It is hoped that the Protected Area Tools will continue to be developed and refined through external funding support A variety of new features have been added to version 3 that we hope you will find useful If you have bugs to report or recommendation to make please send your comments to the authors Steven R Schill Ph D George T Raber Ph D Senior Geospatial Scientist Assistant Professor The Nature Conservancy Department of Geography and Geology Mesoamerica amp Caribbean Region School of Ocean and Earth Sciences sschill tnc org University of Southern Mississippi graber gmail com DISCLAIMER The authors would like to expressly state that these scripts are being placed in the public domain or is Freeware and may be freely used THESE SCRIPTS ARE PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND EXPRESS OR IMPLIED BY STATUTE OR OTHERWISE INCLUDING BUT NOT LIMITED TO
92. re Conservancy August 2009 values expert opinion should be used in assigning a maximum influence distance that the risk element may have on a particular habitat or realm The program calculates intensity decay from the edge of each risk element using the user specified influence distance and distance decay function For example in the file called risk_ag_sugarcane shp there is a terrestrial influence distance of 1000 meters or 1 kilometer If the user chooses to use a linear decay function default the intensity value of 11 will be assigned within close proximity of the boundaries of each sugarcane polygon but as you move away from the polygon the intensity becomes linearly smaller and smaller until you reach a distance of 1000 meters where the intensity is reduced to zero 0 In the figure below there is an example of an ERS model output for a paved road with an intensity value of 30 and an influence distance of 300 meters Notice the linear decay function that is applied like a buffer completely around the risk element in all directions Additional guidance on setting up intensity values and influence distances for a variety of socioeconomic activities can be found in McPherson et al 2008 Higher Risk Areas Lower Risk Areas Intensity RISK ELEMENT PAVED ROAD 30 INTENSITY VALUE 30 as INFLUENCE DISTANCE 300 meters E o An example of ERS model output for a paved road risk element with an intensity value of 30 and an infl
93. ready assigned a status field value 0 1 2 3 in your planning unit file If you are using a layer to calculate the status values choose the layer e g tydixton_protected_areas shp in the drop down menu If you are using the PU field option choose the correct field in the drop down menu Status Value If you are using a layer to calculate the status value choose the status value you want assigned in the drop down menu For locking in planning units the default and most common status value used is 2 The status values are O The planning unit is not guaranteed to be in the initial or seed reserve or portfolio 1 The planning unit will be included in the seed reserve or the initial reserve 2 The planning unit is fixed or locked in the reserve 3 The planning unit is fixed outside or locked out of the reserve Status Overlap Threshold Use this field to indicate the overlap threshold you would like to use for the intersection of the status layer with your planning unit layer This threshold is used to indicate whether or not a planning unit will be chosen and assigned the specified status value The default is set to 50 meaning if the status layer overlaps a planning unit by at least 50 it will be flagged with the TNC Protected Area Tools PAT Version 3 0 63 The Nature Conservancy August 2009 Cost Options Cost Surface Field Output Directory specified status value You can control the percentage
94. ready to add the statistical surface summaries of the Environmental Risk Model ERS and begin to identify planning units that have high RBN values above the mean and low risk values below the mean These planning units could be candidate sites for high conservation value that are in relatively low risk environments according to our modeled ERS surface If you have not already run Zonal Statistics using a modeled ERS surface follow the instructions in the first module using the your_output_name_RBI_LSUMMARY output shapefile as the Zone dataset and join the output statistics table back to the Select By Attributes GIES your_output_name RBI SUMMARY Layer E tydixton_park_rbi_RBL SUMMARY output shapefile Only show selectable layers in this list Method Create a new selection Now determine what the mean values ers_stats MIN are for both the ERS surface and the RBI eh output shapefile This can be done by eae 3 double clicking on each layer and going ers state SUM to Symbology gt Classify Or EE Histogram option In either option the mean for the dataset will be reported For the ERS surface the mean is 72 55 and for the your_output_name_RBI_ gt nd EE _0 SUMMARY output the mean is 1 056 Get Unique Values GoTo Now we will use these numbers to SELECT FROM tydiston_park_rbi_RBISUMMAR Y_ers_stats WHERE threshold out high RBI pockets that have ydiston park bi BL SUMMARY RENT1 21 05
95. reate the output text files spec dat puvspr dat pu dat bound dat if specified and block dat af specified in the specified output directory Processing may take a long time depending on number of planning units targets and options specified TNC Protected Area Tools PAT Version 3 0 64 The Nature Conservancy August 2009 3 2 4 Combining Marxan Input Files If needed the Marxan Tools offer an easy way to combine Marxan input files The Combine Marxan Input Files tool can be used to combine several input files such as puvspr dat and spec dat file as well as the block dat file if running a block definition This is the sixth drop down menu item on the Marxan Tools list Just add the dat files you want to combine specify a new output filename and click OK If you are doing this it s important to keep track of which text files represent which feature types by including the feature type in the file name e g puvspr_points dat spec_polys dat You should only have to combine multiple series of puvspr dat spec dat and block dat files because the pu dat and bound dat files will be the same between features Combine Marxan Input Files Tydixton_Park mxd ArcMap Arcinfo File Edit View Insert Selection Tools Window Help List of Files to Combine Add File D g Wg Eal n ia D workspace marman puyepr_lines dat DD Wwiorkepace nananspuyvepr points dat Do workepacemananspuyvepr pols dat ERs FR MARMAN
