Refine estimates iteratively.

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Description

This is a generic function with currently methods for SLik and SLikp objects (as produced by MSL). Depending on the value of its newsimuls argument, and on whether the function used to generate empirical distributions can be called by R, it (1) defines new parameters points and/or (2) infers their summary likelihood or tail probabilities for each parameter point independently, adds the inferred values results as input for refined inference of likelihood or P-value response surface, and provides new point estimates and confidence intervals.

Usage

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## S3 method for class 'SLik'
refine(object,...)


## Default S3 method:
refine(object, surfaceData, maxit = 1, n = NULL, 
            useEI = list(max=TRUE,profileCI=TRUE,rawCI=FALSE), 
            newsimuls = NULL, useCI = TRUE, level = 0.95, 
            verbose = list(most=interactive(),movie=FALSE),
            precision = Infusion.getOption("precision"),
            method,...)

Arguments

object

an SLik object

surfaceData

A data.frame with attributes, usually taken from the object and thus not specified by user, usable as input for infer_surface.

maxit

Maximum number of iterative refinements (see also precision argument)

n

A number of parameter points (excluding replicates and confidence interval points), which likelihood should be computed (see n argument of sample_volume)

useEI

Cf this argument in rparam

newsimuls

For the SLik_j method, a matrix or data frame, with the same parameters and summary statistics as the data of the original infer_SLik_joint call.

For other methods, a list of simulation of distributions of summary statistics, in the same format as for link{add_simulation}. If no such list is provided (i.e., if newsimuls remains NULL), the attr(object$logLs,"Simulate") function is used (it is inherited from the Simulate argument of add_simulation through the initial sequence of calls of functions add_simulation, infer_logLs or infer_tailp, and infer_surface). If no such function is available, then this function returns parameters for which new distribution should be provided by the user.

useCI

whether to include parameter points near the inferred confidence interval points in the set of points which likelihood should be computed

level

Intended coverage of confidence intervals

verbose

A list as shown by the default, or simply a vector of booleans, indicating respectively whether to display (1) some information about progress and results; (2) a plot of a the likelihood surface, if a one- or two-parameters surface is inferred. verbose$movie controls whether such plots are produced for all iterations. verbose$most controls other verbosity, including whether a final plot is produced.

precision

Requested local precision of surface estimation, in terms of prediction variance of both the maximum summary log-likelihood and the likelihood ratio at any CI bound available. Iterations will stop when either maxit is reached, or this precision is reached for these MSEs. A given precision on the CI bounds themselves might seem more interesting, but is not well specified by a single precision parameter if the parameters are on widely different scales.

method

(A vector of) suggested method(s) for estimation of smoothing parameters (see method argument of infer_surface). The ith element of the vector is used in the ith iteration, if available; otherwise the last element is used. This argument is not always heeded, in that REML may be used if the suggested method is GCV but it appears to perform poorly. The default for SLikp objects is PQL; for SLik objects it is "REML".

...

further arguments passed to or from other methods. refine passes these arguments to the plot method suitable for the object.

Value

An updated SLik or SLik_j object.

Examples

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## see main documentation page for the package