secr (version 5.0.0)

pdot: Net Detection Probability

Description

Compute spatially explicit net probability of detection for individual(s) at given coordinates (pdot).

Usage

pdot(X, traps, detectfn = 0, detectpar = list(g0 = 0.2,
    sigma = 25, z = 1), noccasions = NULL, binomN = NULL,
    userdist = NULL, ncores = NULL) 
CVpdot(..., conditional = FALSE)

Value

For pdot, a vector of probabilities, one for each row in X.

For CVpdot, a named vector with elements `meanpdot' and `CVpdot'.

Arguments

X

vector or 2-column matrix of coordinates

traps

traps object

detectfn

integer code for detection function q.v.

detectpar

a named list giving a value for each parameter of detection function

noccasions

number of sampling intervals (occasions)

binomN

integer code for discrete distribution (see secr.fit)

userdist

user-defined distance function or matrix (see userdist)

ncores

integer number of threads

...

arguments passed to pdot

conditional

logical; if TRUE then computed mean and CV are conditional on detection

Details

If traps has a usage attribute then noccasions is set accordingly; otherwise it must be provided.

The probability computed is \(p.(\mathbf{X}) = 1 - \prod\limits _{k} \{1 - p_s(\mathbf{X},k)\}^{S}\) where the product is over the detectors in traps, excluding any not used on a particular occasion. The per-occasion detection function \(p_s\) is halfnormal (0) by default, and is assumed not to vary over the \(S\) occasions.

From 4.6.11, the detection parameters g0, lambda0 and sigma for point detectors may be detector- and occasion-specific. This is achieved by providing a vector of values that is replicated internally to fill a matrix with dimensions ntraps x noccasions (i.e. in trap order for occasion 1, then occasion 2 etc.)

For detection functions (10) and (11) the signal threshold `cutval' should be included in detectpar, e.g., detectpar = list(beta0 = 103, beta1 = -0.11, sdS = 2, cutval = 52.5).

The calculation is not valid for single-catch traps because \(p.(\mathbf{X})\) is reduced by competition between animals.

userdist cannot be set if `traps' is any of polygon, polygonX, transect or transectX. if userdist is a function requiring covariates or values of parameters `D' or `noneuc' then X must have a covariates attribute with the required columns.

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

CVpdot returns the expected mean and CV of pdot across the points listed in X, assuming uniform population density. X is usually a habitat mask. See Notes for details.

See Also

secr, make.mask, Detection functions, pdotContour, CV

Examples

if (FALSE) {

  temptrap <- make.grid()
  ## per-session detection probability for an individual centred
  ## at a corner trap. By default, noccasions = 5.
  pdot (c(0,0), temptrap, detectpar = list(g0 = 0.2, sigma = 25),
    noccasions = 5)
    
  msk <- make.mask(temptrap, buffer = 100)
  CVpdot(msk, temptrap, detectpar = list(g0 = 0.2, sigma = 25),
    noccasions = 5)
}