2011 Zonae Cogito Manual - University of Queensland
Contents
1. os sos ste ses es E s ES seo w s53 see E sie sce EI nt sor 81 sar s7 kai ud EH E E s72 s15 e e ae E ES s e E E s se s s o pe ss ze 8 E s50 se 24 90 23 w e E ste sat em P s12 sie m se E sos 2 E s an 73 iod s76 97 id s2 w 24 se2 lud s28 se m so 88 E s ss E sez se ow 26 208 000 005 10 Bray Curtis dissimilarity of solutions 84 1 Ei z ER ui 26 H T f 88 i 2 2 8 E ge Iig 3 e a 8 2 Bae E a8 88 uL 28 T 58 amp a8 D 31 i 3g 3 sr DEC 88 58 3 x 23 88 HITLL 83 ag i 23 Reon BE Se lo 58g 58 SE ggi 23 LES 88 85 s5 ki 58 35 Soldions Figure 12 Example dendrogram The Marxan Dashboard 20 of 35 heute comptete Excellence for Environmental Decisions a ied Environmental Decision Analysis Commonwealth F Pfes Commonttion Nelpteg Australia Applied Environmental Decision Analysis Commonwealih J H AUSTRALIA vironmental Research Facility o Aestruilan Government lnirissive THE UNIVERSITY g OF QUEENSLAND ceed QE O p lee Trust The Maran Dashboard is located at Marxan gt Browse Annealing Output This feature allows you to view the annealing2. Project 1 larxan Output to Map Selection Frequency Available Zone ARRE Marzan Dataset Path Ninput brb pu final shp C NZCSbrbNinput dat Run q frequency 0 frequency 100 Marsan Parameter To Edit Edit Value pec s Save Parameter TEKI I Edit All Rows 36424540 113273050 7101400 77563180 5 5 5 5 2811101 1016400370 5 ia mom 540521750 5 130f11 1012 99360010 5 raif1 10 13 405245200 5 132 111014 0 5 183 102 10000000 5 1841 03 380269900 5 5 135 11 10 4 437331880 Figure 3 New ZC project prior to running Marxan If you are opening a creating a new project that has not been run in ZC before the GIS display will initially appear blank See figure 3 After running Marxan for the first time the GIS display will be populated with the planning units and the results from the Marxan runs see Figure 4 E Zonae Cogito Jog File GIS Marxan Applications Convert Data Window Help Project 1 Marxan Output to Map Selection Frequency Available Zone x ARRE Marsan Dataset Path brb_pu_final shp CNZCSbrbNinput dat Bn riot n Marzan Parameter To Edit Edit Value lu d Save Parameter uH o Edit All Rows mi Figure 4 New ZC project after running Marxan 10 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural ipei 4 Excellence for Environmental Decisions aie Environmen
3. ts Comm Environmental Research Facility An Aasernian d Table 4 Functions accessible through the GIS menu and sub menus Menu Zoom Sub Menu Extent Purpose Zooms to full extent of all shapefiles Layer Zooms to full extent of selected shapefile Previous Zooms to previous extent SetZoom Percentage Setthe percentage for zoom in and out cursor modes Zoom to Layer on Resize Zoom to planning unit layer when the window is resized Cursor Mode Zoom In Click and drag on map will zoom in Zoom Out Click and drag on map will zoom out Pan Click and drag on map will pan map in the direction of the drag Select Click and drag on map will select shapes Select Mode Intersection For select mode all shapes intersecting with selected area will be selected Inclusion For select mode all shapes included within selected area will be selected Select With Mouse Click and drag on map will select shapes Query Formulate SQL query on shape table to select shapes Database lookup of selection Mark selection as Not Selected or Place selected Use Selected planning units into nominated zone for use only when dynamically linked to C Selection Planning Units plan Clear Selection Clears the current map selection Invert Selection Inverts the current map selection Post DDE Postto C plan when dynamically linked Export Selection Exports the selected planning units into a n
4. The selected planning units will be posted to C Plan and the selected Click Action will be executed with those planning units 33 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural ipei f Excellence for Cavirenmental Oecislons ci deny onmental Decision Analysis Commnonweath efetes commenttice Metatron anetrette AUSTRALIA vironmental Research Facility o Australian Government lnirissive Key C Plan Functionality Selecting Areas to be Reserved To select areas to be reserved switch to the C Plan interface and in the Click Action box click on Negotiated After setting the click action in C Plan we need to select some areas in ZC and post them to C Plan to have their status updated to reserved Switch to the ZC interface select some sites and post them to C Plan using the instructions above for Selecting and posting sites Selecting Areas to be not Reserved To select areas to be available or not reserved switch to the C Plan interface and in the Click Action box click on Excluded After setting the click action in C Plan we need to select some areas in ZC and post them to C Plan to have their status updated to not reserved We do this in the same way as for Selecting Areas to be Reserved above Querying Site Data To select areas or sites to query fishing and conservation indices switch to the C Plan interface and in the Click Action box click on Lookup After setti
5. To load a previously saved scenario switch to the C Plan interface and click on the File menu then click on the Open Selections menu item Click on a scenario you want to load and click Open Troubleshooting If you experience problems running ZC functions Notify the author so that a bug fix may be provided in a future version Ensure you are using the default names for your Marxan and Marxan with Zones input files such as spec dat and pu dat This may help to alleviate any difficulties Ensure the Marxan dataset runs correctly using the Marxan exe program References Ames D P 2007 MapWinGIS Reference Manual A function guide for the free MapWindow GIS ActiveX map component 194 pages Idaho State Univ Idaho Falls ID Ball R and H P Possingham 2000 MARXAN V1 8 2 Marine Reserve Design Using Spatially Explicit Annealing a Manual Possingham H P I R Balland 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 Acknowledgements This research and development project was generously supported by the Applied Environmental Decision Analysis Centre and through a grant awarded by the Natural Heritage Trust National Competitive Component Continuing work on the project is generously supported by the Australian Research Council funded Centre of E
6. Assign Unique Index Create pu dat MV Create spec dat Use Column Names From Files iter ds Convert metres squared to hectares X cw Figure 19 Table joining tool To run the tool select the folder that contains the dbf files detailing conservation feature abundance in planning units The folder should only contain dbf tables for conservation features to be included in the analysis as all dbfs in the folder will be 30 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural ipei Excellence for Environmental Decisions lieg Environmental Decision Analysis Commonwealth F Pfes Cemeeetites Nelptog Australia Applied Environmental Decision Analysis Cormorweath L n AUSTRALIA vironmental Research Facility o Aesteuilan Government lnirissive added The tool automatically generates the puvspr dat file and provides the user with the option to select other input files that should also be generated If all files are selected the tool will create the Marxan data structure with input and output folders The input files generating will include placeholder values for target spf planning unit cost and other key parameters After generating the input files these values should be updated manually The tool also provides the user with the option of converting from m to hectares dividing by 10 000 Feature index type Two options are available in the join dbf tool for how conservation features should be named i
