esaplotsecr: Mask Buffer Diagnostic Plot (internal)

In secr: Spatially Explicit Capture-Recapture

Mask Buffer Diagnostic Plot (internal)

Description

Internal function used to plot effective sampling area (Borchers and Efford 2008) as a function of increasing buffer width given an ‘secr’ object

Usage

esa.plot.secr (object, max.buffer = NULL, max.mask = NULL,
    thin = 0.1, poly = NULL, poly.habitat = TRUE, session = 1, plt = TRUE, 
    type = "density", add = FALSE, overlay = TRUE, conditional = FALSE, ...)

Arguments

object	secr object output from secr.fit
max.buffer	maximum width of buffer in metres
max.mask	mask object
thin	proportion of mask points to retain in plot and output
poly	matrix of two columns interpreted as the x and y coordinates of a bounding polygon (optional)
poly.habitat	logical as in make.mask
session	vector of session indices (used if object spans multiple sessions)
plt	logical to plot results
type	character; see esa.plot
add	logical to add line to an existing plot
overlay	logical; if TRUE then automatically add = TRUE for plots after the first
conditional	logical; see esa.plot
...	graphical arguments passed to plot() and lines()

Details

esa.plot.secr provides a wrapper for esa.plot that is called internally from esa.plot when it is presented with an secr object. Arguments of esa.plot such as detectfn are inferred from the fitted model.

If max.mask is not specified then a maximal mask of type ‘trapbuffer’ is constructed using max.buffer and the spacing of the mask in object. In this case, if max.buffer is not specified then it is set either to the width of the existing plot (add = TRUE) or to 10 x sigma-hat from the fitted model in object (add = FALSE).

Value

see esa.plot

See Also

esa.plot, mask, pdot, make.mask, mask.check, Detection functions

secr documentation built on Oct. 18, 2023, 1:07 a.m.