secr (version 1.3.0)

make.mask: Build Habitat Mask

Description

Construct a habitat mask object for spatially explicit capture-recapture. A mask object is a set of points with optional attributes.

Usage

make.mask(traps, buffer = 100, spacing = NULL, nx = 64, 
    type = "traprect", poly = NULL, pdotmin = 0.001, ...)

Arguments

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'

Value

• an object of class mask

Details

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 $p.(\mathbf{X})$ (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.

See Also

mask, subset.mask, pdot

Examples

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)