96. red in the RBI calculations Next specify the Output Location as well as an Output Name The output location is a folder geodatabase or feature dataset The Output Name you enter will serve as the root name of the two feature classes that will be created by the model The two new feature classes that will be created in the Output Location will be named your_output_ name_RBI_SUMMARY and your_output_name_RBI_ALL_TARGETS When you click OK another box will appear that will ask you to specify the unique ID fields for each of the target TargetLayer ID Field input layers For the three habitat arget point species TARGET_NAM a shap efiles you will choose the target_line_habitats TARGET_NAM also be a unique number code assigned to each target class or type but it is Cancel easier to interpret the output tables if you use descriptive text for habitats and species such as Wet_Limestone_ Forest Karstic_Streams or Endemic_Fish When using your own data make sure any entry in the target name field does not contain any special characters e g fi 6 or the program may fail Choose Field for Target Layers When you have specified the target field for each of the input layers and press OK the RBI calculations will begin processing The process may run for quite some time depending on number of analysis units total number of unique targets and complexity of TNC Protected Area Tools PAT V
97. red to as the universe domain and the analysis unit is also called the guery domain The target layer must have a unique name or code field that represents each unique target class or type e g forest type stream type The analysis unit layer must have an ID field with a unique code or ID assigned to each planning unit or watershed Biodiversity Index RBI Calculator x Once you have loaded the required layers in es Analysis Unit tydiston_planning_units the m ap view press Larget_point_species gt eee et ate ete Analysis ID Field ID the RBI button and tidixton_planning_units the RBI Calculator tidinton watershed Analysis Extent tydixton_watershed f dialog box will Output Location D Temp REl appear In the left Output Name tydixtom_park bi 0 box click on the targets files that you Cancel_ want to use in the RBI analysis Remember this tool has been designed so you can run simultaneous calculations on point line and polygon features For this exercise choose target_point_species target_line_habitats and target_polygon_habitats Next choose the analysis unit or query domain layer from the drop down list tydixton_planning_units shp Next choose the field from that layer that contains the unique ID for the analysis units ZD In the Analysis Extent drop down list choose the watershed boundary layer tydixton_watershed shp The analysis extent is the universe domain total landscape area to be conside
98. rfaces with varying intensity values and influence distances The dark red areas represent higher combined risk and the lighter blue areas lower risk as modeled by the mapped risk element features Examples of how to assign intensity values influence distances and different distance decay functions are explained in the next sections a Intensity Intensity Intensity Viale Value Value H E iigh ana iji 7 u li 1 p x mm lal 3 Le as TA Low Examples of Environmental Risk Surfaces ERS derived from polygon line and point risk element features Each risk element feature has an intensity influence distance and distance decay function assigned based on the potential threat to biodiversity health Red represents higher risk values which decreases linearly as the distance is increased away from the combined risk element features i e blue represents lower risk TNC Protected Area Tools PAT Version 3 0 11 The Nature Conservancy August 2009 1 0 1 Intensity Value Having identified the risk elements experts then rank each element in relation to each other and assign an intensity value in terms of degree of risk to the focal habitat species For example certain types on mining such as bauxite may have more damaging effect on freshwater systems and thus assigned a higher intensity value compared to limestone excavation which may have less damaging effect Intensity values and influence distances for eac
99. riven by quantitative goals the analysis is repeatable and objective Marxan results can illustrate a pattern of priority sites of low political or social pressure that can still satisfy the explicit biodiversity goals It can also identify a network of sites where resources necessary to implement conservation Strategies or threat abatement are forecast to be lower TNC 2005 Planning units are parts of the land and seascape that are analyzed as the potential building blocks of an expanded system of reserves or areas of conservation priority They allow a comparison between candidate areas Planning units can be systematic units such as hexagons natural areas like watersheds administrative boundaries or arbitrary sub divisions of the landscape They differ widely in size between studies and within regions dependant mostly on scale of analysis and data resolution TNC 2005 TNC Protected Area Tools PAT Version 3 0 42 The Nature Conservancy August 2009 3 0 The MARXAN Algorithm One of the more popular algorithms implemented in Marxan is the simulated annealing site optimization algorithm In order to design an optimal reserve network each planning unit is examined for the values it contains The features within one planning unit may be valuable alone but may not be the best choice overall depending on the distribution and replication of the other features in the wider planning area During the simulated annealing p
