Patch Analyst Manual

Patch Analyst User’s ManualA Tool for Quantifying Landscape Structure

NWST Technical Manual TM-002February 1999

Patch Analyst User’s ManualA Tool for Quantifying Landscape Structure

NWST Technical Manual TM-002February 1999

developed and produced byNorthwest Science & Technology

Philip C. ElkieRobert S. Rempel

Angus P. Carr

by

©1999, Queen’s Printer for OntarioPrinted in Ontario, Canada

ISBN 0-7778-8295-7

Copies of this publication are available from:

Ontario Ministry of Natural ResourcesNorthwest Science &TechnologyRR#1, 25th Side RoadThunder Bay, OntarioP7C 4T9

Phone: (807) 939-2501Fax: (807) 939-1841E-mail: [email protected]

Cette publication spécialiséen’est disponible qu’en anglais

This publication should be cited as:

Elkie,P., R. Rempel and A. Carr. 1999. Patch Analyst User’s Manual. Ont. Min.Natur. Resour. Northwest Sci. & Technol. Thunder Bay, Ont. TM–002. 16 pp +Append.

NWST Technical Report TM-002 v

Acknowledgements and CreditsPatch Analyst was developed by Rob Rempel, Angus Carr and Phil Elkie. Angus Carrwas the lead programmer. Funding and support for the project was provided by theSustainable Forest Management Network (Network of Centres of Excellence) and theOntatio Ministry of Natural Resources (Centre for Northern Forest EcosystemResearch). Thanks to Celine Gilbert and Annalee McColm for layout and design.

NWST Technical Report TM-002 vii

Table of Contents

Acknowledgements .................................................................................................. iiiGetting Started ........................................................................................................... 1

Introduction ............................................................................................................ 1Installation ............................................................................................................. 1Using Patch Analyst ............................................................................................... 2

Features ..................................................................................................................... 3Add Area/Perimeter ............................................................................................... 3Dissolve ................................................................................................................. 4

Dissolving Shape Files .................................................................................... 4Dissolving Grids ............................................................................................. 5

Core areas............................................................................................................... 6Creating Core Area Themes ............................................................................ 7

Mean Proximity Index Threshold .......................................................................... 9Set Contrasted Weighted Edge Weights ............................................................... 10Set Core Buffer Distance...................................................................................... 10Spatial Statistics ................................................................................................... 10

Themes .......................................................................................................... 10Class .............................................................................................................. 11Analyze by .................................................................................................... 11Output Table Name ....................................................................................... 11Add Patch Analysis Theme to View .............................................................. 11

Statistics ............................................................................................................... 11General .......................................................................................................... 11Core Area ...................................................................................................... 11Batch ............................................................................................................. 11Advanced ...................................................................................................... 12

Spatial Statistics Output Table ............................................................................. 12Literature Cited ........................................................................................................ 12

Appendices .............................................................................................................. 13I Patch Analyst Statistic Summary .................................................................. 13II Glossary ........................................................................................................ 14III Dissolve Shape File AML ............................................................................. 20IV Frequently Asked Questions ........................................................................ 21

NWST Technical Manual TM–002 1

Getting Started

IntroductionPatch Analyst consists of several scripts written in Avenue and C code. Collectively

these scripts make up the Patch Analyst extension. Patch Analyst requires ArcView (3.xor higher) and will run on Windows 95, 98 or NT operating systems. Two versions ofPatch Analyst are available; i) vector only version and ii) vector and grid version. Thelatter uses the Fragstats Spatial Pattern Analysis program (McGarigal and Marks, 1994)and requires Arcviews Spatial Analyst extension. A modified version of Fragstats ispackaged and distributed in the Patch Analyst installation files. The Patch Analystextension calculates spatial statistics on both polygon files (e.g., shape files) and rasterfiles (e.g., Arc grids). Generic image files (e.g., Erdas filename.gis, JPEG filename.jpg,etc.) are similar to grid files and can be imported into ArcView and converted to gridfiles for analysis in the Patch Analyst. Patch Analyst can be downloaded from http://flash.lakeheadu.ca/~rrempel/patch/.

Throughout this manual, reference is made to Fragstats Spatial Pattern Analysisprogram (McGarigal and Marks, 1994). The manual for Fragstats can be downloadedfrom, ftp://ftp.fsl.orst.edu/pub/fragstats.2.0/. The frag.zip file contains four postscriptfiles (*.ps): Frag.ps (main body text), FragA.ps (Appendix A), FragB.ps (Appendix B)and FragC.ps (Appendix C). Patch Analyst uses a modified version of Fragstats, whichis included in the patch analyst distribution package.

