make.traps: Build Detector Array

In secr: Spatially Explicit Capture-Recapture

Build Detector Array

Description

Construct a rectangular array of detectors (trapping grid) or a circle of detectors or a polygonal search area.

Usage

make.grid(nx = 6, ny = 6, spacex = 20, spacey = spacex, spacing = NULL,
    detector = "multi", originxy = c(0,0), hollow = FALSE, ID = "alphay", 
    leadingzero = TRUE, markocc = NULL)

make.circle (n = 20, radius = 100, spacing = NULL, 
    detector = "multi", originxy = c(0,0), IDclockwise = TRUE, 
    leadingzero = TRUE, markocc = NULL)

make.poly (polylist = NULL, x = c(-50,-50,50,50),
    y = c(-50,50,50,-50), exclusive = FALSE, verify = TRUE)

make.transect (transectlist = NULL, x = c(-50,-50,50,50),
    y = c(-50,50,50,-50), exclusive = FALSE)

make.telemetry (xy = c(0,0)) 

Arguments

nx	number of columns of detectors
ny	number of rows of detectors
spacex	distance between detectors in ‘x’ direction (nominally in metres)
spacey	distance between detectors in ‘y’ direction (nominally in metres)
spacing	distance between detectors (x and y directions)
detector	character value for detector type - "single", "multi" etc.
originxy	vector origin for x-y coordinates
hollow	logical for hollow grid
ID	character string to control row names
leadingzero	logical; if TRUE numeric rownames are padded with leading zeros
markocc	integer vector of marking or sighting codes; see markocc
n	number of detectors
radius	radius of circle (nominally in metres)
IDclockwise	logical for numbering of detectors
polylist	list of dataframes with coordinates for polygons
transectlist	list of dataframes with coordinates for transects
x	x coordinates of vertices
y	y coordinates of vertices
exclusive	logical; if TRUE animal can be detected only once per occasion
verify	logical if TRUE then the resulting traps object is checked with verify
xy	vector with coordinates of arbitrary point (e.g., centroid of fixes)

Details

make.grid generates coordinates for nx.ny traps at separations spacex and spacey. If spacing is specified it replaces both spacex and spacey. The bottom-left (southwest) corner is at originxy. For a hollow grid, only detectors on the perimeter are retained. By default, identifiers are constructed from a letter code for grid rows and an integer value for grid columns ("A1", "A2",...). ‘Hollow’ grids are always numbered clockwise in sequence from the bottom-left corner. Other values of ID have the following effects:

ID	Effect
numx	column-dominant numeric sequence
numy	row-dominant numeric sequence
numxb	column-dominant boustrophedonical numeric sequence (try it!)
numyb	row-dominant boustrophedonical numeric sequence
alphax	column-dominant alphanumeric
alphay	row-dominant alphanumeric
xy	combine column (x) and row(y) numbers

‘xy’ adds leading zeros as needed to give a string of constant length with no blanks.

make.circle generates coordinates for n traps in a circle centred on originxy. If spacing is specified then it overrides the radius setting; the radius is adjusted to provide the requested straightline distance between adjacent detectors. Traps are numbered from the trap due east of the origin, either clockwise or anticlockwise as set by IDclockwise.

Polygon vertices may be specified with x and y in the case of a single polygon, or as polylist for one or more polygons. Each component of polylist is a dataframe with columns ‘x’ and ‘y’. polylist takes precedence. make.poly automatically closes the polygon by repeating the first vertex if the first and last vertices differ.

Transects are defined by a sequence of vertices as for polygons, except that they are not closed.

make.telemetry builds a simple traps object for the 'telemetry' detector type. The attribute 'telemetrytype' is set to "independent".

Specialised functions for arrays using a triangular grid are described separately (make.tri, clip.hex).

Value

An object of class traps comprising a data frame of x- and y-coordinates, the detector type ("single", "multi", or "proximity" etc.), and possibly other attributes.

Note

Several methods are provided for manipulating detector arrays - see traps.

References

Efford, M. G. (2012) DENSITY 5.0: software for spatially explicit capture–recapture. Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand. https://www.otago.ac.nz/density/.

Efford, M. G., Borchers D. L. and Byrom, A. E. (2009) Density estimation by spatially explicit capture-recapture: likelihood-based methods. In: D. L. Thomson, E. G. Cooch and M. J. Conroy (eds) Modeling Demographic Processes in Marked Populations. Springer, New York. Pp. 255–269.

See Also

read.traps,detector, trap.builder,make.systematic, print.traps, plot.traps, traps, make.tri, addTelemetry

Examples

demo.traps <- make.grid()
plot(demo.traps)

## compare numbering schemes
par (mfrow = c(2,4), mar = c(1,1,1,1), xpd = TRUE)
for (id in c("numx", "numy", "alphax", "alphay", "numxb", 
    "numyb"))
{
    temptrap <- make.grid(nx = 7, ny = 5, ID = id)
    plot (temptrap, border = 10, label = TRUE, offset = 7, 
        gridl = FALSE)
}

temptrap <- make.grid(nx = 7, ny = 5, hollow = TRUE)
plot (temptrap, border = 10, label = TRUE, gridl = FALSE)

plot(make.circle(n = 20, spacing = 30), label = TRUE, offset = 9)
summary(make.circle(n = 20, spacing = 30))

## jitter locations randomly within grid square
## and plot over `mask'
# see also ?gridCells

tr0 <- tr <- make.grid(nx = 7, ny = 7, spacing = 30)
tr[] <- jitter(unlist(tr), amount = spacing(tr)/2)
plot(as.mask(tr0), dots = FALSE, mesh = 'white')
plot(tr, add = TRUE)

secr documentation built on Nov. 4, 2024, 9:06 a.m.