7. C Reserved Excluded Figure 17 Configuration editor window From the configuration editor window you can select an existing configuration to edit or create a new configuration To edit an existing configuration simply highlight the configuration from the list To create a new configuration simply click new and the new configuration window will be opened above When going through the new configuration window with a previously existing scenario you will notice that you have the option to seed the new configuration with any of the previously generated configurations This feature is particularly useful when multiple different branches of changes are being considered Once you have selected the configuration to edit from the configuration list changes can be made either through the GIS or through the query engine Making changes using the interactive GIS From the GIS menu select Cursor Mode gt Select The map is now in select mode clicking holding down while dragging the cursor over the map will highlight the selected planning units Multiple non contiguous sets of planning units can be selected by holding down the shift key between selections Ifthe shift key is not held down each new selection will replace the previous Making changes using queries From the Planning unit configuration window click select by query to launch the query engine The query engine allows you to make changes to a configuration by specifically tar
8. Cost Threshold Mise MaiZone Miscellaneous Repeat Runs f10 Boundaries Boundary Modifier R This Program edits an input file for MARXAN v2 0 and MarZone v1 0 Created by lan Ball 1999 Modified by lan Ball 2000 Modified by Matt Watts 2006 Figure 6 Screen shot of the input editor window Table 3 Functions accessible through the Input editor window Tab Item Purpose Problem Repeat runs Number of repetitions runs or solutions generated Boundary Modifier Boundary Length Modifier Run Options Allows selection of different algorithms Number of Annealing iterations Number of iterations in each run Temperature Decreases Number of temperature decreases When check the annealing schedule will be set adaptively when unchecked the Adaptive annealing schedule will follow the user specified values below Initial Temperature Initial temperature Cooling Factor Cooling factor to be used at the temperature decreases Set cooling from final Temp Allows the user to specify final temperature Input Species File name Name of the species file Planning unit file name Name of the planning unit file Planning unit versus species file Name of the planning unit versus species file Boundary Length Name of the boundary length file Input directory Specifies the location of the input files Output Save each Run If checked will save each run 14 of 35 THE UNIVERSIT
9. R GUI Run R scripts Runs the R scripts that perform cluster analysis The Configuration Editor Interface Reviewing and editing Marxan results From the GIS menu select Edit configuration to open the configuration editor The configuration editor allows you to make planning unit level changes to individual solutions You can save and edit these user defined configurations and then 25 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural BENE Trait 4 Excellence for Environmental Decisions lieg Environmental Decision Analysis Commonwealth F amp fea Cemeeetites Nelptog Australia Applied Environmental Decision Analysis Commonwealih J a AUSTRALIA vironmental Research Facility Ao Anstrsiian Government Laiiatbve generate reports based on target achievement in them It can also be used to interactively design new starting points for Marxan analysis Creating a new configuration If this is the first time you have accessed the configuration editor in the project you will be prompted to create a new configuration see window below To create a new configuration first enter a name and then select a seed configuration The seed configuration specifies the status of planning units to be used in the configuration The status can be loaded from any previously generated Marxan solution or any previously generated configuration You can also start with a blank slate by selecting Blank configuration as seed E
10. Using the ZC Calibration Tools Steps in using parameter calibration Exponential Calibration Adaptive Calibration FPF Detailed Calibration Information View Calibration Summary Report Do Cluster Analysis The Marxan Dashboard cnnic nenn or oh Eee E E R R e 20 The GIS Interface o eee Essi M MTM 21 Viewing Marxan results in the GIS display cccccccccsscessssccsccsessecccseccsesecccescssssecccesessaseceeesssssseeeseess L2 Query Engine Pa Generating new jehapetiesa HE 9 Map color specification e iot reete pter rte ere vei er EP epe REP ree er a Eure SRE KEER I aSa nae 24 Application menu ns HRS The Configuration Editor Interface teen iere dM see DINI ine T 25 Reviewing and editing Marxan results isses nennen nennen nente ener enn tn nennen 25 Creating a new configuration ener eee QO Making changes to a CONFIgUrAatiON ccsseseeseesseeescesecceeeceecceecaaecnaecnaseasecsecsaeeeeceeceeeeeeeeeneeeneenaase 26 Generating Reports from configurations sss nere eere eene QO Table Proce Sing ie EOD EHE QNIN dI Convert data Menu Text Table menu Graphing in ZC Using the C Plan software Downloading and installing C Plan cssc eene nennen nennen etre entente nennen 33 Starting the C
11. a BLM calibration 31 of 35 THE UNIVERSITY dem Wo QUEENSLAND ceed OGOOt Natural Heritage Trust qq Centre of Excellence for Lavironmental Decisions pa siio Environmental Decision Analysis Commonweatth FfPfea Commentttes Melptog Awstratia AUSTRALIA Environmental Research Facility An Mranernian Corus ment nie EJ Graph D ZC_TESTS gup configurations11_summary csv_ t3 7 x axis field Y axis field Save to file Cost Boundary Length x MV Minimum zero v Draw squares Square size E 0 120956123 919999 Boundary Length 13201017 55 512744 618 524157 Cost Figure 20 Example graph of BLM calibration Graphing functionality use notes The size of the squares plotted on the graph can be adjusted using the square size field or removed altogether by un ticking the Draw squares box Save to file function allows you to save the graph to an image file bmp format Close will close the graphing tool 32 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural ipei f Excellence for Cavirenmental Oecislons i aen ronmental Decision Analysis Commnonweath efetes commenttice Metatron anetrette AUSTRALIA vironmental Research Facility o Australian Government lnirissive Using the C Plan software In addition to using Marxan with ZC you can also use C Plan This is a prototype version of ZC for use with C Plan and changes may be made to update the int
12. additional contextual GIS layers that you might want to view with the solutions for example a layer that shows the location of existing protected areas Any layers that are inadvertently added can be removed by highlighting the offending layer and clicking remove Please note that all layers added to the project must be in the same projection If you add multiple layers to the project you will also need to identify which layer is your planning unit layer by selecting it in the Select Planning Unit Shapefile dropdown box Last in the Planning unit key field drop down box you will choose the field that indicates the unique identifier for each planning unit puid When you are done press ok and the project will be loaded into ZC A new project1 zcp file will be created in the same folder as the input dat forthe file The new file contains the configuration settings for the ZC project Atthis point you can save the project main menu File Save in an appropriate place with a descriptive name before moving on to edit files and parameters and to run Marxan 9 of 35 THE UNIVERSITY t dee Wo QUEENSLAND ceed Oe Ol Natural Heritage Trust qs Contre of Excellence for Emironmental Decisions ieg Environmental Decision Analysis Commonwealth Fete Commanttien Melpiag Awatratin AUSTRALIA Environmental Research Facility An Mrasernian Corners ment Ln iet tu Zonae Cogito BAX File GIS Marxan Applications Convert Data Window Help
