LLsurface: Plot Likelihood Surface

In openCR: Open Population Capture-Recapture

Plot Likelihood Surface

Description

Calculate log likelihood over a grid of values of two beta parameters from a fitted openCR model and optionally make an approximate contour plot of the log likelihood surface.

This is a method for the generic function LLsurface defined in secr.

Usage

## S3 method for class 'openCR'
LLsurface(object, betapar = c("phi", "sigma"), xval = NULL, yval = NULL, 
   centre = NULL, realscale = TRUE, plot = TRUE, plotfitted = TRUE, ncores = NULL, ...)

Arguments

object	openCR object output from openCR.fit
betapar	character vector giving the names of two beta parameters
xval	vector of numeric values for x-dimension of grid
yval	vector of numeric values for y-dimension of grid
centre	vector of central values for all beta parameters
realscale	logical. If TRUE input and output of x and y is on the untransformed (inverse-link) scale.
plot	logical. If TRUE a contour plot is produced
plotfitted	logical. If TRUE the MLE from object is shown on the plot (+)
ncores	integer number of cores available for parallel processing
...	other arguments passed to contour

Details

centre is set by default to the fitted values of the beta parameters in object. This has the effect of holding parameters other than those in betapar at their fitted values.

If xval or yval is not provided then 11 values are set at equal spacing between 0.8 and 1.2 times the values in centre (on the ‘real’ scale if realscale = TRUE and on the ‘beta’ scale otherwise).

Contour plots may be customized by passing graphical parameters through the ... argument.

The value of ncores is passed to openCR.fit.

Value

Invisibly returns a matrix of the log likelihood evaluated at each grid point

Note

LLsurface.openCR works for named ‘beta’ parameters rather than ‘real’ parameters. The default realscale = TRUE only works for beta parameters that share the name of the real parameter to which they relate i.e. the beta parameter for the base level of the real parameter. This is because link functions are defined for real parameters not beta parameters.

Handling of multiple threads was changed in version 1.5.0 to align with LLsurface.secr.

The contours are approximate because they rely on interpolation.

See Also

LLsurface.secr

Examples

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openCR documentation built on Sept. 25, 2022, 5:06 p.m.