secr (version 2.5.0)

suggest.buffer: Mask Buffer Width

Description

Determines a suitable buffer width for an integration mask. The `buffer' in question defines a concave polygon around a detector array constructed using make.mask with type = "trapbuffer". The method relies on an approximation to the bias of maximum likelihood density estimates (M. Efford unpubl).

Usage

suggest.buffer(object, detectfn = NULL, detectpar = NULL, 
    noccasions = NULL, ignoreusage = FALSE, RBtarget = 0.001,
    interval = NULL, binomN = NULL, ...)

bias.D (buffer, traps, detectfn, detectpar, noccasions, binomN = NULL,
    control = NULL)

Arguments

object

`secr', `traps' or `capthist' object

detectfn

integer code or character string for shape of detection function 0 = halfnormal etc. -- see detectfn

detectpar

list of values for named parameters of detection function -- see detectpar

noccasions

number of sampling occasions

ignoreusage

logical for whether to discard usage information from traps(capthist)

RBtarget

numeric target for relative bias of density estimate

interval

a vector containing the end-points of the interval to be searched

binomN

integer code for distribution of counts (see secr.fit)

...

other argument(s) passed to bias.D

buffer

vector of buffer widths

traps

`traps' object

control

list of mostly obscure numerical settings (see Details)

Value

• suggest.buffer returns a scalar value for the suggested buffer width in metres, or a vector of such values in the case of a multi-session object. bias.D returns a dataframe with columns buffer and RB.D (approximate bias of density estimate using finite buffer width, relative to estimate with infinite buffer).

Details

The basic input style of suggest.buffer uses a `traps' object and a detection model specified by `detectpar', `detectfn' and `noccasions', plus a target relative bias (RB). A numerical search is conducted for the buffer width that is predicted to deliver the requested RB. If interval is omitted it defaults to (1, 100S) where S is the spatial scale of the detection function (usually detectpar$sigma). An error is reported if the required buffer width is not within interval. This often happens with heavy-tailed detection functions (e.g., hazard-rate): choose another function, a larger RBtarget or a wider interval. Convenient alternative input styles are --

• secrobject containing a fitted model. Values of `traps', `detectpar', `detectfn' and `noccasions' are extracted fromobjectand any values supplied for these arguments are ignored.
• capthistobject containing raw data. Ifdetectparis not supplied thenautoiniis used to get `quick and dirty' values ofg0andsigmafor a halfnormal detection function.noccasionsis ignored.autoinitends to underestimatesigma, and the resulting buffer also tends to be too small.

bias.D is called internally by suggest.buffer.

See Also

mask, make.mask, mask.check, esa.plot

Examples

temptraps <- make.grid()
detpar <-  list(g0 = 0.2, sigma = 25)
suggest.buffer(temptraps, "halfnormal", detpar, 5)

RB <- bias.D(50:150, temptraps, "halfnormal", detpar, 5)
plot(RB)

detpar <-  list(g0 = 0.2, sigma = 25, z=5)
RB <- bias.D(50:150, temptraps, "hazard rate", detpar, 5)
lines(RB)

## compare to esa plot
esa.plot (temptraps, max.buffer = 150, spacing = 4, detectfn = 0,
  detectpar = detpar, noccasions = 5, as.density = F)

## compare detection histories and fitted model as 
suggest.buffer(ovenCH)
suggest.buffer(ovenbird.model.1)