13. ceed QEOOl Natural Heritage Trust qq Centre of Excellence for Emvironmental Decisions cci Environmental Decision Analysis Commonwealth W lefaa Commentites Met peg Awstratia AUSTRALIA Environmental Research Facility An Aanensen Gorversment mirtantve Table of Contents Introduction to Zonae COBIO eee cc ceeecceccsseecceccsseeeaeccsseesaeccssnsaaeseseeeaueceseneaaes 4 Decision Support SYSTEM sisse eene eene enne eene ernannt nennen enne eere enne eee eene eed Free SoftWare feo Mem EE 4 What can you do with ZC eeesisssssssessseeene eee eene entre enn TSE entes nennt ernannt eese teens nennen 4 Whatdoes Z loolkliKe unirse e terr De PERO o aee rese ei OR Dee pua ioa Fecerunt delet 5 Downloading and setting up Zonae Cogito sss ener tenentes 5 lancing ZC ee X 8 Creating a New ZE proje tarra E aa E eee A E EOAR as 8 Opening an existing ZC project file lisse eene enne ener nennen nennen nnne 11 Arranging the GIS and Marxan Wind OWS cccccccssssseccecccsssesceecesseseeececssseeesescsacsneceeccnsceneececsaeeneaeeses 11 The Marxan Interface cccccccccccsssscceecseeecescsseeceesceueeeeccsseeeecesenesseceseneseeesseneea 11 Editing Marxan files and ParaMeters ccccccssseccscccssseeeescccsseesseccsssseeueccssseescseccescensaececssessensecceseneeas 11 Advanced parameter editing Calibrating Marxan parameters
14. process for one solution along with the impact of the changes in the process on the score cost connectivity and penalty If you set the NUMITNS to 1000 and NUMREPS to 1 you can view each individual step in the annealing process the planning unit being considered for a change in status is highlighted in yellow You can speed up or slow down the process by using the slide bar The GIS Interface ZC uses the MapWinGIS ActiveX component which is an application programming interface for MapWindow GIS It allows developers to embed the MapWindow software within their own application and directly access the GIS objects in an efficient way from their choice of programming languages Ames 2007 The MapWindow ActiveX component is directly embedded into ZC allowing direct access to some GIS capabilities facilitating custom high performance GIS processing and display MapWindow is a powerful and user friendly open source GIS package It can be downloaded from the MapWindow web site MapWindow org There are a number of GIS functions accessible through the GIS menu item on the main window These functions represent a subset of the MapWindow functions that are useful for working with Marxan See Table 4 for a list of these functions 21 of 35 THE UNIVERSITY err OF QUEENSLAND ceed Centre of Excellence for Lovironmental Decisions AUSTRALIA OL OQL Natur nl e Trust Applied Environmental Decision Analysis Commonwealth
15. re d gt Install R packages to use cluster analysis function e KSA Ensure you are logged in as an administrative user Download the correct packages labdsv rgl tkrgl and vegan from http cran ms unimelb edu au or if you are not in Australia from your closest CRAN page find this by clicking on CRAN under Download Packages on the main R website page Save the packages locally as zip files Launch the R application from the start menu Within the R application from the Packages menu click Install package s from local zip files Browse to the folder where you saved the zip files Select the 4 zip files you might have different versions labdsv_1 3 1 zip rgl 0 81 zip tkrgl O 6 zip and vegan 1 15 0 zip Click Open The 4 packages will now be installed 7 d ete e d te ate P P 7 KS 5 Install C Plan to use C Plan within Zonae Cogito te tis not necessary to install C Plan if you are only using Marxan Ensure you are logged in as an administrative user Download C Plan version 4 from http www ugq edu au ecology index html page 106842 t ate 6 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural ipei f Excellence for Cavirenmental Oecislons i aen ronmental Decision Analysis Commnonweath efetes commenttice Weraroa anetrette AUSTRALIA vironmental Research Facil
16. J New Planning Unit Configuration OE New Configuration Name SecondConfiauratiorl Seed Configuration Blank configuration X x Cancel Figure 16 New configuration window Making changes to a configuration Once aconfiguration is open changes to the configuration can be made either though the clicking on the interactive GIS display or by a query of specific attributes If you have created multiple configurations ensure you highlight the correct configuration when you wish to edit that configuration Table 7 Functions accessible through the configuration editor window Button Action New Creates a new configuration Report Starts the reporting editor Sends the current user defined configuration to Marxan so you Send to Marxan can run Maran with these planning units locked in or out Stop Editing Closes the configuration editor window Saves the specified changes to the current user defined Save configuration 26 of 35 Centre of Excellence for Environmental Decisions lieg Environmental Decision Analysis Commonwealth F Pfea Commonttion Nelpteg Australia Aonlled Environmental Decision Analysis Cormorweath J H AUSTRALIA vironmental Research Facility Ao Anstrsiian Geversmoot Laiiative THE UNIVERSITY t dem g OF QUEENSLAND ceed OLEOO Natural Heritage Trust 2 Edit Planning Unit Configurations E Report Send to Marran Stop Editing Assign To Not Selected
17. Plan dataset with Zonae Cogito eene entente 33 Selecting and posting Sites ccc ccecscccccccecececceeeceaeaeenaaeessecssecseceeesseceseeeeecneeesaecaseesasetatsttetsteneee D Key C Plan Functionality Lesen aaan i onin eai een ee ense en senes es dD Troubleshooting sisir eccentric ratore See Od eee o E Ed a reb esse 35 References s ooereiomsor miei eene ee eaedem eM IM 35 Acknowledgements i eoe EHE ar nA I E VLA ETRAS Fea ER EE Teens 35 3 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural ipei Excellence for Environmental Decisions aie Environmental Decision Analysis Commonwealth F Pfes Cemeeetites Nelpteg Australia Applied Environmental Decision Analysis Cormorweath L n AUSTRALIA vironmental Research Facility o Australian Government lnirissive Introduction to Zonae Cogito Decision Support System ZC is a decision support system written in the object Pascal programming language It features an interface to the Marxan family of software and an integrated geographic information system It is designed as a simple and robust way to run Marxan analyses and view the results Due to the integration of open source GIS software it eliminates the need foran individual or organisation to purchase costly GIS software in order to use Marxan The Ecology Centre is continuing development on ZC and new features will be incorporated into later versions of the software We encourage you to assist w
18. S P 5 of 35 Run the Map Window Active X control executable exe Usealldefault settings to complete the install Download the Map Window Active X 4 5 control from the Zonae Cogito www uq edu au marxan index html page 106746 f Excellence for Cavirenmental Oocilens i aen ronmental Decision Analysis Commnonweath efetes commenttice Weraroa Anstatt THE UNIVERSITY g OF QUEENSLAND ceed QE Q Natural mn Trust AUSTRALIA vironmental Research Facility Jo Aestesllan Government Laiissbve It may also be necessary to issue the following command in a startup script to register the Map Window active X component regsvr32 CAProgram Files Common Files MapWindow MapWinGIS ocx If during the installation you get an Error message similar to Unable to register OCX MapWinGIS ocx please select the Ignore option 2 Install Zonae Cogito P Ensure you are logged in as an administrative user Download Zonae Cogito from the Zonae Cogito download page http www uq edu au marxan index html page 106746 Run the Zonae Cogito setup executable exe Use all default settings to complete the install P e 7 v ous 3 Install R if you do notalready have it on your computer to use cluster analysis function e d Ensure you are logged in as an administrative user Download R from http www r project org Run the R setup executable exe Use all default settings to complete the install e
