Build Habitat Mask
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, ny = 64, type =
c("traprect", "trapbuffer", "pdot", "polygon", "clusterrect",
"clusterbuffer", "rectangular", "polybuffer"), poly = NULL, poly.habitat = TRUE,
cell.overlap = c("centre","any","all"), keep.poly = TRUE, check.poly = TRUE,
pdotmin = 0.001, random.origin = FALSE,
...)traps |
object of class |
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) |
cell.overlap |
character string for cell vertices used to determine overlap with ‘poly’ |
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 |
random.origin |
logical; if TRUE the mask coordinates are jittered |
... |
additional arguments passed to |
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. 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.
The ‘polybuffer’ method cnstructs a mask by buffering around the polygon specified in the ‘poly’ argument. If that inherits from ‘SpatialPolygons’ then the buffering is performed with rgeos::gBuffer. Otherwise, buffering is approximate, based on the distance to points on an initial discretized mask enclosed by ‘poly’ (points at half the current ‘spacing’).
If poly is specified, points outside poly are dropped (unless type = "polybuffer"). The default is to require only the centre to lie within poly; use cell.overlap = "all" to require all cell corners to lie within poly, or cell.overlap = "any" to accept cells with any corner in poly. 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 SpatialPolygons or SpatialPolygonsDataFrame object as defined in the package ‘sp’, possibly imported by reading a shapefile with readOGR() from package rgdal.
If spacing is not specified then it is determined by dividing the
range of the x coordinates (including any buffer) by nx.
random.origin shifts the origin of the mask by a uniform random displacement within a spacing x spacing grid cell, while ensuring that the mask also satisfies the buffer requirement. random.origin is available only for ‘traprect’, ‘trapbuffer’, ‘polygon’, and ‘rectangular’ types, and spacing
must be specified.
An object of class mask. When keep.poly = TRUE,
poly and poly.habitat are saved as attributes of the
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.
The function buffer.contour displays the extent of one or more
‘trapbuffer’ zones - i.e. the effect of buffering the detector array
with varying strip widths.
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 `rgdal' package of Roger Bivand, Tim Keitt and Barry Rowlingson
## Not run:
datadir <- system.file("extdata", package = "secr")
possumarea <- rgdal::readOGR(dsn = datadir, layer = "possumarea")
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!
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.