R/hyperpar.R

In inbo/INLA: Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations

## Export: inla.hyperpar

##!\name{inla.hyperpar}
##!\alias{inla.hyperpar}
##!\alias{hyperpar.inla}
##!
##!\title{Improved estimates for the hyperparameters}
##!\description{
##! Improve the estimates of the  posterior marginals
##! for the hyperparameters of
##! the model using the grid integration strategy.
##!}
##!\usage{
##! inla.hyperpar(
##!         result,
##!         skip.configurations = TRUE,
##!         verbose = FALSE,
##!         dz = 0.75,
##!         diff.logdens = 15,
##!         h = NULL,
##!         restart = FALSE,
##!         quantiles = NULL, 
##!         keep = FALSE)
##!}
##!
##!\arguments{

`inla.hyperpar` =
    function(

        ##!\item{result}{An object of class
        ##!\code{inla},  ie a result of a call to
        ##!\code{inla()}}
        result,

        ##!\item{skip.configurations}{ A boolean variable; skip
        ##!configurations if the values at the main axis are to
        ##!small. (Default TRUE)}
        skip.configurations = TRUE,

        ##!\item{verbose}{Boolean indicating wheather the inla
        ##!program should run in a verbose mode.}
        verbose = FALSE,

        ##!\item{dz}{Step length in the standardized scale used
        ##!in the construction of the grid, default 0.75.}
        dz = 0.75,

        ##!\item{diff.logdens}{The difference of the
        ##!log.density for the hyperpameters to stop numerical
        ##!integration using int.strategy='grid'.  Default 15}
        diff.logdens = 15,

        ##!\item{h}{The step-length for the gradient
        ##!calculations for the hyperparameters. Default 0.01.}
        h = NULL,

        ##!\item{restart}{A boolean defining wheather the
        ##!optimizer should start again to ind the mode or if it
        ##!should use the mode contained in the \code{object}}
        restart = FALSE,

        ##!\item{quantiles}{A vector of quantiles,
        ##!to compute for each posterior marginal.}
        quantiles = NULL, 

        ##!\item{keep}{A boolean variable indicating the
        ##!working files (ini file, data files and results files)
        ##!should be kept}
        keep = FALSE
        )
{
    ##!}
    ##!\value{
    ##!The object returned is the same as  \code{object} but the
    ##!estimates of the hyperparameters are replaced by improved estimates.}
    ##!\references{
    ##!See the references in \code{inla}}
    ##!\author{Havard Rue \email{hrue@r-inla.org}}
    ##!\note{This function might take a long time or if the number of
    ##!hyperparameters in the model is large. If it complains and says \code{I cannot get enough memory},
    ##!try to increase the value of the argument \code{dz} or decrease \code{diff.logdens}.}
    ##!\seealso{\code{\link{inla}}}

    result.tmp = result
    stopifnot(class(result.tmp) == "inla")

    ## only arguments that we need to change,  is changed...
    result.tmp$.args$quantiles = inla.ifelse(missing(quantiles) || is.null(quantiles), result.tmp$.args$quantiles, quantiles)
    result.tmp$.args$verbose = verbose
    result.tmp$.args$only.hyperparam = TRUE
    result.tmp$.args$keep = keep

    result.tmp$.args$control.compute$hyperpar=TRUE
    result.tmp$.args$control.compute$return.marginals = TRUE
    result.tmp$.args$control.compute$dic = FALSE
    result.tmp$.args$control.compute$mlik = TRUE
    result.tmp$.args$control.compute$cpo = FALSE
    result.tmp$.args$control.compute$po = FALSE
    result.tmp$.args$control.compute$q = FALSE
    result.tmp$.args$control.compute$graph = FALSE
    
    result.tmp$.args$control.predictor$compute = FALSE

    result.tmp$.args$control.inla$int.strategy = "grid"
    result.tmp$.args$control.inla$strategy = "gaussian"
    result.tmp$.args$control.inla$h = inla.ifelse(is.null(h), result.tmp$.args$control.inla$h, h)
    result.tmp$.args$control.inla$dz = dz
    result.tmp$.args$control.inla$diff.logdens = diff.logdens
    result.tmp$.args$control.inla$print.joint.hyper = TRUE
    result.tmp$.args$control.inla$force.diagonal = TRUE
    result.tmp$.args$control.inla$adjust.weights = FALSE
    
    result.tmp$.args$control.results$return.marginals.random = FALSE
    result.tmp$.args$control.results$return.marginals.predictor = FALSE
    
    result.tmp$.args$control.mode$result = result.tmp
    result.tmp$.args$control.mode$restart = restart
    
    ## cannot use this function with inla.call="submit", if so, then
    ## replace this into inla.call="remote"
    result.tmp$.args$inla.call = sub("inla.submit", "inla.remote", result.tmp$.args$inla.call)
        
    ## call itself
    result.tmp = inla.rerun(result.tmp, plain = TRUE)
    
    ## these are the entries that we want to replace
    replace.names = c("summary.hyperpar", "marginals.hyperpar", "internal.marginals.hyperpar",
        "internal.summary.hyperpar", "joint.hyper", "mlik", "version", "cpu.used")

    for (nm in replace.names) {
        idx.result = which(names(result) == nm)
        idx.result.tmp = which(names(result.tmp) == nm)
        if (length(idx.result) > 0 && length(idx.result.tmp) > 0) {
            result[[idx.result]] = result.tmp[[idx.result.tmp]]
        }
    }
    ## from $misc, we only want this one.
    result$misc$configs = result.tmp$misc$configs

    return(result)
}