19. SITY alie Wo QUEENSLAND ceed QE O Natural eS Excellence for Environmental Decisions aie Environmental Decision Analysis Commonwealth F Pfea Commonttion Nelpteg Australia Applied Environmental Decision Analysis Commonwealih J H AUSTRALIA vironmental Research Facility Ao Anstrsiian Gevers mont Laiiathve Using the ZC Calibration Tools Note that before you open the calibration tool the number of repetitions runs that you have set in the input dat file or through the Marxan Parameter to edit NUMREPS file will be the number of repetitions that are run within your calibration Make sure this number is sufficiently high to run a meaningful calibration To start calibration select calibration from the Marxan menu A new window called Parameter calibration will appear see below Parameter Calibration BAX 1 Choose Input to Calibrate 2 Choose number of values 3 Choose range of values C Zone BLM Number 6 Minimum 0 o C Target Maximum 10 C Zone Target Cost Use exponential values for calibration C Probability Weighting A Run Calibration X Cancel Figure 7 Screen shot of the parameter calibration window Steps in using parameter calibration Set 1 Choose input parameter to calibrate i e BLM Set 2 Choose number of values to test i e 9 Set 3 Choose range of values i e a Minimum of 0 and a Maximum of 0 1 Next enter Run Calibration The Choose number of Values field all
20. THE UNIVERSITY alie Wo QUEENSLAND ceed QEOOl Natural Heritage Trust f Excellence for Environmental Decisions oic Eny ronmental Der nana alysis Commonwealth Mets AUSTRALIA rwronmaental Reseatah Fac vO hs tania Erud cho Using the Zonae Cogito Decision Support System A manual prepared by Applied Environmental Decision Analysis Centre Matt Watts Romola Stewart Dan Segan and Lindsay Kircher The Ecology Centre University Of Queensland March 2011 1 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural BENE Trai Excellence for Environmental Decisions a ie Environmental Decision Analysis Commonwealth F f amp fes Cemeeetites Nelpteg Australia Applied Environmental Decision Analysis Commonwealih J H AUSTRALIA vironmental Research Facility Ao Anstrsiian Gevernmest Laiiatbve Introduction This software was written by Matthew Watts and Romola Stewart from The Ecology Centre University of Queensland Zonae Cogito comes from the Latin Zonae meaning zones and Cogito meaning to think or reflect on In other words the title means to think about zones Within this manual we will refer to Zonae Cogito as ZC The purpose of the software is to act as a decision support system and database management system for the family of Marxan software It incorporates open source GIS software components and is a freely available software package 2 of 35 THE UNIVERSITY E Wo QUEENSLAND
21. Y y OF QUEENSLAND AUSTRALIA Save overall Best ui OEOCL sum Centre of Excellence for Lovironmental Decisions Heritage Trust tog Awstvatia Applied Environmental Decision Analysis Commonwealth ts Comment Environmental Research Facility T If checked will save the overall best run Save Summary If checked will save summary information for all runs Save Scenario Details If checked will save save scenario details Save Missing values info If checked will save the missing values information for each conservation feature ArcView format ArcView format ArcView format csv type ArcView format csv type Save Summed Solution If checked will save the summed solution file Species missing if proportion of target lower than Species the percentage of target achievement at which the feature will be considered to have missed its target in the summary reports A value of 1 means that a feature has to achieve 100 of the target Save file name Name to be appended to the beginning of each output file for the scenario Output directory Folder in which the output will be placed Cost Threshold Threshold enabled Checked specifies use of the threshold unchecked the threshold will not be used Threshold Actual threshold value Penalty Factor A Multip lier for cost threshold penalty A Penalty Factor B Multip lier for cost threshold pen
22. alty B Starting Prop Proportion of planning units to start in the protected zone MarZone Enable MarZone Checked turns on Marxan with Zones unchecked runs Marxan Zones Inputfile for zones Zone target Inputfile for zone targets Costs Inputfile for costs Zone cost Inputfile for zone costs Planning unitZone Inputfile for planning unit zones not required Zone Cost Boundary Inputfile for zone boundary costs not required Advanced parameter editing Advanced users of Marxan will recognize that not all parameters are editable through the ZC user interface We have tried to make ZC user friendly to all levels of user and have thus chosen not to reveal functionality that is only utilized by a small subset of advanced users Please note that no functionality has been removed and all parameters are still editable by directly editing the input files Calibrating Marxan parameters Calibration is the process of achieving the desired output e g minimum cost by varying the input parameters In Marxan the BLM is often varied to explore different levels of compactness Too little compactness and reserves are highly fragmented and unmanageable Too much compactness and the reserves may become large and costly to other uses You can use the ZC Calibration tool to find an efficient range of BLM values and the tool automates the calibration process for a variety of other Marxan parameters as well 15 of 35 THE UNIVER
23. an run Marxan Menu The Marxan menu in ZC provides access to additional functionality that is not available through the Marxan window of ZC Table 2 Asummary of functions accessible through the Marxan menu and sub menus 12 of 35 THE UNIVERSITY OF QUEENSLAND Ceed e Centr AUSTRALIA e of Excellence id OL OQL Natural ee Trust Applied Environmental Decision Analysis Commonwealth Environmental Research Facility for Environmental Decisions Menu Sub Menu Purpose Run Marxan Method for starting Marxan Save Run Saves a copy of the Marxan database Load Run Restore a copy of the Marxan database that has been saved Calibration Allows you to use an assisted calibration tool for key Marxan parameters Adaptive Calibration FPF Allows you to use an assisted calibration tool for the Marxan FPF parameter View Output Calibration Report If you have run an assisted calibration this opens the report for viewing Summary Report After a Marxan run you can view the summary report sum txt file Best solution features After a Marxan run you can view the bestsolution features report mvbest txt file Input Editor Allows you to edit the input parameter file using the classic Marxan InEdit interface Hide Marxan console Allows you to view the progress of classic Marxan interface as it runs orto hide it Do Cluster Turns on and off the cluster analysis feature for solutions re
24. ction Figure 13 Screen shot of the GIS toolbar Table 5 Guide to functionality of map tools sS D 5 c Purpose Zoom to fullextent Zoom to layer extent Zoom to extent of selected features Return view to previous extent Zoom in Zoom out Pan Select tool Post DDE Selection TTT Post selection to C plan Query Engine The query engine can be launched from the GIS menu by choosing select with query From the query window you can build queries that will select planning units based on any attribute in the planning unit shapefile This includes selection based on selection frequency in Marxan After highlighting the field you would like to base the selection on the unique values from that field can be populated in the values field by clicking the check box next to load values this can take some time if you are using a large number of planning units After you have highlighted a field and operator eg gt and a value the query can be generated by clicking add After a query is added it will appear in the query box To execute the query and replace the currently selected planning units click New Selection If you would like to add the query results to the existing selection set click Add to Selection 23 of 35 THE UNIVERSITY alie Wo QUEENSLAND 7 ceed OEOM Natural Heritage Trust Centre of Excellence for Covironmental D
