Description Usage Arguments Details Value Note Examples
Calculate log likelihood over a grid of values of two beta parameters from a fitted secr model and optionally make an approximate contour plot of the log likelihood surface.
1 2 3 
object 

betapar 
character vector giving the names of two beta parameters 
xval 
vector of numeric values for xdimension of grid 
yval 
vector of numeric values for ydimension 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 (inverselink) scale. 
plot 
logical. If TRUE a contour plot is produced 
plotfitted 
logical. If TRUE the MLE from 
ncores 
integer number of cores available for parallel processing 
... 
other arguments passed to 
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.
If ncores > 1
the parallel package is used to create
processes on multiple cores (see Parallel for more).
Invisibly returns a matrix of the log likelihood evaluated at each grid point
LLsurface.secr
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.
The contours are approximate because they rely on interpolation. See Examples for a more reliable way to compare the likelihood at the MLE with nearby points on the surface.
1 2 3 4 5 6 7 8 9 10 11 12  ## Not run:
LLsurface.secr(secrdemo.CL, xval = seq(0.16,0.40,0.02),
yval = 25:35, nlevels = 20)
## now verify MLE
## click on MLE and apparent `peak'
xy < locator(2)
temp < LLsurface.secr(secrdemo.CL, xval = xy$x,
yval = xy$y, plot = FALSE)
temp
## End(Not run)

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