100. roan 65727 conservation values read Reading in the Block Definition File Marxan writes the results to text files ie EEEE RTA Pre processing Section that can be found in the specified output AESAC folder These files can be viewed using Run 1 Using Calculated Tinie 258917208 811 Tcool 99980118 Notepad Or Excel If you decide to i 3031592 5 Penclty 286925361678 PUs 71 Boundary 216 60 Missing 19 Shortfal Nalue 285925367842 8 Cost 107 PUs 71 Boundary 216 0 Missing 19 Shortfall 3631 22 e e 5 G change the settings in the feature oe ine eet eet ioe calcein co bie ie Md Annealing Completed Time passed so secs Value 182058 9 Cost 82358 9 PUs 4516 Boundary 3988 0 Missing 1 Shortfall 6 66 attribute tables it iS beast to reextract the j ace 82358 9 PUs 4516 Boundary 3988 0 Missing 1 Shortfall 6 66 Pe nalty 6 661695 values and create new input files in a Best Ualue 182058 9 Cost 82358 9 PUs 4516 Boundary 3988 0 Missing Shortfall 6 66 Penalty 6 6 182058 9 Cost 82358 99 PUs 4516 Boundary 3988 0 Missing Shortfall O A Pe new directory 8 000000 182058 9 Cost 82358 9 PUs 4516 Boundary 3988 0 Missing Shortfall 6 66 Pe 4 6 182058 9 Cost 82358 9 PUs 4516 Boundary 3988 6 Missing Shortfall O A Pe 6 6660000 Using Calculated Tinit 226358132 6148 Tcool 6 99981466 Creating the initial reserve InitValue 285925367842 8 Cost 1075 0 PUs 71 Boundary 216 6 Missing 19 Shortfal 1 3631522 65 Penalty 285925361367 8 Value
101. rocedure an initial portfolio of planning units is selected Planning units are then added and removed in an attempt to improve the efficiency of the portfolio Early in the procedure changes in the portfolio that do not improve efficiency can be made in order to allow the possibility of finding a more efficient overall portfolio The requirement to accept only those changes that improve efficiency becomes stricter as the algorithm progresses through a set of iterations Note that for any set of conservation targets and goals there may be many efficient and representative portfolios that meet all conservation goals but most of these networks would have a number of planning units in common Many runs of the algorithm are used to find the most efficient portfolio and to calculate a measure of irreplaceability used here to indicate the number of times a particular unit is chosen In some cases conservation targets are only found in limited sites areas of high irreplaceability that are always chosen in any representative portfolio Additionally areas of high irreplaceability also include planning units whose exclusion would require a proportionally larger conservation area network to achieve the same level of representation resulting in a loss of portfolio efficiency The algorithm attempts to minimize portfolio total cost whilst meeting conservation goals in a spatially compact network of sites This set of objectives constitutes the o
102. ror We will be creating this file so the next time you launch Inedit the error will not appear O O O H COMBINE MARZAN INPUT FILES O O O ai Input File Editor for Marxan Problem Run Opti Annealing Input Output Cost Threshold Mi 1 The first screen is to set the Problem The un Options Annealing Input Output Cost Threshold Mise options consist of the number of runs to be Miscellaneous performed and the level of clustering desired Repeat Runs 100 Type 100 runs in the first Miscellaneous Repeat Runs box 200 runs are also often used Boundaries but take twice as long to run 100 runs are used Eo here due to time constraints Type 0 into the r Boundary Modifier box as shown here The type Tradional Formatted Style of input file to be used is the New Freeform SU k Style This program edits an input file for MARXAN v1 6 Created by lan Ball 1999 Modified by lan Ball 2001 Save As Exit Deworkspace marxant inpuk dat TNC Protected Area Tools PAT Version 3 0 66 The Nature Conservancy August 2009 ai Input File Editor for Marxan 2 Click onto the Run Options tab positioned Problem Fun Options Annealing Input Output Cost Threshold Misc second in line at the top of the Inedit screen You should see options for the type of Simulated Annealing algorithm to be run by Marxan Click the box Options for Simulated Annealing appear on next tab for Simulated Annealing and for Iterat
103. rs most often between input rasters on a cell by cell basis MEDIAN Takes the median value that corresponds to a cumulative proportion of 0 5 If each input cell value was arranged in increasing order 50 percent of the values would lie below the median and 50 percent of the values would lie above the median The median provides another measure of the center of the distribution MINORITY Takes the value that occurs the least often between input rasters on a cell by cell basis RANGE Takes the range of values highest to lowest between input rasters on a cell by cell basis STD Takes the standard deviation of the values between input rasters on a cell by cell basis The standard deviation is the square root of the variance It describes the spread of the data about the mean in the same units as the original measurements The smaller the variance and standard deviation the tighter the cluster of measurements about the mean value VARIETY Takes the number of unique values between input rasters on a cell by cell basis g You can also use the Scale Output feature to rescale the final output model to a specified range This is useful for defining scale ranges in cost surfaces to be used in Marxan For example to keep a tight cost range use the area of a hexagon as the base and then five times the area as the maximum cost value i e 260 1300 For the tutorial example we will not use this option but it may be useful if you are trying