25. ecisions Lcd Environmental Decision Analvsis Commonwealth efPfeg Cemmeetites Metpieg Australia Applied Environmental Decision Analysis Cormorweath J H AUSTRALIA vironmental Research Facility An Mraseraian Corversment nie e SelectShapesQuery Jog Fields Values w Load Values New Selection Add To Selection X Cancel Figure 14 Example query that selects all planning units with a selection frequency greater than 75 SSOLN gt 75 User note When making selections from a single solution within Marxan the user will note that planning unit status used by ZC are slightly different to those of the raw Marxan output files To be compliant with Marxan with Zones ZC uses a status of 2 to specify a selected planning unit and a status of 1 for a non selected planning unit Thus if you are using Marxan and want to create a selection based on solution 8 the appropriate query would be SOLN8 2 Generating new shapefiles ZC offers two options for generating shapefiles The first option is in the GIS menu under Export Selection and the second is in the configuration editor and is detailed later Export selection will export the selected planning units to a new shapefile with only the planning unit id in the attribute table The option can be used to generate new shapefiles from individual Marxan runs by using the select by query option It can also be used to interactively create a new shapefile usi
26. erface Downloading and installing C Plan You will need to obtain the install set for C Plan version 4 Email Matt Watts m watts uq edu au to obtain this software OR http www uq edu au ecology index html page 101951 OR http www uq edu au uqmwatts cplan html Unzip the file CPlan4 zip To install C Plan run the SETUP EXE program from the CPlan4 folder that was created when unzipping the zip file Starting the C Plan dataset with Zonae Cogito 1 Launch Zonae Cogito but don t open and files or projects e Click on the Start menu click Programs click Zonae Cogito then Zonae Cogito 2 Launch C Plan with the required dataset e Click on the Start menu click Programs then C Plan e Click Locate Database then browse to your cplan ini file and click Open e Click on your cplan ini to select and highlight the database then click Start C Plan The GIS window will open in ZC and the systems will be dynamically linked If you experience problems shut down both systems and restart them Selecting and posting sites When the systems are launched and dynamically linked 1 Click on the Select Cursor Mode button Ey or select GIS gt Cursor Mode gt Select from the menu system 2 Select the required sites by clicking and dragging on the GIS 3 Post the selected sites to C Plan by clicking on the Post DDE Selection button or selecting GIS Selection Post Select DDE from the menu system
27. ew ESRI compatible shapefile Colour Select colours for map display and selection Add Shape Add a shape to the map Remove All Shapes Remove all shapes from the map Export Map Allows you to save the current map as a bitmap file Shape Outlines Adds or removes the outlines of your planning units Edit configurations Opens the configuration editor Report Configurations Opens the configuration reporting editor Viewing Marxan results in the GIS display The GIS display allows you to view maps of your Marxan solutions After running Marxan through the Marxan display window review the solutions using the drop down menu in the GIS display The outputs that you can view are e Selection frequency when using standard Marxan reserve zone refers to planning units included in Marxan solutions while available zone refers to planning units that are not included in Marxan solutions e Best Solution e Each individual solution 22 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QEOOl Natural Heritage Trust mire of Excellence for Levironmental Decisions no Environmental Decision Analveis Commarwealth Welpies Commentiios Melpteg Australie Applied Environmental Decision Analysis Commonwealth Hd AUSTRALIA vironmental Research Facility Ao Anstrsiian Government Laiiatbve Al Zonae Cogito File GIS Marxan Applications Convert Data Window Help Analysis One upone Selection Frequency Available Zone AURAA QAWL Post DDE Sele
28. from the Marxan Parameter to Edit drop down menu 11 of 35 THE UNIVERSITY alie Wo QUEENSLAND 7 ceed OEOO Natural Heritage Trust Contre of Excellence for fawironmental Decisions a p lettmwionment Decir Anas Commonweal Meteten commenttios Weirton Aureli AUSTRALIA vironmental Research Facility An Kennen Corners ment Ln nie l Marsan Dataset Path C ZC brb input dat Run Marxan Parameter To E dit Edit Value P H Save Parameter B Edit All Rows ies Figure 5 Marxan window in ZC To edit one value click on it and then change the value in the Edit value box If you would like to edit an entire field click on one of the values in that field then tick the Edit All Rows box and change the value in the Edit Value box but remember to un tick this box when you are finished to avoid accidentally changing entire columns of other data If you would like to edit several values at a time highlight the cells using the shift key or clicking and dragging with the mouse and change the cell value in the Edit Value box When you finish editing a file or parameter press the Save Parameter button If you forget to save your edits ZC will prompt you to save them when you attempt change to a different Marxan parameter or run Marxan To run Marxan press the Run button and Marxan will start After the Marxan run is complete the GIS display will be refreshed with the results of the new Marx
29. geting Marxan results or another attribute of the shapefile User suggestion 27 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QEOOl Natural Heritage Trust Excellence for Environmental Decisions lieg Environmental Decision Analysis Commonwealth F Pfes Commonttion Melpiog Australia Applied Environmental Decision Analysis Cormorweath J H AUSTRALIA vironmental Research Facility An Aaserniian Government Linie Prior to editing any configurations we suggest that you make a back up copy of your Marxan database so you don t lose information To do so simply select Marxan Save Run from the main menu and then name the current run Save Run will copy the current Input Output files and input parameter file into the scenarios folder for the project Then if you decide that you would like to abandon all changes you ve made during configuration editing you can still copy a clean version of the input files back into the project folder Generating Reports from configurations Clicking Report from the configuration window will open the reporting window EJ Report on Planning Unit Configu Joe 1 Select Planning Unit Configurations for Reporting 2 Select reports to create target achievement summary v planning unit detail X Cancel Figure 18 Reporting window To generate a report highlight the configuration you wish to report on and select the reports you would like to generate Note here that mul
30. he base ZC has two windows a Marxan display for viewing and editing Marxan files and running the Marxan software and another for the Geographic Information System GIS display The size of each window can be customized by the user by simply selecting the edge of the window with the mouse and dragging the mouse until the window reaches the desired size EJ zonae C ogito Jog File GIS Marxan Applications Convert Data Window Help Marxan Output to Map Selection Frequency Available Zone ee ele Marsan Dataset Path m NZCNbrbNinput dat brb pu final shp C rb input dal BE frequency 0 Y frequency 50 lad Marsan Parameter To Edit Edit Value Save Parameter a Ee Edit All Rows Figure 1 Screen shot of Zonae Cogito Downloading and setting up Zonae Cogito You will need to complete these steps when preparing your computer to use Zonae Cogito It is necessary to complete steps 1 2 and 6 Steps 3 5 are optional and are for specific functionality within Zonae Cogito 3 4 for cluster analysis and 5 for using C Plan in Zonae Cogito Note it is necessary to have Marxan version 2 1 1 or above and or Marxan with Zones 1 0 1 or above to use Zonae Cogito http www uq edu au marxan index html page 77064 1 Install Map Window Active X control Ensure you are logged in as an administrative user download page htt You must use version 4 5 P lt 7 K
