expected.n {secr}

R Documentation

Expected Number of Individuals

Description

Computes the expected number of individuals detected across a detector layout or at each cluster of detectors.

Usage

expected.n(object, session = NULL, group = NULL, bycluster
    = FALSE, splitmask = FALSE, ncores = NULL)

Arguments

object	secr object output from secr.fit
session	character session vector
group	group – for future use
bycluster	logical to output the expected number for clusters of detectors rather than whole array
splitmask	logical for computation method (see Details)
ncores	integer number of threads to be used for parallel processing

Details

The expected number of individuals detected is E(n) = \int p.(X) D(X) dX where the integration is a summation over object$mask. p.(X) is the probability an individual at X will be detected at least once either on the whole detector layout (bycluster = FALSE) or on the detectors in a single cluster (see pdot for more on p.). D(X) is the expected density at X, given the model. D(X) is constant (i.e. density surface flat) if object$CL == TRUE or object$model$D == ~1, and for some other possible models.

If the bycluster option is selected and detectors are not, in fact, assigned to clusters then each detector will be treated as a cluster, with a warning.

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

By default, a full habitat mask is used for each cluster. This is the more robust option. Alternatively, the mask may be split into subregions defined by the cells closest to each cluster.

The calculation takes account of any fitted continuous model for spatial variation in density (note Warning).

Value

The expected count (bycluster = FALSE) or a vector of expected counts, one per cluster. For multi-session data, a list of such vectors.

Warning

This function changed slightly between 2.1.0 and 2.1.1, and now performs as indicated here when bycluster = TRUE and clusters are not specified.

Clusters of detectors are assumed to be independent (always true with detector types ‘proximity’, ‘count’ etc.). The computed E(n) does not apply when there is competition among clusters of detectors.

The prediction of density at present considers only the base level of density covariates, such as cell-specific habitat variables.

See Also

region.N

Examples

## Not run: 

expected.n(secrdemo.0)
expected.n(secrdemo.0, bycluster = TRUE)
expected.n(ovenbird.model.D)

## Clustered design
mini <- make.grid(nx = 3, ny = 3, spacing = 50, detector =
    "proximity")
tempgrids <- trap.builder (cluster = mini , method = "all",
    frame = expand.grid(x = seq(1000, 9000, 2000),
    y = seq(1000, 9000, 2000)), plt = TRUE)
capt <- sim.capthist(tempgrids, popn = list(D = 2))
tempmask <- make.mask(tempgrids, buffer = 100,
    type = "clusterbuffer")
fit <- secr.fit(capt, mask = tempmask, trace = FALSE)
En <- expected.n(fit, bycluster = TRUE)

## GoF or overdispersion statistic
p <- length(fit$fit$par)
y <- cluster.counts(capt)
## scaled by n-p
sum((y - En)^2 / En) / (length(En)-p)
sum((y - En)^2 / En) / sum(y/En)


## End(Not run)

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