104. rts identifying efficient portfolios of planning areas that combine to satisfy a number of ecological social and economic goals Ball and Possingham 2000 Marxan is used by over 1100 registered users from 600 organizations government academia and NGOs in 95 countries as a decision support tool to consider options in terrestrial and marine reserve design It is perhaps the most popular site selection optimization software available and is widely published It is a stand alone program that requires no other software to run although GIS makes it simpler to prepare the data generate the required input files and view the results For the latest information about Marxan users should register and download the software at http www uq edu au marxan Early conservation assessments depended on manual mapping to delineate sites and were often reliant on expert opinion to prioritize conservation areas The large number size and diverse types of datasets describing the targets eventually required the use of a more systematic and efficient site selection procedure Marxan software is an optimization program and provides decision support for teams of experts choosing between hundreds of biodiversity targets and thousands of candidate areas planning units It identifies efficient portfolios of planning units and has a measure of flexibility that allows the teams to adapt efficient solutions to real world situations Using a transparent process that is d
105. rvation areas It is suggested that planning units HIGH RBI HIGH RBI LOW RISK HIGH RISK LESS MOST URGENT URGENT LOWRBI LOW RBI LOW RISK HIGH RISK RISK containing both high nRBI i e have relatively high target abundance scores and high Marxan irreplaceability are areas that should receive first attention in sequencing conservation actions These are areas that are potentially rich in rare intact or otherwise important ecosystem habitats Additionally rare habitat in high risk areas can be delineated by selecting areas above the median nRBI value and below the median risk ERS value The figure on the next page shows an example RBI and risk analysis recently conducted for terrestrial habitats in Jamaica Additional analysis can be done within strata to identify a more geographically distributed range of areas TNC 2005 TNC Protected Area Tools PAT Version 3 0 33 The Nature Conservancy August 2009 E o B medium P High L HIGH RBI HIGH RBI LOW RISK f HIGH RISK MEDIAN LOW RBI HIGH RISK E o B Medium E High HIGH RBI HIGH RISK MOST URGENT MEDIAN LOW RBI HIGH RISK oO uJ HIGH RBI HIGH RBI LOW RISK HIGH RISK LESS MOST URGENT URGENT MEDIAN LOW RBI HIGH RISK HIGH RBI HIGH RBI LOW RISK HIGH RISK MOST URGENT MEDIAN Results from an RBI and risk analysis for terrestrial habitats in Jamaica This type of quartile analysis can be combine
106. s Prior to launching the ERS module you must also think about how to resolve overlay areas within the influence distance and make sure that each risk element is in the same projection with the projection information properly defined Risk element overlay functions should be determined by experts who understand the how these elements interact spatially E Attributes of risk_roads FID Shape HAME Class Terr_Inten Terr_Dista Polyline Road TRACK 50 1 Polline Roag TRACK 50 2 Pobvline Road TRACK 50 3 Pohvline Road TRACK 20 4 Polling Road OTHER 30 5 i i 1 ee aa aa a a aa a an 6 Polyline Roag TRACK T Pobvline Road TRACK 6 Pobvline Road TRACK 9 Pobvline Road CLASS B 10 Polyvline Road TRACK E E o 5 Polyline Road CLASS E E E E E Record 14 1 fal Show Al Selected Records 0 out of 781 An example of the attribute table for risk_roads shp indicating class road type and corresponding intensity and influence distance values 1 3 Executing the ERS Module Once risk element features have all been assigned intensity and influence distance values and the layers are in the same projection the user is ready to execute the ERS module Prior to clicking on the ERS button in the PAT toolbar make sure all the risk element TNC Protected Area Tools PAT Version 3 0 18 The Nature Conservancy August 2009 features have been added to the map view and that the Spatial Analyst E
107. s 1 0 and 2 0 have less functionality and are no longer supported Once you have downloaded and unzipped the patv2 zip file double click on the setup exe file and the wizard will walk you through the installation process When the installation is complete launch ArcMap and turn on the extension by going to View gt Toolbars gt TNC Protected Area Tools You will see the following icon appear in your ArcMap window Ere Ry MARZAN Tools You can drag this icon by clicking on the left sidebar and positioning anywhere in your ArcMap toolbar This new toolbar gives you access to all the functionality in the three modules of the Protected Area Tools ERS Environmental Risk Surface RBI Relative Biodiversity Index and the Marxan Tools The Protected Area GAP Assessment Process Identifying gaps in protected areas is Steps in conducting a gap assessment one step in the demanding and often daunting process of creating country a EOE a BE SS ay i f level ecologically representative T ks Evaluate amd map the cccurmrence aind protected area networks Although status of there are a variety of ways and 4 Analyse and Map the Gocunmence and f methods that protected area gap x slatus of protected areas F assessments can be conducted several Sge s the infarmation dentity ga principles and guiding methods are ee a outlined in Dudley and Parrish 2006 posse aha tes The tools presented in this tutorial are aimed at s
