| make.mask {secr} | R Documentation |
Construct a habitat mask object for spatially explicit capture-recapture. A mask object is a set of points with optional attributes.
make.mask(traps, buffer = 100, spacing = NULL, nx = 64,
type = "traprect", poly = NULL, pdotmin = 0.001, ...)
traps |
object of class traps |
buffer |
width of buffer in metres |
spacing |
spacing between grid points (metres) |
nx |
number of grid points in 'x' direction |
type |
character string for method to use ('traprect', 'trapbuffer', 'pdot', 'polygon') |
poly |
matrix of two columns interpreted as the x and y coordinates of a bounding polygon (optional) |
pdotmin |
minimum detection probability for inclusion in mask when type = 'pdot' (optional) |
... |
additional arguments passed to pdot when type = 'pdot' |
The 'traprect' method constructs a grid of points in the rectangle
formed by adding a buffer strip to the minimum and maximum x-y
coordinates of the detectors in traps. Both 'trapbuffer' and
'pdot' start with a 'traprect' mask and drop some points.
The 'trapbuffer' method restricts the grid to points within distance
buffer of any detector.
The 'pdot' method restricts the grid to points for which the net
detection probability p.(X) (see
pdot) is at least pdotmin. Additional parameters
are used by pdot (detectpar, noccasions). Set these with the
... argument; otherwise make.mask will silently use the
arbitrary defaults.
The 'polygon' method places points on a rectangular grid clipped to the
polygon (buffer is not used).
If spacing is not specified then it is determined by dividing the
range of the x coordinates (including any buffer) by nx.
an object of class mask
A warning is displayed if type = 'pdot' and the buffer is too small to include all points with p. > pdotmin.
A habitat mask is needed to fit an SECR model and for some related
computations. The default mask settings in secr.fit may be good
enough, but it is preferable to use make.mask to construct a mask
in advance and to pass that mask as an argument to secr.fit.
Murray Efford murray.efford@otago.ac.nz
temptrap <- make.grid(nx = 10, ny = 10, spacing = 30)
## default method: traprect
tempmask <- make.mask(temptrap, spacing = 5)
plot(tempmask)
summary (tempmask)
## make irregular detector array by subsampling
## form mask by 'trapbuffer' method
temptrap <- subset (temptrap, sample(nrow(temptrap), size = 30))
tempmask <- make.mask (temptrap, spacing = 5, type = 'trapbuffer')
plot (tempmask)
plot (temptrap, add = TRUE)
## form mask by 'pdot' method
temptrap <- make.grid(nx = 6, ny = 6)
tempmask <- make.mask (temptrap, buffer = 150, type = 'pdot',
pdotmin = 0.0001, detectpar = list(g0 = 0.1, sigma = 30),
noccasions = 4)
plot (tempmask)
plot (temptrap, add = TRUE)