fxTotal: Activity Centres of Detected and Undetected Animals

Description

The summed probability densities of both observed and unobserved individuals are computed for a fitted model and dataset.

Function fx.total was replaced by method fxTotal in secr 5.0.0.

Usage

# S3 method for secr
fxTotal(object, sessnum = 1, mask = NULL, ncores = NULL, ...)

Value

An object of class `Dsurface' (a variety of mask) with a `covariates' attribute that is a dataframe with columns --

D.fx: sum of fxi over all detected individuals
D.nc: expected density of undetected (`not caught') individuals
D.sum: sum of D.fx and D.nc

All densities are in animals per hectare (the `scale' argument of plot.Dsurface allows the units to be varied later).

Arguments

object: a fitted secr model
sessnum: session number if object$capthist spans multiple sessions
mask: x- and y- coordinates of points at which density will be computed
ncores: integer number of threads to be used for parallel processing
...: other arguments passed to detectpar and thence to predict.secr

Details

This function calls fxi for each detected animal and overlays the results to obtain a summed probability density surface D.fx for the locations of the home-range centres of detected individuals.

A separate calculation using pdot provides the expected spatial distribution of undetected animals, as another density surface: crudely, D.nc(X) = D(X) * ( 1 -- pdot(X)).

The pointwise sum of the two surfaces is sometimes used to represent the spatial distrbution of the population, but see Notes.

Setting ncores = NULL uses the existing value from the environment variable RCPP_PARALLEL_NUM_THREADS (see setNumThreads).

References

Borchers, D. L. and Efford, M. G. (2008) Spatially explicit maximum likelihood methods for capture--recapture studies. Biometrics 64, 377--385.

Examples

Run this code


if (FALSE) {

tmp <- fxTotal(secrdemo.0)

## to plot we must name one of the covariates:
## the Dsurface default 'D.0' causes an error 

plot(tmp, covariate = 'D.sum', col = terrain.colors(16),
   plottype = 'shaded')
plot(tmp, covariate = 'D.sum', col = 'white', add = TRUE,
   plottype = 'contour')
if (interactive()) {
    spotHeight(tmp, prefix = 'D.sum')
}

fxsurface <- fxTotal(ovenbird.model.D, sessnum = 3)
plot(fxsurface, covariate = 'D.sum')

}

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