InstallationThe Patch Analyst extension and other necessary scripts are contained in the zip

archive file named patch.zip. Within the zipped file there are several files that need tobe installed. Installation includes unzipping the patch.zip file into a directory of yourchoice. Once the files have been unzipped, double click on the install.apr file. This willcopy the Patch Analyst extension into the “C:\ESRI\AV_GIS30\ARCVIEW\EXT32”directory. If you are using the vector and grid version Fragstats.exe and Trimgrid.exewill also be copied into the “EXT32” directory. The install routine will also copy partsof the Dialogue Designer extension, if not already there, into the ArcView directorystructure. An alternative method of installation is a manual installation, i.e., unzip thebin, lib, ext.zip files to their respective ArcView directories. The respective ArcViewdirectories include:

• C:\ESRI\AV_GIS30\ARCVIEW\BIN32 for bin.zip

• C:\ESRI\AV_GIS30\ARCVIEW\LIB32 for lib.zip

• C:\ESRI\AV_GIS30\ARCVIEW\EXT32 for ext.zip

Either method is valid and will install the Patch Analyst extension properly. Oncethe extension is installed, start ArcView, open a view, choose Extensions from theViews file menu, and ensure that the Patch Analyst extension is enabled. The Patchmenu is now available and you are ready to begin using the Patch Analyst.

2 NWST Technical Manual TM–002

Using Patch Analyst

Click on Patch to activate the Patch Analyst menu. The menu consists of sevenoptions: Add Area/Perimeter, Dissolve, Create Core Areas, Set MPI Threshold, SetCWED Weights, Set Core Buffer Distance and Spatial Statistics. An About PatchAnalyst information box lists the Patch Analyst extension credits.


Features

Add Area/Perimeter

The Add Area/Perimeter feature adds two fields (columns) to the shapes attributetable, if not already present. The first field is an Area field that represents, in map units,the corresponding shape areas. The second field is a Perimeter field that represents, inmap units, the corresponding shape perimeters. If either of the fields already exist theywill not be overwritten. To update fields with new values existing fields must bedeleted first.

As with most ArcView features, and for most features in the Patch Analyst, therequested action will be performed on the theme or themes that have been selected.This does not mean the themes have to be displayed within the view, just that the thememust be selected. For example, in the ‘Moose Young Old’ View legend window below,the lower theme (Moose Habitat Map) is selected and the top theme (Moose HabitatMap Dissolved...) is not selected. The selected theme(s) are “embossed”in the viewstable of contents. Several themes can be selected at one time. Patch Analyst alsofollows ArcView protocol in that the selected action is performed on the entire theme ifno records are selected. If a set of records are selected, the action will be restricted tothat set.


Dissolve

Dissolve removes boundaries between polygons (shape files) that have the sameattributes. It is also used to clump contiguous pixels in grid files.

Dissolving Shape FilesThe dissolve features are typically used when the data source(s) contain polygons

with more than one feature attribute and analyses are performed on a feature attributethat includes groups of polygons that are adjacent to each other. When two polygonsare adjacent to each other and they have the same meaning the boundary between thetwo polygons must be dissolved. Boundaries of same-class polygons must be dissolvedor the number of patches will be artifically high. Dissolve differs from the routineprovided in ArcView’s GeoProcessing wizard in that every patch has a unique record inthe attribute table.

To dissolve polygons in a shape file choose Dissolve from the main Patch pull-downmenu, select the field that you want to dissolve the polygons by, and click on OK. Anew theme with the dissolved polygons will be added to the view. The new theme isplaced in the project working directory.


The dissolve routine can be time consuming. Dissolving shape files with greater than1,000 polygons is, at least, an overnight job. Faster computers with more memory willhandle larger data sets more efficiently. However, the dissolve routine in Arc/Info mightbe a more efficient route to take, and a simple dissolve AML is included in AppendixIII. Converting vector data to a grid is an alternative approach, that is much quicker.

Dissolving GridsClumping grids (analogous with dissolve for shape files) is complex and requires

that careful attention be paid to the process. Performing a landscape pattern analysis ona grid file is often faster than on a shape file. Clumping grids is not necessary whenperforming a spatial analysis in Patch Analyst because this is done by the fragstatsroutine. However, clumping is required when information for each patch within thesame class is needed (i.e., producing patch histograms). When creating a grid from ashape file or Arc/Info coverage, the user is prompted for the grid resolution, the featurefield to use to create the grid, the grid name, the location to store the grid and whetherall the original feature attributes should be joined to the grid. The result is a grid with atable of feature attributes. The table contains one row for each class. To produce patchhistograms, calculate the number of patches etc., a row is needed for each patch(contiguous clump of pixels) within each class. Dissolving a grid will simplify the tableand create a row for each patch.

To dissolve a grid, select the desired gridto dissolve, from the Patch pull-down menuselect dissolve, choose the field to clump byand select the clumping method (4N - Useorthogonals or 8N - Use Diagonals).


