secr (version 2.9.4)

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, ny = 64, type =
    c("traprect", "trapbuffer", "pdot", "polygon", "clusterrect",
    "clusterbuffer", "rectangular"), poly = NULL, poly.habitat = TRUE,
    keep.poly = TRUE, check.poly = TRUE, 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

ny

number of grid points in `y' direction (type = `rectangular')

type

character string for method

poly

bounding polygon to which mask should be clipped (see Details)

poly.habitat

logical for whether poly represents habitat or its inverse (non-habitat)

keep.poly

logical; if TRUE any bounding polygon is saved as the attribute `polygon'

check.poly

logical; if TRUE a warning is given for traps that lie outside a bounding polygon

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. When keep.poly = TRUE, poly and poly.habitat are saved as attributes of the 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. pdot is currently limited to a halfnormal detection function. The `clusterrect' method constructs a grid of rectangular submasks centred on `clusters' of detectors generated with trap.builder (possibly indirectly by make.systematic). The `clusterbuffer' method resembles `trapbuffer', but is usually faster when traps are arranged in clusters because it starts with a `clusterrect' mask. The `rectangular' method constructs a simple rectangular mask with the given nx, ny and spacing. If poly is specified, points outside poly are dropped. The `polygon' method places points on a rectangular grid clipped to the polygon (buffer is not used). Thus `traprect' is equivalent to `polygon' when poly is supplied. poly may be either

• a matrix or dataframe of two columns interpreted as x and y coordinates, or
• a SpatialPolygonsDataFrame object as defined in the package `sp', possibly from reading a shapefile with readShapePoly() from package `maptools'.

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, read.mask, subset.mask, pdot, buffer.contour, deleteMaskPoints

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)

## Using an ESRI polygon shapefile for clipping (shapefile
## polygons may include multiple islands and holes).
## Requires the `maptools' package of Nicholas J. Lewin-Koh, Roger
## Bivand, and others; `maptools' uses the `sp' package of spatial
## classes by Ed Pebesma and Roger Bivand.

library(maptools)
setwd(system.file("extdata", package = "secr"))
possumarea <- readShapePoly("possumarea")  ## possumarea.shp etc.
possummask2 <- make.mask(traps(possumCH), spacing = 20,
    buffer = 250, type = "trapbuffer", poly = possumarea)
par(mar = c(1,6,6,6), xpd = TRUE)
plot (possummask2, ppoly = TRUE)
plot(traps(possumCH), add = T)
par(mar = c(5,4,4,2) + 0.1, xpd = FALSE)

## if the polygon delineates non-habitat ...
seaPossumMask <- make.mask(traps(possumCH), buffer = 1000, 
    type = "traprect", poly = possumarea, poly.habitat = FALSE)
plot(seaPossumMask)
plot(traps(possumCH), add = T)
## this mask is not useful!