108. s 30m Remember that the smaller the cell size the longer the computation time exponentially and the more hard disk space required Run time also depends on the scale you are working at and the number of unique intensity values that you have defined It is a good idea to experiment with cell sizes to get an idea of run time and space requirements All input distances need to be specified in the same units as the input data i e all inputs should use the same units Also if you have defined an influence distance less than the cell size TNC Protected Area Tools PAT Version 3 0 20 The Nature Conservancy August 2009 the output will automatically default to the user defined cell size For example if roads have an influence distance of 15m and a cell size of 30m is used the cell size will override the system and the road influence distance will be 30m For the tutorial example we will use a cell size of 30 which corresponds with the scale of the input data You can experiment using different cell sizes to get an idea of how the resolution and file size correspondingly change Specify the Overlay Function This is where to specify the map algebra function that you want used when combining all of the output risk element groups A risk element group means all of the risk elements created by a single input layer e g roads towns quarries Later you will be given the option of specifying the overlay function within a risk element group e g typ
109. sure that conservation goals are met Can be adjusted Der ere accordingly for priority targets Total field length is 16 numbers Total field length is 16 numbers Target Occurrence The number of occurrences of the conservation target required This can be used in INTEGER conjunction with or instead of the goal Total field length is 16 numbers Minimum Clump Size If a clump of a number of OCC INTEGER planning units with the given conservation target is below this size then it does not count toward the goal TNC Protected Area Tools PAT Version 3 0 57 The Nature Conservancy August 2009 es GT Total field length is 16 numbers Separation Number Goal number of mutually separated planning units in valid clumps Total field length is 16 numbers Separation Distance Minimum distance at which planning units holding the conservation target are ene a considered to be separated Total field length is 16 numbers Proportion An alternative to the GOAL and used in the block definition file This is the proportion of the total amount of the conservation target which must be FLOAT i a oe ae PROE preserved Expressed in 0 1 If this is specified it is used instead of the number specified in the GOAL field Total field length is 15 numbers NOTE In using the Marxan manual by Ball amp Possingham 2000 please note that the authors use the term Conservation Feature for what we are referring to as the Target
110. t 1s scaled by the BLM There is no theoretically good value to give it because the cost measure and the length measure are both arbitrary Ball amp Possingham 2000 The BLM can be confusing to understand but serves several important purposes e To specify the relative importance of fragmentation in the cost function Smaller values will make fragmentation less important than meeting goals and minimizing area If the BLM is set to zero then the boundary length will have no impact on the selection of the portfolio and the output solution will be highly fragmented The more you increase the BLM the more you increase the importance of compactness for the modeled portfolio solution e To convert units If the base analysis unit cost is specified as hectares and boundary length as kilometers the BLM must serve the purpose of converting the boundary into comparable units TNC Protected Area Tools PAT Version 3 0 A8 The Nature Conservancy August 2009 e To make area and length comparable The least fragmented shape possible is a circle and the area to circumference ratio can serve as a guide for this Because of the many conflicting factors inherent in the BLM the best way to arrive at a good number is via experimentation There are some key things to look at to test the BLM s accuracy at meeting goals particularly in how the mvbest file is set up Adjusting BLM is all about how goals are met under precisely overrepresented F
111. t 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 or by specifying the Number of hexagons 3 If specifying the area enter the desired area in hectares for each hexagon The default is 100ha If specifying the number of hexagons enter the number of hexagons 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 0 55 The Nature Conservancy August 2009 5 If you uncheck Include Only Overlap Hexes the program will return the complete set of planning units contained within the upper left and lower right coordinates of the Extent Layer Most users leave the box checked since they only want the planning units that overlap with the features of the extent layer e g watershed targets 6 Specify a Step interval for the calculation of the unique IDs The default is an interval of 1 e g 1 2 3 4 etc This is often useful when combining hexagon IDs at a later time using multiples of ten 1 e using a step interval of 10 or 100 7 Specify an Output File This will be the name of the new hexagon 8 Click OK to execute The process may run for quite some time depending on the size and number of hexagons Extent Laver tydixtor_ watershed required to generate The bot