A

B

25 metres

25metres

The difference between 4N and 8N is the number of neighbours (N) used in clump-ing contiguous pixels. For instance, in the example below, two patches are present, Aand B (white cells). If 4N - Use Orthogonals is selected, a search around each pixel willinclude the four sides of each pixel. If a pixel with the same value is found on any ofthe four sides of pixel, the two pixels will be clumped together. In the example belowthere are two distinct patches when the 4N - Use Orthogonals method is used (Patch Aand Patch B). In contrast, if 8N - Use Diagonals is selected the searches will includethe four sides of each pixel and the diagonals of each pixel, or each surrounding pixel,hence eight neighbours. In the example, only one discrete patch would be defined usingthe 8N - Use Diagonals method, and it would include all the white pixels.

Core AreasCreate Core Areas works the same for both shape and grid themes. A core area is

the interior area of a landscape patch and is defined by a core area buffer distance. Theexample below shows two core areas (black cells) from a grid file. This grid consistsof 144 pixels, each 25 metres by 25 metres. The two core areas were created bychoosing a core area buffer distance of 25 metres.

Core Areas


In the case of grid files you may be warned that the cells are not square and the ‘X’dimension is going to be used. Grids can be made up of pixels that are either square orrectangular. Buffer in grids uses a count of pixels, so grids that have rectangular cellswill not always be buffered the same distance in both directions. In either case PatchAnalyst will use the ‘X’ dimension in the buffer distance algorithm when creating corearea themes.

Detatching multiple cores is a routine that allows the user to treat several core areasthat are derived from the same patch as one core area and vice-versa. If Detachedmultiple cores is selected the feature attribute table associated with the core area themewill include a record (row) for each core area polygon regardless of what patch it wasderived from. In contrast, if Detach multiple cores is not selected the feature attributetable will include a row for each original polygon (providing it is large enough to havecore area) that the core area theme was derived from. For instance, in the followingview the active theme consists of four polygons: i) conifer, ii) deciduous, iii) mixed-wood, and iv) swamp. The conifer polygon has an irregular shape and is the largestpolygon. Whether or not Detach multiple cores is selected, the result is a new themewith the same core area polygons .

When creating core area themes for grids it is important to consider the size ofpixels when specifying core area buffers. For instance, in the example (pixel size - 25m x 25 m), if a buffer of 10 metres was specified, Patch Analyst would round-up andcreate the core areas at the minimum distance possible based on pixel size. In this casethe actual distance used would be 25 metres or one pixel width. To create a finerbuffer, resample grid at a finer pixel resolution and convert to grid. When creating coreareas in shape files there are no constraints on core area buffer distances.

It is not necessary to create core area themes when core area statistics for gridthemes are required. Instead, from the Patch pull-down menu, choose, Set Core BufferDistance, and input the buffer distance. When statistics are calculated through thespatial statistics dialogue, the core area statistics will use the input buffer distance. Ifcore area statistics are required for shape themes a core area theme must be created.

Creating Core Area ThemesTo create a core area theme: (i) from the Views table of contents select the theme(s)

for which core areas are to be created, (ii) choose Patch from the main menu, (iii)select Create Core Areas, (iv) choose the field for which core area themes are to becalculated, (v) enter a core area theme file name, (vi) enable Detach multiple cores (ifdesired), and (vii) enter a core Buffer Size.


C


The difference is in the feature attribute table. If Detach multiple cores is selected thefeature attribute table will consist of five rows, one for each core area polygon.

In contrast, if detach multiple cores is unselected, the feature attribute table consistsof four rows, one for each original polygon.

The PatchArea field represents the area of the original patch from which the coreoriginated. The values in this field will occur twice or more in the table if more than onedetached core area has originated from the same polygon or set of cells. The CoreAreafield is the sum of all the core areas originating from the same polygon. This value canalso occur more than once in the table. The Area field is the area of the individualdisjunct core polygon or cells. When creating core areas from Grid themes the attributetable will also include Value, Count, Link, OldValue and Perimeter fields.

The method used to create core areas also impacts the calculation of some spatialstatistics. In the example below, core areas were created from a single polygon. Theresulting polygons, regardless of whether Detach multiple cores is selected, is threediscrete core areas (i.e., core area polygon ‘a’, core area polygon ‘b’, and core areapolygon ‘c’). When calculating mean core area if Detach multiple cores is selected themean core area will be calculated as: MCA = Sum of area of all core polygons/n, wheren is the number of core area polygons in the landscape. If detach multiple cores is notselected the mean core area will be calculated as: MCA = Sum of area of all corepolygons/n, where n is the number of polygons from which core area polygons origi-nated. These differences will be reflected in all core area statistics derived from vectorthemes.

Mean Proximity Index ThresholdThe Set MPI threshold option allows the user to enter a mean proximity threshold

distance. The MPI distance must be in map units and is used in calculating proximityindices. The default value is 1,000,000.


