make.mask {secr} | R Documentation

## 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'

### 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.(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`.

### Value

an object of class `mask`

### Note

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`.

### Author(s)

Murray Efford murray.efford@otago.ac.nz

### 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)

[Package secr version 1.2.11 Index]