31. he registry editor 1 Runthe registry editor RegEdit by typing regedit at command prompt or at startmenu gt run 2 Locate following registry key HKEY_LOCAL_MACHINE Software Microsoft Windows CurrentVersion Policies Syst em 3 Locate the following REG DWORD value EnableLUA 4 Setthe value of EnableLUA to O 5 Reboot the computer Register the active X control On a 64 bit OS regsvr32 exe c Program Files x86 Common Files Map Window MapWinGIS ocx On a 32 bit OS regsvr32 exe c Program Files Common Files MapWindow MapWinGIS ocx 7 of 35 THE UNIVERSITY t dem g OF QUEENSLAND ceed Oe Ol Natural Heritage Trust e i ire of Excellence for Levironmental Decisions Loa Environmental Decision Analvsis Commonwealth MefPfeg Commentites Nolptog Australie Applied Environmental Decision Analysis Commonwealth J H AUSTRALIA vironmental Research Facility Ae Aaserniian Government nini Enable UAC by setting EnableLUA to 1 with the registry editor Reboot the computer You have now completed the install of Zonae Cogito and support software and it is ready to use Launching ZC ZC can be launched either by clicking directly on the executable file ZonaeCogito exe or by navigating to ZC through the start menu Creating a new ZC project After you have created a Marxan database you will need to make a new Zonae Cogito project file zcp to load the database into ZC This file loads the appropriate p
32. inimum proportion of targets met MPM for all solutions 3 Ifthe MPM is less than the desired amount increase the FPF by an order of magnitude 17 of 35 4 Excellence for Environmental Decisions goood Env ronmental Dern nales commonwealth Felbtes Eemmnntnter wetPiey axetratte AUSTRALIA vironmental Research Facility Annerein Government Loi THE UNIVERSITY alie g OF QUEENSLAND ceed QE O p Heritage Trust 4 Run the system and view the MPM for all solutions 5 Repeat steps 3 and 4 until MPM exceeds the desired amount 6 Reduce the FPF value to that used in the previous run of the system 7 Increase the FPF by a very small number 0 00001 8 Run the system and view the MPM for all solutions 9 Ifthe MPM is less that the desired amount increase the FPF by an amount one order of magnitude greater than the increase used in previous run of the system then go to step 10 If the MPM is greater than the target amount go to step 6 10 Run the system and view the MPM for all solutions 11 Go to step 9 Users should note that adaptive calibration FPF can be quite slow for large datasets With Marxan it only works for scenarios where all target objectives are achievable whereas for Marxan with Zones it only works for scenarios where all target objectives are simultaneously achievable The graph below illustrates how the adaptive calibration algorithm systematically searches from low values of FPF to higher ones then progre
33. ith this development process by emailing your suggestions to the authors Matt Watts m watts Qug edu au or Romola Stewart Rom Stewart gmail com Free Software Tools Marxan is the world leading systematic conservation planning software and we present a methodology for performing state of the art conservation planning using entirely free software tools The one proviso ofthis is that users must have a copy of a Microsoft Windows operating system or compatible software emulator such as WINE that runs in the Linux operating system to run the software A future version of Zonae Cogito may have native compatibility with the Linux operating system to eliminate the need for an emulator What can you do with ZC e Edit Marxan parameters and input files e Run Manan analyses e interactively view the results of Marxan analyses e interactively make changes to Marxan solutions e Calibrate Marxan parameters e UseitasaGIS for the C Plan Conservation Planning System e Run the full range of Marxan software including standard Marxan Marxan with Zones Threat Probability and cluster analysis of Marxan solutions 4 of 35 THE UNIVERSITY 3t Wy OF QUEENSLAND ceed AUSTRALIA Excellence for Environmental Decision What does ZC look like a QE A Natural opus Trust nvironmental Research Facility Applied Envi fon mental Decision Analysis Commonwealth M amp fea Commantttes Nelphog Australia Ae Aasesiian Goversiment instr T
34. ity o Australian Government lnirissive ate Run the C Plan setup executable exe Use alldefault settings to complete the install 6 Finalising the Install We perform the following steps in order to register the MapWindow ActiveX control Reboot the computer so all the application installed are ready for use Ensure you log in as an administrative user RunZonae Cogito with the administrative login Start menu gt All programs gt Zonae Cogito When running Zonae Cogito ensure you load an existing project with a map shapefile or create a new project that displays a map details in Creating a New ZC Project in the next section of this manual This is so that the MapWindow ActiveX component will load and execute at least once with the administrative login If this does not happen when a non admin user attempts to use the MapWindow ActiveX component it will fail to initialise and Zonae Cogito will not function o gt P 7 Windows 7 and Vista User Access Control If you are using Windows7 or Vista you may need to temporarily disable UAC User Access Control in to register the Map Window ActiveX control This will be necessary if step 6 above does not register the map control on your system This may be apparent as very slow performance of the map control or as a runtime error when attempting to use the map control Ensure you log in as an administrative user Disable UAC with t
35. lanning unit GIS file and the input dat file from the Marxan database along with any other GIS layers that you want to be able to view with the Marxan solutions From the ZC main menu choose File gt New Project and the following window will appear EJ Create A New Zonae Cogito Project BAX Specify Project Name Include C Plan Database paeem Locate ESRI Shapefiles for GIS display Browse Remove Select Planning Unit Shapefile Select Planning Unit Key Field X X Cancel Figure 2 Screen shot of create a new ZC project window 8 of 35 Excellence for Environmental Decisions lieg Environmental Decision Analysis Commonwealth F fPfea Commonttion Nelpteg Australia Applied Environmental Decision Analysis Commonwealih L n AUSTRALIA vironmental Research Facility o Aesteuilan Government lnirissive THE UNIVERSITY E g OF QUEENSLAND ceed QE O Natural sis Trust In the box at the top of this window you can specify a project name It is best to use a name that describes the scenario you are building Next tick the Include Marxan Database box and browse to the appropriate input dat file Next select the GIS Planning Unit shapefile for the project ZC will use this layer to display planning unit status in the maps of the Marxan solutions Click on the Browse button to the right of the Locate ESRI Shapefiles for GIS display and then browse to the appropriate planning unit shapefile You can also add
36. n the spec dat and puvspr dat files 1 Assign Unique Index will assign a unique id to each of the column header 2 Use Column names from files will use the unique id in each of the column headers For example if the column name is Value 243 the conservation feature id will be 243 Text Table menu When a table is highlighted in ZC for example after a report is generated the text table menu will appear in the main ZC menu Table 13 Functions accessible through the Text Table menu and submenus Sub Menu Auto fit Entire Table Adjusts the column size of the entire table Selection Adjusts the column size for the selected columns ofthe table Save non zero rows Saves only those rows and columns that contain some non zero values rows or and columns columns populated only with zeros will not be saved Graph Table Opens up the graphing editor Compact Marxan Matrix Removes zero value column Graphing in ZC ZC provides the user with a simple graphical interface for creating graphs that can be useful with assisted parameter calibration Navigate to the Text Table in the Marxan main menu this option appears after a table is open such as when assisted calibration is run Select Graph table to automatically graph the calibration results Two fields are shown the X axis field and the Y axis field Choose the X axis and Y axis fields you would like to graph from the drop down boxes See Figure 15 below for an example of
