Random Landscape
The Modified Random Cluster algorithm of Saura and Martinez-Millan (2000) is used to generate a mask object representing patches of contiguous ‘habitat’ cells (pixels) within a ‘non-habitat’ matrix (‘non-habitat’ cells are optionally dropped). Spatial autocorrelation (fragmentation) of habitat patches is controlled via the parameter ‘p’. ‘A’ is the expected proportion of ‘habitat’ cells.
randomHabitat(mask, p = 0.5, A = 0.5, directions = 4, minpatch = 1, drop = TRUE, covname = "habitat", plt = FALSE, seed = NULL)
mask |
secr mask object to use as template |
p |
parameter to control fragmentation |
A |
parameter for expected proportion of habitat |
directions |
integer code for adjacency (rook's move 4 or queen's move 8) |
minpatch |
integer minimum size of patch |
drop |
logical for whether to drop non-habitat cells |
covname |
character name of covariate when |
plt |
logical for whether intermediate stages should be plotted |
seed |
either NULL or an integer that will be used in a call to |
Habitat is simulated within the region defined by the cells of mask. The region may be non-rectangular.
The algorithm comprises stages A-D:
A. Randomly select proportion p of cells from the input mask
B. Cluster selected cells with any immediate neighbours as defined by
directions
C. Assign clusters to ‘non-habitat’ (probability 1–A) and ‘habitat’ (probability A)
D. Cells not in any cluster from (B) receive the habitat class of the majority of the <=8 adjacent cells assigned in (C), if there are any; otherwise they are assigned at random (with probabilities 1–A, A).
Fragmentation declines, and cluster size increases, as p increases up to the ‘percolation threshold’ which is about 0.59 in the default case (Saura and Martinez-Millan 2000 p.664).
If minpatch > 1 then habitat patches of less than minpatch
cells are converted to non-habitat, and vice versa. This is likely to
cause the proportion of habitat to deviate from A.
If drop = FALSE a binary-valued (0/1) covariate with the
requested name is included in the output mask, which has the same extent
as the input. Otherwise, non-habitat cells are dropped and no covariate
is added.
An object of class ‘mask’. By default (drop = TRUE) this
has fewer rows (points) than the input mask.
The attribute “type” is a character string formed from paste('MRC p=',p, ' A=',A, sep='').
Single-linkage clustering and adjacency operations use functions
‘clump’ and ‘adjacency’ of the package raster; ‘clump’ also
requires package igraph0 (raster still uses this
deprecated version). Optional plotting
of intermediate stages (plt = TRUE) uses the plot method for
rasterLayers in raster.
A non-rectangular input mask is padded out to a rectangular rasterLayer for operations in raster; cells added as padding are ultimately dropped.
The procedure of Saura and Martinez-Millan (2000) has been followed as far as possible, but this implementation may not match theirs in every detail.
This implementation allows only two habitat classes. The parameter A is the expected value of the habitat proportion; the realised habitat proportion may differ quite strongly from A, especially for large p (e.g., p > 0.5).
Anisotropy is not implemented; it would require skewed adjacency filters (i.e. other than rook- or queen-move filters) that are not available in raster.
Hijmans, R. J. and van Etten, J. (2011) raster: Geographic analysis and modeling with raster data. R package version 1.9-33. https://CRAN.R-project.org/package=raster.
Saura, S. and Martinez-Millan, J. (2000) Landscape patterns simulation with a modified random clusters method. Landscape Ecology, 15, 661–678.
## Not run:
tempmask <- make.mask(nx = 100, ny = 100, spacing = 20)
mrcmask <- randomHabitat(tempmask, p = 0.4, A = 0.4)
plot(mrcmask, dots = FALSE, col = "green")
pop <- sim.popn(10, mrcmask, model2D = "IHP")
plot(pop, add = TRUE)
## plot intermediate steps A, C, D
par(mfrow = c(1,3))
mrcmask <- randomHabitat(tempmask, p = 0.4, A = 0.4, plt = TRUE)
par(mfrow = c(1,1)) ## reset to default
## keep non-habitat cells
mrcmask <- randomHabitat(tempmask, p = 0.4, A = 0.4, drop = FALSE)
plot(mrcmask, covariate = "habitat", dots = FALSE,
col = c("grey","green"), breaks = 2)
## effect of purging small patches
opar <- par(mfrow=c(1,2))
mrcmask <- randomHabitat(tempmask, p = 0.4, A = 0.4, minpatch = 1)
plot(mrcmask, dots = FALSE, col ="green")
mrcmask <- randomHabitat(tempmask, p = 0.4, A = 0.4, minpatch = 5)
plot(mrcmask, dots = FALSE, col ="green")
par(opar)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.