112. t id or the same as dani id1 for an irremovable boundary CRITICAL The values are separated by commas The file structure looks like id1 id2 boundary 1 2 33453 5 1 3 334536 2 3 2 2 Generating Hexagons HexGen Tydixton_Park mxd ArcMap ArcInfo Hexagons are the most often used polygon feature that serve as planning units for Marxan analyses go Ele HOO Wee eae ies e GE Ecologists have adopted hexagons because they D Hg Eal i have more facets for connectivity and can Pe aran Tto E represent a more continuous and natural surface Om EXEM The HexGen tool has been designed as a simple way to generate hexagons based on a user defined M MARZAN INPUT GENERATOR l Oo size and attribute them with customized unique Lay Mer MARMAN TARGET PREP n a O E COMBINE MARXAN INPUT FILES n IDs Ll RUN CONVERT TO MATRIX FILE rH T RUN INEDIT You will not need to create hexagons to run the F RUN MARXAN tutorial data since they are already provided In JOIN AND DISPLAY MARXAN OUTPUT order to create hexagons for a new Marxan analysis 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 the spatial boundaries of your extent layer This layer represents the total area where you would like hexagons to be created Before you click on the HexGen button make sure that you have the Exten
113. t list table that should be prepared prior to running the Marxan Target Prep tool Remember that you can use either the GOAL field or the PROP proportion field to define your goals but choose one or the other If you choose PROP you must define a block definition file taRGet Nam TaRceTiD Goat _ Tyee sper _ occ cLump sepnum sePpis PROP _ taes ee orei a e a a a o a a ER E e e E e e E af af oso Blk_Bill_ Parrot 3 00 47 100000 a 1 p foe f f rof es ooo e a a r oan eol 70 somo rf a af foo 1 e Turtle 2 00 100000 1 1 0 50 o nenn ro O 720 84221 2 2 4 32 Only use the PROP proportion field if you are not entering exact goal amounts in the GOAL field If using PROP you must check the box in the Marxan Input Generator to create a block definition file TNC Protected Area Tools PAT Version 3 0 59 The Nature Conservancy August 2009 In addition to adding the target name and ID fields you may want to make sure that all targets to be used in the Marxan analysis have been properly screened by experts and stratified if necessary For example stratification is needed if the user wants to assign different goals to the same target class that is spread across different geography settings e g political boundaries elevations or geologic zones These stratified targets must have both a unique name and ID defined At a minimum the targets should have the conservation goals d
114. tematic and repeatable manner PAT will continue to be developed based on user s needs and refined for investigations into a habitat species vulnerability to risk elements such as land cover change fragmentation and changes to PA boundaries or management practices b distributions of habitats species in the landscape to ensure that there are sufficient occurrences across their environmental range within PAs and c overall level of protected status to site irreplaceability as modeled by Marxan TNC Protected Area Tools PAT Version 3 0 4 The Nature Conservancy August 2009 Mandatory Requirements Needed to Run the Protected Area Tools l The user needs to have ArcGIS 9 3 Desktop installed e Farlier versions of the tool e g ArcGIS 9 1 and 9 2 can be downloaded from Attp www gispatools org You can check what version and level of ArcGIS you are running by going to Help gt About ArcMap e An ArcView Level is required to run the ERS and RBI modules e An ArcInfo Level is required to run the Marxan Tools you also need to have ArcInfo Workstation installed Make sure the Coverage Tools Toolbox is loaded this is the default setting during installation This toolbox is usually found in C arcgis arcexe9x Toolboxes If the user has installed it to the default location e To ensure full functionality of these tools please install the latest ArcGIS Service Packs from www esri com Version 3 0 requires that Microsoft NET Framew
115. that planning unit was chosen based on 100 runs Table 3 Analysis of Marxan output tydixton_100runs_mvbest txt which lists several model outcomes by feature including amount of the target that was held and if the goal was met Remember the term Target in this output is the same as the conservation goal Conservation Amount Occurrence Occurrences Separation Separation Feature Feature Name Target Held Target Held Target Achieved Target Met 5172 Wet_Limestone_Forest 2422 14 2440 04 0 21 0 Oyes 5132 Wet_Alluvial_ Forest 61 39 60 76 0 4 0 Ono 5112 Dry_Limestone_Forest 472 05 549 85 0 6 0 Oyes 5082 Dry_Alluvial_ Forest 34 91 38 48 0 3 0 0 yes 639 Spring 3 3 0 3 0 Oyes 91 Huitas 4 4 0 4 0 O yes 80 Endemic_ Turtle 2 2 0 2 0 O yes 70 Endemic_Fish 2 2 0 1 0 O yes 638 Cave 7 13 0 7 0 0 yes 47 BIk_Bill_Parrot 3 3 0 3 0 0 yes 524 Bat_Pteronotus 1 1 0 1 0 Oyes 531 Bat_Phyllonycter 2 2 0 2 0 0 yes 720 Small_Rivers_Non_Karstic 8442 21 9570 59 0 6 0 Oyes 710 Medium_River_Non_Karstic 11270 7 12538 22 0 12 0 0 yes 700 Karstic_Streams 11606 12 18360 14 0 8 0 0 yes TNC Protected Area Tools PAT Version 3 0 73 The Nature Conservancy August 2009 References Araujo M B P H Williams and A Turner 2002 A sequential approach to minimize threats within selected conservation areas Biodiversity and Conservation 11 1011 1024 Ball I R and H P Possingham 2000 MARXAN V1 8 2 Marine Reserve Design Using Spatially Explicit Annealing a Man
116. tom left will report SpecityHexArea Specify Number of Hexes the current row of hexagons the program is Area Hectares 0 processing and the status bar will show percent Stat UNITI O complete It is best not to work on the computer or M Include Only Overlap Hexes Step 1 click on ArcMap while the model is executing It Output Dataset C Tempitydixton_park_pus shp takes approximately 1 minute to generate 100 Input Area in units 10000 e g in hectares if meters hexagons depending on the computer Once the ox Cancel _ model is compe a text box stating Processing Complete will appear and the results will be loaded into the map view 3 2 3 Marxan Target Prep Having reviewed the basics of Marxan and the required input files we are now ready to start the process of preparing the conservation target data Tydixton_Park mxd ArcMap ArcInfo File Edit View Insert Selection Tools Window Help for creating Marxan input files If the user already Lae el amp E a has their planning units 1 e hexagons created ERs Fey MARXAN Tools Spatial Analyst the first step in using the Marxan Tools is creating d Hexcen Hae ARAN TARGET PREP hy MARYAN INPUT GENERATOR COMBINE MARZAN INPUT FILES F RUN CONVERT TO MATRIX FILE IF RUN INEDIT ME RUN MARSAN 42 JOIN AND DISPLAY MARYAN OUTPUT and populating the target layer with the correct fields that Marxan will use to produce the input files It is not nec