Set Contrasted Weighted Edge WeightsThe Set CWED weights option allows the user to provide a text file name. The text

file should contain all the edge-to-edge class combinations and the weights associatedwith them. For example:

1, 2, .451, 3, .51, 4, .52, 3, .322, 4, .453, 4, .75Weights represent the magnitude of contrast between adjacent patches and must

range between zero and one. If a file name is not provided contrasted weighted edgeswill not be calculated.

Set Core Buffer DistanceThe Set Core Buffer Distance option allows the user to enter the buffer distance to

use in core area statistics. This option is only applicable on grid themes. The minimumdistance that should be used is the width of one pixel. The default is nil.

Spatial StatisticsThe spatial statistics option activates a dialogue box that contains spatial statistics

inputs and selections.

ThemesIn the Themes menu area (top left), the theme(s) selected from the Views table of

contents will appear. Each theme that is present in the Themes menu can be analyzed;however, only one theme can be analyzed at a time. Select the theme that you wish toanalyze.


ClassThe Class box allows selection of the class field from the feature attribute table to be

analyzed. Both character and numeric classes can be analyzed.

Analyze byThe Analyze By option allows calculation of spatial statistics at either the Landscape

or Class level. If the theme is being analyzed at the landscape level, all patches, regard-less of the class they belong to, will be analyzed and a single value will be reported foreach statistic. In contrast, if the theme is analyzed at the class level, the statistics will bereported for each class within the landscape.

Output Table NameOutput Table Name is the name of the Arcview table that will be created containing

the spatial statistics. Spatial Statistics Output is the default name, althougth any namecan be entered. If the table already exists, Overwrite becomes available, otherwise it isnot available. The default is Append.

Add Patch Analysis Theme to ViewAdd Patch Analysis theme to view will create a new theme with the results of the

statistics for each patch. Add Patch Analysis theme to view is only available whenanalyzing vector themes.

Statistics

GeneralThere are six categories of statistics available in the Patch Analyst: i) area, ii) patch

size and density, iii) edge metrics, iv) shape metrics, v) diversity and interspersionmetrics, and vi) core area metrics. Simply select the statistics to be calculated andreported in the Spatial Statistics Output Table. Choose Select All to select all thestatistics or choose Select None to clear the selection. Certain statistics are only applica-ble at the landscape level. Similarly, certain statistics are only applicable on shapethemes. For a listing of statistic applicability and abbreviations refer to Appendix I.

Core AreaCore Area Metrics from the spatial statistics dialogue are only available for grid

themes. When core area statistics are required for vector themes, Create Core Areas(create a core area theme) from the Patch pull-down menu and then treat the core areatheme as a normal patch theme. Choose the desired statistics (i.e., Mean Patch size, etc.)from the spatial statistics dialogue and the result will be core area statistics. Whencreating core area themes two fields are added to the feature attribute table: i) Core Areaand ii) Patch Area. Therefore be sure to choose the proper field to calculate statisticswhen analyzing core area themes (see discussion on core areas).

BatchThe Batch option is available in both the Spatial Statistics and Create Core Area

menus. The Batch option allows the user to automatically create Avenue batch scripts.To create a batch file, make all the selections necessary to calculate spatial statistics on aspecific theme as outlined above, then click on batch. Next, click on clear all and makea new selection of statistics, then click on batch again. Continue making selections andclicking on batch. When all the selections have been made, click on Cancel. Close theactive view and click on Scripts from the Projects table of contents. Highlight the Scriptcalled Batch script and click on Run from the top menu. The batch script will run andthe appropriate Spatial Statistics Output table(s) will be created.


Literature Cited

Environmental Systems Research Institute Inc. 1996. Using ArcView GIS. ESRIRedlands, CA 350 p.

McGarigal and Marks. 1994. Fragstats: Spatial pattern analysis program forquantifying landscape structure. Reference manual. For. Sci. Dep. Oregon StateUniversity. Corvallis Oregon 62p.+Append.

Ritters, K.H., R.V. O’Neill, C.T. Hunsaker, J.D. Wickham, D.H. Yankee, S.P. Timmins,K.B. Jones, and B.L. Jackson. 1995. A factor analysis of landscape pattern andstructure metrics. Landscape Ecology 10(1) 23-29.

AdvancedThe Advanced button activates the Advanced Properties for Patch Analysis box and

allows the user to make specific requests at the current stage of processing. For instance,shape files can be dissolved and grids can be dissolved (clumped) with diagonals (i.e.,eight neighbours). The Analyze Vectors As option allows the user to analyze shape files(vector themes) as grid files. This is used when a shape file has been created from a gridfile. Depending on what software was used to create the shape file, The shape file can beblocky. Patch Analyst will apply the proper correction factor to account for the blocki-ness inherited from the original grid file.

The State areas in _______ option will show up as hectares or acres depending onthe settings in the View properties. For instance, if the View properties map units are setto metres the State areas in hectares option will become active. If the View propertiesmap units are set to feet, the State areas in acres option will become active. If map unitsare not set in View properties, then areas will be reported in the native map units of thetheme. Native map units will also be used if the checkbox is not selected. The Stateareas in _______ option is only available if a vector theme is used.