37. nfiguration name Cost Total cost of the configuration Connectivity Boundary Length Shortfall Summed representation shortfall for all conservation features Target achievement re port Table 11 Fields in the Target achievement report Field Feature Name Explanation Feature name Feature Key Feature Id as entered in spec file Initial Reserve Amount of feature locked into the reserved zone at the beginning of the scenario Totalin region Target 96 Total amount of the feature in the region same units as puvsp file Percent of feature targeted for protection Target amount Feature target amount same units as puvsp file Target in MPA Amount in MPA Target Amount Amount in MPA Amount of feature in MPA same units as puvsp Missed Target 96 Target Amount Amount in MPA Target Amount Missed Target Amount Target Amount Amount in MPA same units as puvsp Sharing results 29 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural BENE Trai Excellence for Environmental Decisions aie Environmental Decision Analysis Commonwealth F fPfes Cemeeetites Nelpteg Australia Applied Environmental Decision Analysis Commonwealih J M AUSTRALIA vironmental Research Facility Ao Anstraiian Geversmoot Laiiative In addition to generating reports the configuration tool can also be used to generate ESRI compatible shapefiles to share resul
38. ng the interactive GIS selection tool Map coluor specification You can change the colours associated with the solutions in the GIS by clicking on the colours in the left hand menu or through the Main Menu GIS gt Colour and the window shown below will open 24 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural BENE Trait 4 Excellence for Environmental Decisions aie Environmental Decision Analysis Commonwealth F fPfes Cemeeetites Nelptog Australia Applied Environmental Decision Analysis Commonwealih J H AUSTRALIA vironmental Research Facility Ao Anstesiian Gevers mont Laiiatbve Specify Marxan Map Colours Joey C Summed Solution I8 m n C Single Solution m E i FG Colour to Ee Selection Colour Accept Changes x Cancel Changes Figure 15 Screen shot of the Specify Marxan Map Colours window Select the type of display you would like to edit from the Colour to edit section and then select the colour you would like to use in the display When you are finished making changes click Accept Changes or click cancel changes to abandon all changes You can add contextual GIS layers to the window at anytime by using the GIS gt Add Shape option from the main menu Application menu Table 6 Functions accessible through the Applications menu and sub menus Menu Purpose Validate Marxan Validation of Marxan family of software and input files R Starts preferred
39. ng the click action in C Plan we need to select some areas in ZC and post them to C Plan to query their indices We do this in the same way as for Selecting Areas to be Reserved above Querying Feature Data To select areas to query feature irreplaceability switch to the C Plan interface and in the Click Action box click on Features After setting the click action in C Plan we need to select some areas in ZC and post them to C Plan to have their status updated to reserved or not reserved We do this in the same way as for Selecting Areas to be Reserved above To see the proportion of each feature target that has been met switch to the C Plan interface and click on the Show menu then click the Features To Target menu item A form is displayed that lists features in the dataset the proportion of each feature target that has been met You can use the Sort Order and Sort Field controls to change the way this information is displayed Saving and Loading Scenarios To save a scenario switch to the C Plan interface and click on the File menu then click on the Save Selections menu item Enter a name for your scenario and click Save 34 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural ipei 4 Excellence for Cavirenmental Oecislons ci deny tonmenta Decision Analysis Commnonweath efetes Commenttice Helbins Anstatt AUSTRALIA vironmental Research Facility o Aesteuilan Government lnirissive
40. ows the user to specify the number of intervals to be used in the calibration The Choose range of values allows the user to specify the range of values to be used in the calibration For example if you specify 4 in the number of values field and a range from 1 10 the parameter will be calculated at 4 intervals between 1 amp 10 1 4 7 10 The parameter will always be calculated for both the minimum and maximum value specified in the range Running this calibration may take a few minutes but the GIS display will be updated with the different configurations as the runs progress Once calibration is complete the Calibration Summary Report will automatically appear The calibration report can also be viewed by going to the main menu and choosing Marxan gt View Output gt Calibration Report 16 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural spac Excellence for Environmental Decisions io Environmental Decision Analysis Commonwealth F Pfea Commonttion Nelpteg Australia Applied Environmental Decision Analysis Commonwealih J H AUSTRALIA vironmental Research Facility Ao Anstrsiian Gevernmest Laiiatbve The calibration report is also saved as calibrate csv in the output folder for retrieval at a later date Exponential Calibration Exponential calibration allows testing within an exponential range rather than within the equal interval range of base calibration functionality Building on the above exam
41. ple where we specified 4 intervals between the 1 10 range instead of using the values 1 4 7 10 directly in the calibration the exponent e of that value is calculated and used for the calibration So the final range of values used in the calibration is 2 7 54 1096 22026 After clicking exponential calibration a box will appear that specifies the range of values and their exponents prior to calibration This allows the user to ensure that the exponential values used for calibration have an appropriate range Adaptive Calibration FPF The adaptive Calibration FPF function is a tool for calibration of the Feature Penalty Factor FPF previously called the Species Penalty Factor SPF Instead of requiring the user to specify a range in which the penalty factor should fall the user specifies a minimum percentage of target achievement After specifying this level of minimum achievement ZC incrementally increases or decreases the FPF for all features until converging on an efficient FPF that meets the desired target level Bi Adaptive Calibration FPF Jicleg Minimum proportion of targets required 0 99 Minimum Proportion Met LabelMPM Proportion of Features Done LabelProgress Steps LabelSteps Figure 8 Screen shot of the adaptive feature penalty factor calibration window The pseudo code for adaptive calibration of the FPF is as follows 1 Start with a very small FPF 0 00001 2 Run the system and view the m