117. toolbar This will bring up the ERS interface that looks like this Environmental Risk Surface Generator Input Layers risk_ag_small_scale isk_ag_ sugarcane rsk_Bausite_ mines nsk_quarnies nsk_roads tisk_urban_areas Output Faster al Raster Catalog Item SSS Intensity Scale Max 100 Output Cell Size Do D Overlay Functor SUM Scale Output Min 7 Mam 5000 Expand Extent by 1000 Cancel TNC Protected Area Tools PAT Version 3 0 19 The Nature Conservancy August 2009 a Select the risk layers that you want to include in the ERS analysis by clicking on them in the ERS interface window Once selected they appear highlighted and will be used in the model Click to unselect Specify an Output Raster This should be a valid raster name You can save your output GRID IMG personal geodatabase file geodatabase ArcSDE geodatabase or non georeferenced formats BMP GIF JPEG JPEG 2000 PNG TIFF When storing a raster dataset in a geodatabase no file extension should be added to the name of the raster dataset When storing the raster dataset in a file format you need to specify the file extension bmp for BMP gif for GIF img for an ERDAS IMAGINE file jpg for JPEG jp2 for JPEG 2000 png for PNG tif for TIFF or no extension for GRID The output grid should not be written to a directory that has a space in the name or in the directory path e The output grid name cannot be over 13 characters long e
118. ual Convention on Biological Diversity 2001 Global Biodiversity Outlook CBD Montreal Canada Dudley N and J Parrish 2006 Closing the Gap Creating ecologically representative protected area systems A guide to conducting gap assessments of protected area systems for the Convention on Biological Diversity Secretariat of the Convention on Biological Diversity Montreal Technical Series no 24 vi 108 pages Ervin J and J Parrish 2006 Toward a Framework for Conducting Ecoregional Threats Assessments In Monitoring Science and Technology Symposium Unifying Knowledge for Sustainability in the Western Hemisphere Proceedings C Aguirre Bravo J P Pellicane P D Burns and S Draggan eds Fort Collins CO U S Department of Agriculture Forest Service Rocky Mountain Research Station p 105 112 Ferdana Z 2006 Personal communication Game E T and H S Grantham 2008 Marxan User Manual For Marxan version 1 8 10 University of Queensland St Lucia Queensland Australia and Pacific Marine Analysis and Research Association Vancouver British Columbia Canada Huggins A 2006 Personal communication Huggins A 2005 Marxan Conservation Planning Decision Support Software Tutorial for GIS Beginners The Nature Conservancy 18 pages Huggins A E S Keel P Kramer F N ez S Schill R Jeo A Chatwin K Thurlow M McPearson M Libby R Tingey M Palmer and R Seybert 2007 Biodiversity C
119. uence distance of 300m Notice the linear decay function that is applied like a buffer completely around the risk element in all directions TNC Protected Area Tools PAT Version 3 0 16 The Nature Conservancy August 2009 1 1 1 Overlay Function Another item to consider is how to resolve the overlaying areas of influence distances between neighboring risk element features The ERS tool allows users to specify how risk elements will be combined based on map algebra statistical functions e g mean majority maximum median minimum minority range standard deviation and variety These are further explained in the next section but if influence distance overlay between risk element features is anticipated it is important to think about the best way to resolve this type of aggregation prior to executing the tool The default function for influence distance overlay is SUM calculating the sum for all layer values Most often either SUM or MAX are the most typical functions used Examples of each are given in the figure below Overlay Type SUM Overlay Type MAXIMUM Examples of the most commonly utilized overlay function types Maximum and Sum for resolving overlaying areas of influence distance between neighboring risk element features Notice the differences in how each function handles the computation on the intensity values within the overlay areas TNC Protected Area Tools PAT Version 3 0 17 The Nature Conservancy August
120. upporting several steps of Agreeona hi b h strategy and this process but the user must always take action remember that the model output is only as good as the quality of the input data The rule of garbage in garbage out cannot be emphasized enough It is recommended that 80 90 of the total gap process work should involve careful thought and consideration with in country experts TNC Protected Area Tools PAT Version 3 0 7 The Nature Conservancy August 2009 for focal habitats species delineation conservation goal setting and defining ranking of risk elements that threaten the health of targeted habitats or key species The guiding principles for conducting a protected area gap analysis include Dudley and Parrish 2004 l 2 Ensure full representation across biological scales species and ecosystems and biological realms terrestrial freshwater and marine Aim for redundancy of examples of species and ecosystems within a protected area network to capture genetic variation and protect against unexpected losses Design for resilience to ensure protected area systems to withstand stresses and changes such as climate change Consider representation gaps ecological gaps and management gaps in the analysis Representation gaps refer to species ecosystems and ecological processes that are missed entirely by the protected area system Ecological gaps relate to biodiversity that exists within protected ar