Spatial Statistics Output TableThe spatial statistics output table created from a landscape pattern analysis contains

the results of the analysis. The first four columns/fields will always be the same regard-less of whether a grid or vector theme was analyzed. The four fields are: i) (the name ofthe theme analyzed), ii) Run Date (the date of the analysis), iii) Run (the Run number),and iv) Class ( the class that the statistics for a particular row represent). If an analysis isperformed at the landscape level the Class field will report full. The following fields inthe table will contain the statistics that were selected in the Spatial Statistics dialoguebox. For a complete listing including abreviations and units that the statistics arereported in refer to Appendix I and II.

The output table can be exported as a dBase, Info, or delimited text file by selectingExport under the Tables File menu or can be exported directly to an Excel worksheetwith Excel Export. The output table is located in the system temp directory under thename statsx.dbf.

For grid analyses the native fragstats output tables are located in the system tempdirectory under frag.av.full, frag.av.class,and frag.av.land. A subset of these statisticsare imported to the output table.


Appendix I

Patch Analyst Statistic Summary

Statistic Name Statistic Applicable on Applicable onAbbreviation Shape Theme Grid Theme

Area MetricsClass Area CA Y YTotal Landscape Area TLA Y Y

Patch Density & Size MetricsNo. of Patches NumP Y YMean Patch Size MPS Y YMedian Patch Size MedPS Y NPatch Size Coefficient of Variance PSCoV Y YPatch Size Standard Deviation PSSD Y Y

Edge MetricsTotal Edge TE Y YEdge Density ED Y YMean Patch Edge MPE Y YContrasted Weighted Edge CWED Y Y

Shape MetricsMean Shape Index MSI Y YArea Weighted Mean Shape Index AWMSI Y YMean Perimeter-Area Ratio MPAR Y NMean Patch Fractal Dimension MPFD Y YArea Weighted Mean Patch Fractal Dimension AWMPFD Y Y

Diversity & Interspersion MetricsMean Nearest Neighbour Distance MNN Y YMean Proximity Index MPI Y YInterspersion Juxtoposition Index IJI Y YShannons Diversity Index* SDI Y YShannons Eveness Index* SEI Y Y

Core Area Metrics**Total Core Area TCA ** YMean Core Area MCA ** YCore Area Standard Deviation CASD ** YCore Area Density CAD ** YTotal Corea Area Index TCAI ** Y

NotesAll core area metrics are per disjunct cores.* applicable only at the landscape level** core area metrics are directly applicable for grid themes. For vector themes create a core area theme.


Appendix II

Glossary

Hierarchy in Patch Analyst TerminologyLandscapeA landscape includes all patches, polygons, contiguous cells or shapes in a view ora theme.ClassA class includes all patches, polygons, contiguous cells or shapes in a theme, a view ora landscape that have the same value for a given attribute.PatchEach individual polygon, contiguous set of cells, or shape is a patch. Each patch has aseperate record, or row, in the theme attribute table.

Example: The landscape below is made up of 14 individual polygons/patches. Thelandscape is made up of three classes; Conifer, Mixedwood and Deciduous. TheConifer class includes four patches (2, 3, 11 and 13), the Deciduous class includes fivepatches (4, 7, 8, 10 and 14) and the Mixedwood class includes five patches (1, 5, 6, 9and 12). When Patch Analyst generates statistics at the class level it calculates valuesfor each class. In contrast, at the landscape level it calculates a single value for allpatches, irrespective of class.


StatisticsThe attribute table for the 14 patch landscape is shown below. This table and the

corresponding landscape view is used to illustrate basic landscape statistics. For a moredetailed discussion of landscape quantification read Fragstats Users Manual(McGarigal and Marks 1994) and A factor analysis of landscape pattern and structuremetrics (Riitters et al. 1995).

ImportantIn the case of vector themes, for all statistics that report indices representing

areas, the standard reporting is in hectares if metres are selected as the Map Unitsand acres if feet are selected as Map Units. Analyses of grids only work in metricand the resulting area statistics or any statistics that use area will be reported inhectares. It is important that grid theme properties, especially cell size, are set inmetres. Similarily, statistics that use area (e.g., edge density m/ha) will use thearea of all classified pixels in the grid theme. Therefore, if a landscape includesclassified pixels that should not be used as landscape area (i.e., water), thesevalues should first be classified as No Data. Note that native maps units bothUTM and Lambert projections is meters. Map values are displayed in the upperright corner of the view.

Class AreaSum of areas of all patches belonging to a given class.

