View source: R/contagpixelgrid.R
contagpixelgrid  R Documentation 
Function for calculating the classic pixeladjacency contagion landscape metric from a binary map (O'Neill, 1988).
contagpixelgrid(xi, obswin, normalise = FALSE)
adjacency(xi, obswin = NULL)
xi 
A raster binary map (as an 
obswin 
If 
normalise 
If 
The unnormalised contagion landscape metric of categorical map is defined as
\sum_i \sum_j Qij ln(Qij),
where Qij
is the probability of
randomly selected adjacent pixels being in class i
and class j
respectively, and m
is the number of classes.
Here m = 2
as xi
is a binary map and we have defined 'adjacent'
pixels using the 4neighbourhood regime.
Contagion is calculated from an adjacency matrix created using the function adjacency
.
The adjacency matrix is a 2 by 2 table containing the number of pairs of neighbouring pixels (where order matters) such that:
Second pixel in xi  Second pixel not in xi 

First pixel in xi     
First pixel not in xi     
The computed pixeladjacency contagion value. If normalise
is TRUE
then the value will be between 0 and 1. Otherwise the value will be negative.
contagpixelgrid()
: Pixeladjacency contagion landscape metric of a binary map.
adjacency()
: Calculates the adjacency matrix used in the pixel contagion
Will fail if map is either all foreground or all background.
O'Neill, R.V., Krummel, J.R., Gardner, R.H., Sugihara, G., Jackson, B., DeAngelis, D.L., et al. (1988) Indices of landscape pattern. Landscape Ecology, 1, 153162.
xi < heather$coarse
obswin < owin(xrange = c(0,7),yrange=c(0,16))
adjmat < adjacency(xi,obswin)
pixeladjcontagion < contagpixelgrid(xi,obswin)
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