convertRaster: Create a habitat mask from a raster

In mikemeredith/makeJAGSmask: Construct a Habitat Matrix for Use with SECR Analysis in JAGS or BUGS

Description

Create a habitat mask suitable for JAGS from a raster in which non-habitat is indicated by NAs. The raster is converted to a look-up matrix and included in the output.

Usage

convertRaster(raster, traps, plot = TRUE)

Arguments

raster	An object of class RasterLayer or RasterStack, possibly with covariates to be used for the analysis, where pixels corresponding to non-habitat have NA values. It must use a projected CRS, not lat/long.
traps	A 2-column matrix or data frame with the x and y coordinates of the traps.
plot	If TRUE, the resulting mask and trap locations will be plotted.

Value

An object of class JAGSmask, a list where the first elements are matrices corresponding to habMat with the values of the covariate in the original raster layer or stack. NA values in the raster are replaced with 0. If raster is a RasterLayer, this will be names 'covMat', otherwise the names of the layers will be retained.

This is followed by the following items

habMat	A 1/0 matrix, habMat[x, y] = 1 if location (x, y) is in good habitat.
trapMat	A 2-column matrix with the x and y coordinates of the traps in the same units as habMat
upperLimit	A length 2 vector giving the upper limit of x and y for habMat in pixel units (the lower limit for each is always 1).
pixelWidth	The width and height of the cells in habMat in the original units (usually metres).
area	The area of suitable habitat in the original units, typically square metres.

It will also have the following attributes, which can be used to convert JAGS output back to the original coordinate system:

boundingbox	A 4x2 matrix with coordinates of the 4 corners of habMat in the original units (usually metres).
origin	A vector of length 2 giving the location in the original coordinates of point 0, 0 in pixel units.

Author(s)

Mike Meredith

See Also

convertMask

Examples

require(raster)
data(simSCR)
plot(simSCR$patchR)
points(simSCR$traps, pch=3, col='red')
plot(simSCR$patchRS)

# Create the 'JAGSmask' object from the raster:
mymask1 <- with(simSCR, convertRaster(patchR, traps, plot=TRUE))
str(mymask1)  # covariate is called "covMat"
mymask2 <- with(simSCR, convertRaster(patchRS, traps, plot=TRUE))
  # only the first covariate is shown
str(mymask2) # covariates retain the names in the RasterStack

mikemeredith/makeJAGSmask documentation built on May 19, 2021, 1:10 a.m.