plot1Dprof  R Documentation 
These functions plot 1D and 2D profiles from an SLik object
plot1Dprof(object, pars=object$colTypes$fittedPars, type="logLR", gridSteps=21, xlabs=list(), ylab, scales=NULL, plotpar=list(pch=20), control=list(min=7.568353, shadow_col="grey70"), decorations = function(par) NULL, ...) plot2Dprof(object, pars=object$colTypes$fittedPars, type="logLR", gridSteps=17, xylabs=list(), main, scales=NULL, plotpar=list(pch=20), margefrac = 0, decorations = function(par1,par2) NULL, ... )
object 
An 
pars 
The parameters for which profiles will be computed. For 2D plots, all pairs of parameters in 
type 
Character: 
gridSteps 
The number of values (in each dimension for 2D plots) which likelihood should be computed. For 1D plots,

xlabs 
A list of alternative axis labels. The names of the list elements should be elements of 
xylabs 
Same as 
ylab 
Same as 
main 
Same as 
scales 
A named character vector, which controls ticks and tick labels on axes, so that these can be expressed as (say) the exponential of the parameter inferred in the SLik object.
For example if the likelihood of 
plotpar 
arguments for 
control 
Control of 
decorations 
A function with formals parameters as shown by the default (being parameters names represented as character strings), implementing graphic directives added to the plot. 
margefrac 
For development purposes, not documented. 
... 
Further arguments passed by another function. Currently these arguments are ignored. 
A "zoom"
plot shows only the top part of the profile, defined as points whose yvalues are above a threshold minusloglikelihood ratio control$min
, whose default is 7.568353, the 0.9999 pvalue threshold.
A "dual"
plot displays both the zoom, and a shadow graph showing the full profile. The dual plot is shown only when requested and if there are values above and below control$min
. The shadow curve color is given by control$shadow_col
.
Both functions return a list, which currently has a single element MSL_updated
which is a boolean indicating whether the summarylikelihood maximum (but not the intervals) has been recomputed.
if (Infusion.getOption("example_maxtime")>40) { data(densv) slik < infer_surface(densv) ## infer a loglikelihood surface slik < MSL(slik) ## find the maximum of the loglikelihood surface plot1Dprof(slik,pars="s2",gridSteps=40,xlabs=list(s2=expression(paste(sigma^2)))) }
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