42. quires R and R Analysis packages to be installed Browse Annealing Allows you to view the annealing process spatially and the impact on the score Output cost connectivity and penalty Save Run Makes a copy of the existing Marxan database including all output files and any changes you have made to the input files Files are saved into a scenarios folder inside the existing Marxan database If this is the first scenario you have saved the scenarios folder will be generated for you Input Editor It is important to recognize that not all parameters in Marxan can be edited through the Marxan window of ZC The additional parameters that are not editable through the main Marxan window of ZC can be accessed through the classic Marxan InEdit interface window or can be directly edited in the input dat To launch the input editor window select Input editor from the Marxan menu see below Additional documentation for parameters in the input editor is available in the Marxan manuals on the Marxan website www uq edu au marxan 13 of 35 a OLEOQL Natural Heritage Trust Applied Environmental Decision Analysis Commonwealth M Pfes Cemmsetites Mel pres 4btivaMa Environmental Research Facility Ao Ansertium Covers ment inire THE UNIVERSITY eer OF QUEENSLAND ceed Centre of Excellence for Lovironmental Decisions AUSTRALIA a Input File Editor for Marxan and MarZone aes Problem Run Options Annealing Input Output
43. ssively narrows its search until converging to the most efficient FPF value that ensures that the user specified 96 of targets for allour features are met FPF test Figure 9 Fluctuations of FPF during the course of adaptive calibration Detailed Calibration Information Each calibration run is saved individually in the scenarios folder inside the project In the above example 9 different intervals are used for BLM calibration the result will be 9 folders inside the scenarios folder titled Scenario1 Scenario2 etc Within each folder will be the input dat and Input Output folders used for that calibration These files can be used to more closely inspect results from each calibration run or to restore a specific scenario on request with the Marxan Load Run function 18 of 35 THE UNIVERSITY alie Wo QUEENSLAND ceed QE O Natural BENE Trait Excellence for Environmental Decisions lieg Environmental Decision Analysis Commonwealth F Pfea Commonttion Nelpteg Australia Applied Environmental Decision Analysis Commonwealih J a AUSTRALIA vironmental Research Facility Ao Anstrsiian Gevernmest Laiiatbve View Calibration Summary Report The Calibration Summary Report reports on the performance of the reserve system at different parameter values Do Cluster Analysis How to use the cluster analysis function The cluster analysis function is located in the main menu under Marxan gt Do Cluster Analysis This feature is a
44. tal Decision Analysis Commonwealth F Pfea Cemeeetites Nelpteg Australia Applied Environmental Decision Analysis Cormorweath L n AUSTRALIA vironmental Research Facility o Australian Government lnirissive Opening an existing ZC project file To open a previously created ZC project file zcp selectFile Open from the ZC main menu Both the GIS and the Marxan windows will automatically open If you cannot see the map in the GIS window go to the main menu and choose GIS gt Zoom gt Layer Table 1 Summary of the functions accessible through the File menu and sub menus Menu Sub Menu Purpose New Project Create new ZC projects New Window Launches a second instance of ZC Open Open an existing ZC project Recent Files Allows you to browse to recently used ZC projects Save Saves the current project Exit Closes ZC Arranging the GIS and Marxan windows To arrange the GIS and Marxan windows in ZC select Windows Arrange from the Main Menu Choose vertical horizontal or cascade as the arrangement type and press ok to apply the change The window functions can help you to locate a window that may have been inadvertently lost when viewing another window The Marxan Interface Editing Marxan files and parameters In the Marxan window pictured below you can review and edit your input files and the most commonly used Marxan Parameters To edit a file or parameter choose the appropriate selection
45. tiple reports for the same configuration can be generated at the same time After selecting the appropriate configuration and reports click OK to generate the reports After a report is generated it will appear in ZC and will also be saved as a csv file in the main project folder Table 8 Three different types of reports are available from within the reporting tool Report Explanation Summary detail Summary statistics about the configuration Planning unit detail Individual status of each planning unit in the configuration Target achievement Detailed information on the representation of each 28 of 35 LJ tre of Excellence for Eavironmental Decisions applied Environmental Decision Analysis Commonwealth FefPfea Commeattion Metptog Anstratta THE UNIVERSITY dem ao QUEENSLAND ceed OEOOC Natural Heritage Trust AUSTRALIA Environmental Research Facility Ae Aasernian Convers ment Liane conservation feature Planning unit detail re port Table 9 Fields in the Planning unit detail report Field Explanation Planning unit Planning unit ID Configuration Name Displays the status of each planning unit in the configuration Note the name ofthis field is dynamic The name will be the name you have given the configuration Summary detail report Table 10 Fields in the Summary detail report Field Explanation Summary Co
46. ts or perform additional processing To generate a shapefile from a configuration click on the check box next to planning unit shapefile in the reporting window When this option is selected shapefile of the configuration will be exported to the main project folder when the reports are generated The shapefile name will be given the same name as the configuration Table Processing Convert data menu The convert data menu provides a couple of tools for the manipulation of data tables that can be useful when preparing input files or reviewing Marxan output Table 12 Functions accessible through the Convert data menu and submenus Menu Sub Menu Purpose Tables Transpose CSV Transposes the active table Transpose anneal Transposes the annealzones outputtable Anneal zones is an optional output of Tables zones table Marxan with zones Join DBF tables Tables puvspr Join dbf tables to generate a puvspr file for Marxan Join DBF tables puvspr The join table function can assist with the creation of new Marxan databases The function allows the user to specify a folder which contains a set of dbf tables that contain species information summarized by planning units These files can be generated by running the zonal statistics or tabulate area function in ArcGIS EJ Join DBF Tables To Marxan PUVSPR File Joe Folder containing files to be joined Browse Feature Index Type Create summary information file
47. utomatic if Do Cluster Analysis is ticked and you have installed R and the appropriate R packages details in the Downloading and setting up Zonae Cogito section at the beginning of this manual What is the cluster analysis function used for The purpose of including the cluster analysis function is to make it easy to identify dissimilar solutions from your Marxan runs in order to compare the full range of spatial configuration in your solutions Some Marxan users in the past have performed cluster analysis of Marxan solutions by manually creating the solutions matrix and using it with statistical analysis software Airam 2005 and ZC automates this process making the ability to perform a cluster analysis on Marxan solutions available to more Marxan users Outputs from cluster analysis The outputs include a 3 dimensional plot of the solution space this appears in a pop up a 2 dimensional plot of the solution space and a dendrogram showing the dissimilarity of the Marxan solutions these are automatically placed in the output folder after a Marxan run finishes Figure 10 Example 3 D plot 19 of 35 THE UNIVERSITY OF QUEENSLAND AUSTRALIA ARC g LEOOL sani his Trust ioak DEL NMS of solutions Centre of Excellence for Covironmental Decisions ootisd Environmental Decision Analysis Commonwealth Wetetea Commences Environmental Research Facility
48. xcellence for Environmental Decisions CEED the National Environmental Research Program NERP funded Terrestrial Hub 1 and The Nature Conservancy We thank Trevor Ward who assisted with software evaluation and development 35 of 35
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