PatchStat: Landscape Patch Statistics

In SDMTools: Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises

Description

PatchStat calculates the patch statistics for individual patches identified in a matrix of data. The matrix can be a raster of class 'asc' (adehabitat package), 'RasterLayer' (raster package) or 'SpatialGridDataFrame' (sp package).

Usage

PatchStat(mat, cellsize = 1, latlon = FALSE)

Arguments

mat	a matrix of data with individual patches identified as with ConnCompLabel; The matrix can be a raster of class 'asc' (this & adehabitat package), 'RasterLayer' (raster package) or 'SpatialGridDataFrame' (sp package)
cellsize	cell size (in meters) is a single value representing the width/height of cell edges (assuming square cells)
latlon	boolean value representing if the data is geographic. If latlon == TRUE, matrix must be of class 'asc', 'RasterLayer' or 'SpatialGridDataFrame'

Details

The patch statistics are based on statistics calculated by fragstats http://www.umass.edu/landeco/research/fragstats/fragstats.html.

Value

a data.frame listing

patchID	the unique ID for each patch.
n.cell	the number of cells for each patch, specified in square meters.
n.core.cell	the number of cells in the core area, without the edge area.
n.edges.perimeter	the number of outer perimeter cell edges of the patch.
n.edges.internal	the number of internal cell edges of the patch.
area	the area of each patch comprising a landscape mosaic.
core.area	represents the interior area of the patch, greater than the specified depth-of-edge distance from the perimeter.
perimeter	the perimeter of the patch, including any internal holes in the patch, specified in meters.
perim.area.ratio	the ratio of the patch perimeter (m) to area (m2).
shape.index	the shape complexity, sum of each patches perimeter divided by the square root of patch area.
frac.dim.index	fractal dimension index reflects shape complexity across a range of spatial scales; approaches 2 times the logarithm of patch perimeter (m) divided by the logarithm of patch area (m2).
core.area.index	quantifies core area as a percentage of patch area.

Author(s)

Jeremy VanDerWal [e-mail]

References

McGarigal, K., S. A. Cushman, M. C. Neel, and E. Ene. 2002. FRAGSTATS: Spatial Pattern Analysis Program for Categorical Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following web site: www.umass.edu/landeco/research/fragstats/fragstats.html

See Also

ClassStat, ConnCompLabel

Examples

#define a simple binary matrix
tmat = { matrix(c( 0,0,0,1,0,0,1,1,0,1,
                   0,0,1,0,1,0,0,0,0,0,
                   0,1,NA,1,0,1,0,0,0,1,
                   1,0,1,1,1,0,1,0,0,1,
                   0,1,0,1,0,1,0,0,0,1,
                   0,0,1,0,1,0,0,1,1,0,
                   1,0,0,1,0,0,1,0,0,1,
                   0,1,0,0,0,1,0,0,0,1,
                   0,0,1,1,1,0,0,0,0,1,
                   1,1,1,0,0,0,0,0,0,1),nr=10,byrow=TRUE) }

#do the connected component labelling
ccl.mat = ConnCompLabel(tmat)
ccl.mat
image(t(ccl.mat[10:1,]),col=c('grey',rainbow(length(unique(ccl.mat))-1)))

#calculate the patch statistics
ps.data = PatchStat(ccl.mat)
ps.data

Example output

      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    0    0    0    1    0    0    2    2    0     3
 [2,]    0    0    1    0    1    0    0    0    0     0
 [3,]    0    1   NA    1    0    1    0    0    0     4
 [4,]    1    0    1    1    1    0    1    0    0     4
 [5,]    0    1    0    1    0    1    0    0    0     4
 [6,]    0    0    1    0    1    0    0    4    4     0
 [7,]    4    0    0    1    0    0    4    0    0     4
 [8,]    0    4    0    0    0    4    0    0    0     4
 [9,]    0    0    4    4    4    0    0    0    0     4
[10,]    4    4    4    0    0    0    0    0    0     4
  patchID n.cell n.core.cell n.edges.perimeter n.edges.internal area core.area
1       0     60           1               122              118   60         1
2       1     17           0                60                8   17         0
3       2      2           0                 6                2    2         0
4       3      1           0                 4                0    1         0
5       4     19           0                54               22   19         0
  perimeter perim.area.ratio shape.index frac.dim.index core.area.index
1       122         2.033333    3.812500       1.669487      0.01666667
2        60         3.529412    3.333333       1.911646      0.00000000
3         6         3.000000    1.000000       1.169925      0.00000000
4         4         4.000000    1.000000            NaN      0.00000000
5        54         2.842105    3.000000       1.767868      0.00000000

SDMTools documentation built on Jan. 11, 2020, 9:23 a.m.