LLsurface | R Documentation |
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.
## 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, ...)
object |
|
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 |
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.
The value of ncores
is passed to openCR.fit
.
Invisibly returns a matrix of the log likelihood evaluated at each grid point
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.
LLsurface.secr
# not yet
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