121. used by just typing in the percentage value There are four ways to assign a cost value to each planning unit a Specify a grid e g ERS model that is currently in your map view b Select Planning Unit Area to assign the area of the planning unit to each corresponding planning unit c Select Planning Unit Field to choose a pre defined field in the planning unit layer that contains a cost value and d type in a flat cost that will be assigned to every planning unit Method If you choose a grid to calculate the cost per planning unit you must choose a zonal grid function Sum Mean or Maximum that will be used for each planning unit The default is Sum which assigns the sum of all underlying grid cells within each planning unit as the cost for that planning unit Mean assigns the mean value and Maximum assigns the maximum value of the cost on a per planning unit basis If you choose the Planning Unit Field option for the cost you must then specify the Cost Field in the drop down menu Specify the directory where the new Marxan output files will be written If you are running multiple scenarios it is helpful to assign descriptive names to the folders e g high_goals_no_lock_with_cost It is best not to use a directory that has a space in the path e g C Document and Settings User When all the parameters have been set double check them and then click the OK button This will execute the program and c
122. value average based on the sum of total number of targets found in the universe domain i e total landscape RBIT2 Non normalized RBI value average based on the sum of total number of targets found in the guery domain i e hexagon planning unit Normalized RBI value average based on the sum of total number of targets found in the universe domain i e total landscape Normalized RBI value average based on the sum of total number of targets found in the query domain i e hexagon planning unit As part of the RBI output another feature class is created called your_output_name_ RBI_LALL_TARGETS If we look at the RBI model output planning unit number 76 came out the highest in the RBNT1 score If we open the your_output_name_RBI_All_ TARGETS table we can see the list of targets and their associated RBI scores within planning unit 76 TNC Protected Area Tools PAT Version 3 0 37 The Nature Conservancy August 2009 BH Attributes of tydixton_RBI_SUMMARY _ FID Shape mf RBIT2 RENTI RBNT2 36 Polygon 76 9 657478 20694596 12808401 27 446574 65 Polygon 65 7 211372 1 02843 9 564555 23 911388 70 Polygon a rine T m oo og T3 Polygon Gf Attributes of tydixton_RBI_ALL_TARGETS 44 Folygon 71 Folygon FD Shape TCOUNT RBI REN RBI TARGET 72 Polygon _ 132 Polygon 4474841 5934838 Dry Limestone Forest 75399559 62 Polygon 187 Polygon 4090171 5 424661 Wet Limestone Forest 75399559 1 P
123. xtension is turned on by going to Tools gt Extensions Remember that shapefiles geodatabases and grids can all be used in the ERS module When using grids the grid value is used as the intensity value For this exercise add the risk element features that are included in the figure below to the map view These features are part of the Tydixton Park tutorial sample dataset and are in the same projection JAD2001 with the projection information defined i e prj file Tydixton_Park mxd ArcMap Arclinfo File Edit View Insert Selection Tools Window Help el a gt lal EP i K Ey MARXAN Tools Spatial Analyst _ x i 8 i m ayers risk_ag_small_scale risk_ag sugarcane risk bauxite mines risk_ quarries risk_roads risk_ urban areas lt K E 5 K It is important to note that since ArcGIS calculates projection on the fly layers can appear to be in the same projection but may not actually be in the same projection This is important to understand because when executing an ERS model all layers are ultimately turned into grids before a series of map calculations are made Since Spatial Analyst does not do projection on the fly having the same coordinate system for all input layers is critical for success in these map calculations 1 3 1 Launch the ERS Module and Specify Input Layers and Output Parameters You are now ready to launch the ERS module by clicking on the ERS button in the
124. ygon shapefile by right clicking on the planning unit shapefile and going to Joins and Relates gt Join When the Join Data dialog box appears choose ID as the field that the join will be based on make sure that the zstat output table is the table to join and then choose the OID field in the table to base the join on If you are using the habitat polygons and want to spatially equalize your ERS mean values you may consider area weighting the ERS mean values by creating an area field e g hectares or meters sq in the habitat polygon attribute table and dividing the polygon mean value by the area of the polygon Tydixton_Park mxd ArcMap Arcinfo Once you have File Edit View Insert Selection Tools Window Help joined the table 0 ms Bx eo fine Vi OSONw QQruTS eO Bc k hL statistics to th e be Edta p lanning unit j e eee _planning_units Mean Risk 1 2 55 pri i ou shapefile close the mas cotta oe 2 554501 ey ee andard Deviation Site table and double 9 567311 16 353701 aa E 16 353702 25 874800 click on the an ers Se Hig her Mean Risk planning unit layer ae Planning Units to br ing up the 30 ee N m Layer Properties O risk_ag_sugarcane Click on the C riek bande rine Symbology tab and specify Quantities gt Graduated color Choose the Field Value of Lower Mean Risk zstat MEAN or Planning Units the area weighted O risk_roads O risk_urban_areas

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