Example: Conifer Class Area (CA) = 359047.844+......+65819.984CA = 69.6626 hectares

If the map units are not specified (i.e., View Properties) and State Area in Hecatresor Acres has not been selected from the Advanced box in the Spatial Statistics Menu,then the resulting statistics will be reported in native map units (vector themes only).In the example; CA = 696626.012 (map units). This is the case for most statistics.

Landscape AreaSum of areas of all patches in the landscape.

Example: Landscape Area (TLA) = 46872.719 + 359047.844 +... + 62423.574TLA = 184.11 hectares


Number of PatchesTotal number of patches in the landscape if ‘Analyze by Landscape’ is selected, orNumber of Patches for each individual class, if ‘Analyze by Class’ is selected.

Example: Class Level: Number of Patches (NumP)Mixedwood = 5, Conifer = 4, Deciduous = 5

Landscape Level: Number of Patches (NumP) = 14

Mean Patch SizeAverage patch size.

Example: Mean Patch Size of Conifer Patches (Class Level)MPS = (359047.844 + 139531.484 ...+ 65819.984)/4MPS = 17.42 hectares

Example: Mean Patch Size of Patches (Landscape Level)MPS = (46872.719 + 359047.844 + ... + 62432.574)/14MPS = 13.15 hectares

Median Patch SizeThe middle patch size, or 50th percentile .

Example: Median Patch size of Conifer Patches (Class Level)MedPS = 13.22 hectares

Example: Median Patch size of all patches (Landscape Level)MedPS = 7.59 hectares

Patch Size Standard DeviationStandard Deviation of patch areas.

Example: Patch Size Standard Deviation of Conifer Patches (Class Level)PSSD = 11.05 hectares

Example: Patch Size Standard Deviation of all patches (Landscape Level)PSSD = 9.51 hectares

Patch Size Coefficient of VarianceCoefficient of variation of patches.

Example: Coefficient of Variation of Conifer patches (Class Level)PSCoV = PSSD/MPS

= (11.05 hectares / 17.42 hectares) *100 = 63Example: Coefficient of Variation of all patches (Landscape Level)

PSCoV = (9.51 hectares / 13.15 hectares)*100 =72

Total EdgePerimeter of patches.

Example: Total Edge Conifer (Class Level)TE = Sum of perimeter of all conifer patches.TE = 10858.88 metresUnits are expressed in native maps units.

Example: Total Edge all patches (Landscape Level)TE = Sum of perimeter of all patchesTE = 28607.27 metres


ImportantIn the case of vector themes, edge calculations include all the edge on the land-scape including boundary edge. The contrasted weighted edge feature allows edgeweight at the boundaries to be set to zero. In the case of grid themes, edge calcula-tions do not include the edges that surround the landscape boundary edge or anyinterior edges that include pixels classified as No Data.

Edge DensityAmount of edge relative to the landscape area.

Example: Edge Density Conifer (Class Level)ED = TE / TLAED = 10858.88 metres/184.11 hectares = 58.98 metres/hectare

Example: Edge Density of all Patches (Landscape Level)ED = 28607.27 metres/184.11 hectares = 155.38 metres/hectare

Mean Patch EdgeAverage amount of edge per patch.

Example: Mean Patch Edge Conifer (Class Level)MPE = TE / NumPMPE = 10858.88 metres/4 patches = 2714.72 metres/patch

Example: Mean Patch Edge all Patches (Landscape Level)MPE = TE / NumPMPE = 28607.27 metres/14 patches = 2043.38 metres/patch

Mean Perimeter-Area RatioShape Complexity.

Example: Mean perimeter-area ratio Conifer (Class Level)MPAR = Sum of each patches perimeter/area ratio divided by

number of patches.MPAR = (132 m/ha + 112 m/ha + 201 m/ha + 84 m/ha)/4 patchesMPAR = 182 metres/hectare

Example: Mean perimeter-area ratio all patches (Landscape Level)MPAR = (200 m/ha + 132 m/ha + ... + 175 m/ha)/14 patchesMPAR = 185 metres/hectare

Mean Shape IndexShape Complexity.MSI is greater than one, MSI = 1 when all patches are circular (polygons) or square(grids).MSI = sum of each patches perimeter divided by the square root of patch area (hec-tares) for each class (Class Level) or all patches (Landscape Level), and adjusted forcircular standard (polygons), or square standard (grids), divided by the number ofpatches (McGaril and Marks 1994).

Mean Patch Fractal DimensionShape Complexity.Mean patch fractal dimension is another measure of shape complexity. Mean fractaldimension approaches one for shapes with simple perimeters and approaches two whenshapes are more complex (McGaril and Marks 1994).


Area Weighted Mean Patch Fractal DimensionShape Complexity adjusted for shape size.Area weighted mean patch fractal dimension is the same as mean patch fractal dimen-sion with the addition of individual patch area weighting applied to each patch.Because larger patches tend to be more complex than smaller patches, this has theeffect of determining patch complexity independent of its size. The unit of measure isthe same as mean patch fractal dimension (McGaril and Marks 1994).

Mean Nearest NeighborMeasure of patch isolation.The nearest neighbor distance of an individual patch is the shortest distance to a similarpatch (edge to edge). The mean nearest neighbor distance is the average of thesedistances (metres) for individual classes at the class level and the mean of the classnearest neighbor distances at the landscape level.

Interspersion Juxtaposition IndexMeasure of patch adacencyApproaches zero when the distribution of unique patch adjacencies becomes unevenand 100 when when all patch types are equally adjacent.

Interspersion requires that the landscape be made up of a minimum of three classes.At the class level interspersion is a measure of relative interspersion of each class. Atthe landscape level it is a measure of the interspersion of the each patch in the land-scape.

Mean Proximity IndexMeasure of the degree of isolation and fragmentation.Mean proximity index is a measure of the degree of isolation and fragmentation of apatch. MPI uses the nearest neighbor statistic. The distance threshold default is1,000,000. If MPI is required at specific distances, select Set MPI Threshold from themain Patch pull-down menu and enter a threshold distance.

Both MNN and MPI use the nearest neighbor statistic of similar polygons in theiralgorithm. Occasionally a blank or zero will be reported in MNN and MPI fields. Thishappens when one polygon vertex touches another polygons border but the two similarpolygons do not share a common border. When this happens a manual edit (move) ofthe touching vertex will correct the problem in the theme. This problem will not happenwhen analyzing grid themes.

Shannon’s Diversity IndexMeasure of relative patch diversity.Shannon’s diversity index is only available at the landscape level and is a relativemeasure of patch diversity. The index will equal zero when there is only one patch inthe landscape and increases as the number of patch types or proportional distribution ofpatch types increases (McGaril and Marks 1994).

Shannon’s Evenness IndexMeasure of patch distribution and abundance.Shannon’s evenness index is equal to zero when the observed patch distribution is lowand approaches one when the distribution of patch types becomes more even. Shan-non’s evenness index is only available at the landscape level.

Core Area DensityMeasure of relative distribution of core areas.Number of disjunct core areas per hectare of total landscape area.


ImportantDirect analyses of Core Area through the spatial statistics dialogue are onlyavailable for grid themes. If core area statistics are required for vector themes,first Create Core Areas (create a new core area theme) from the Patch pull-downmenu and then calculate statistics for the new theme as you would for a normalvector theme. The results will be core area statistics.

Mean Core AreaThe average size of disjunct core patches.The mean size of disjunct core area patches (hectares).

Core Area Standard DeviationThe standard deviation of disjunct core areas (hectares).The standard deviation of disjunct core areas (hectares).

Core Area DensityThe relative number of disjunct core patches relative to the landscape area.The total number of all disjunct patches divided by the landscape area (number ofdisjunct core patches /hectare).

Total Core Area IndexMeasure of amount of core area in the landscape.Total core area index is a measure of the amount of core area in the landscape. Totalcore area index is a proportion of core area in the entire landscape and is equal to zerowhen no patches in the landscape contain core and approaches one as the relativeproportion of core area in the landscape increases.


Appendix IIIAML to dissolve a shape file USAGE: &run shpdslv.aml <shapefile basename> <dissolve field> For a shapefile the shapefile basename is the name of the shapefile without the .shp

&args bname dissfield&type Convert shape to ArcInfo coverageshapearc %bname%.shp dcov dissolve_id DEFAULT&type clean the coverageclean dcov dcov # 0.0001 poly&type convert regions to polygonsregionpoly dcov dcovpoly dissolve_id %bname%tab&type dissolve the coverage by specified fielddissolve dcovpoly %bname%d %dissfield%arcshape %bname%d poly %bname%d.shp DEFAULT&type kill the temporary coverageskill dcovkill dcovpolykill %bname%d&s delouttab:= [DELETE %bname%tab -INFO]&return


Appendix IV

Frequently Asked Questions

1. What level of expertise do I need to use Patch Analyst? To effectively use PatchAnalyst and understand the points made in this FAQ, you need only be familiar with thestandard functions and terminology used in ArcView, and the standard terminology andconcepts used in landscape GIS analysis.

2. What is Dissolve? Dissolve is a function that removes boundaries of like-classifiedpolygons or pixel clumps, and then retains a separate record for each patch in theattribute table. To conduct a valid landscape analysis, the theme must be dissolved firstto remove artificial patch boundaries.

3. ArcView 3.1 and ARC/INFO both have a Dissolve function. Are they the sameas the one in Patch Analyst? The ArcView dissolve is different. The dissolve (ormerge) function in the Geoprocessing wizard of ArcView 3.1 removes polygonboundaries of like-classified polygons, but then merges all records by class in theattribute table. A dissolve on a 4-class habitat theme would result in an attribute tablewith only four records, so patch-specific information is lost. The ARC/INFO dissolvecan be used to create the type of dissolve required by Patch Analyst, and can be muchfaster. An example AML is available from the download site. Jeffrey Lane has modifiedthe AV 3.1 Geoprocessing wizard so it will perform an Arc/Info type dissolve as inPatch Analyst. Go to the ESRI site to obtain geopwaid.avx.

4. My resource inventory is in shapefile format, but I want to analyse the datausing grid. How do I do this? To do this, the original polygon theme is first con-verted to grid; select the analysis theme (e.g., HU in the example data). There is noneed to join the attribute table to the theme. Ensure the new grid theme is active, thenrun Patch Statistics, selecting “value” as the class field. You must set MPI threshold,buffer distance, and identify the Contrast Weighted Edge weights file, if you wish youcalculate stats for MNN, core area, and CWED.

5. My 7-class landcover data (grid format) was derived from a satellite image,and the value attribute table has only seven records in it. How do I calculate statsfor individual patches? In ArcView, a raster-based grid file normally has an attributetable with one record for each raster class value. To create the new theme and table,simply run Dissolve on the original grid theme. This will activate the grid clumpingprocedure and structure the data properly. It is not necessary to run the dissolve on gridthemes before using the Spatial Statistics dialog box, however, because fragstats.exeperforms the “dissolve” internally.

6. How does analysis differ between grids and shapefiles? Grid analyses run muchfaster than polygon analyses. Experience has shown that for forest managementapplications, differences in results between polygons versus grids are relatively small ifa grid cell size of about 50 metres is used.

7. The computer seems hung? ArcView begins to slow down if processing is done onthemes with more than 5,000 polygons. Dissolve is most affected by this limitation, solarge dissolves may have to be done overnight. Some software developers have figuredways around this AV limitation, but we did not implement any such “work arounds”.Alternatively, an ARC/INFO dissolve runs much faster, and working with grids is alsomuch faster. We have included the dissolve function in Patch Analyst because it may bethe only alternative for some users.


8. Are statistical formulas different for grids? Yes, some formulas are adjusted forthe stair-case effect of grid perimeters. Alternatively, if a polygon has been createdfrom a grid and thus has a “jagged edge”, then spatial statistics must also adjust for thestair-case effect of this artificially high perimeter. You can do this by calculating patchstatistics for polygons using the grid formulas. Choose this option in the advanceddialog box.

9. I have run the Patch Statistics dialog box, but once it is finished, nothinghappens. The output statistics table does not open automatically. Go to Tables, thenselect and open the output statistics table.

10. Units for the patch metrics seem wrong. Set map units in the View propertiesdialog box.

11. The Core Areas statistics are greyed out. You must select a Core Areas shapefile theme, or any grid theme to make these statistics active. Use Patch > Create CoreAreas, select your dissolved habitat shapefile, and specify the edge distance. A newtheme will be created and added to your View. All statistics, including the specific corearea statistics, can then be run on the core areas theme. Grid themes are automaticallyenabled for core area stats.

12. What does “detach core areas” mean? When creating Core Areas (e.g.,delineating interior forest), processing of the original stand might result in creation ofmore than one separate core area. If “detach” is selected, then these multiple corescreated from the original polygon are treated separately, although information on thesize of the original patch from which it was created is retained in the table. This isequivalent to “disjunct” core areas in fragstats. Grid theme statistics for core areasreport “disjunct” core area metrics.

13. There is not enough flexibility to calculate ratios, create graphs, and displaymy results, or, How do I export tables to Excel? Spatial Analyst captures spatialinformation in table format, which can then be subject to traditional statistical analysis,spreadsheet calculations, and graphing. Go to Tables, File menu, then select ExcelExport. Alternatively, the standard Export...will allow you to create a dBase, ASCII, orINFO table.

14. The entire landscape is too big an area for my analysis. How do I analyse bysubunits? For many ecological applications, analysis of the entire landscape (e.g.,Forest Management Unit) is too coarse. Alternatively, create subunits by selectingMake Hexes from the Habitat menu item, then intersect your habitat theme with thehexagon theme. Now run spatial statistics on this intersected theme, and selectIDCODE as the analysis class. This is explained in greater detail in the Habitat Analystsection of the FAQ.

15. Can I automate the proceedure to run multiple analyses, or What is the Batchbutton for? The batch button can be used to send analysis requests to a script file,much the way the paste button allows you to save syntax in an SPSS session. Afterselecting options in the Spatial Statistics dialog box (including the advanced dialog,which allows you to request a DISSOLVE of the shapefile), or the Create Core Areasdialog box, push the Batch button. Once selections have been made, push the Cancelbutton. Now go to the Scripts area, open Batchscript, and you will see the compiledscript file used to run the procedures. This script can of course be edited andrecompilied to further automate your analyses. A single quote marks a commented line.

51263(.3k P.R. 99 02 19)ISBN 0-7778-8295-7

Documents

Patch Analyst Manual