Nothing
#####################################################################################
## Author: Daniel Sabanes Bove [daniel *.* sabanesbove *a*t* ifspm *.* uzh *.* ch]
## Project: Bayesian FPs for GLMs
##
## Time-stamp: <[GlmBayesMfp-methods.R] by DSB Fre 07/12/2012 11:10 (CET)>
##
## Description:
## Additional convenience methods for GlmBayesMfp class objects.
##
## History:
## 12/02/2010 modify from bfp package
## 15/03/2010 adapt print.GlmBayesMfp to new S4 gPrior element
## 07/12/2012 change default for freq in as.data.frame.GlmBayesMfp
#####################################################################################
##' @include posteriors.R
{}
##' Extract method for GlmBayesMfp objects
##'
##' Extract a subset of models from a \code{\link{GlmBayesMfp}} object.
##'
##'
##' @method [ GlmBayesMfp
##' @param x valid \code{\link{GlmBayesMfp}} object
##' @param \dots transports the indexes of the models
##' @return The subsetted object.
##' @export
##'
##' @name Extract.GlmBayesMfp
##' @aliases Extract.GlmBayesMfp [.GlmBayesMfp
##' @keywords methods
##' @seealso \code{\link{glmBayesMfp}}
##' @author Daniel Sabanes Bove \email{daniel.sabanesbove@@ifspm.uzh.ch}
'[.GlmBayesMfp' <- function (x, ...)
{
y <- NextMethod("[")
mostattributes (y) <- attributes (x)
names (y) <- names (x)[...]
class(y) <- oldClass(x)
y
}
##' Print a GlmBayesMfp object.
##'
##'
##' @method print GlmBayesMfp
##' @param x valid \code{\link{GlmBayesMfp}} object
##' @param \dots unused
##' @return Only used for its side effect
##'
##' @export
##'
##' @keywords methods
##' @seealso \code{\link{glmBayesMfp}}
##' @author Daniel Sabanes Bove \email{daniel.sabanesbove@@ifspm.uzh.ch}
print.GlmBayesMfp <- function (x, ...)
{
cat ("------------------------------ GlmBayesMfp-Output ------------------------------\n")
cat (length (x), "multivariable fractional polynomial model(s) of total (visited/cached)",
attr (x, "numVisited"), "for following covariates:\n\n")
cat ("fixed: ", paste(attr (x, "termNames")$fixed, collapse = ", "), "\n")
cat ("uncertain fixed form: ", paste(attr (x, "termNames")$uc, collapse = ", "), "\n")
cat ("fractional polynomial:", paste(attr (x, "termNames")$bfp, collapse = ", "), "\n")
pr <- attr (x, "priorSpecs")
cat ("\nPrior for g was,", class(pr$gPrior),
"\nand a ", pr$modelPrior, " prior on the model space was used.",
"\n")
}
##' Convert a GlmBayesMfp object into a data frame
##'
##'
##' @method as.data.frame GlmBayesMfp
##' @param x valid \code{\link{GlmBayesMfp}} object
##' @param row.names optional rownames (default is to keep the names of the
##' \code{\link{GlmBayesMfp}} list)
##' @param \dots unused
##' @param freq should empirical frequencies of the models in the sampling
##' path be given? (not default)
##' @return The data frame with the following columns:
##' \describe{
##' \item{posterior}{the posterior model probabilities}
##' \item{logMargLik}{the log marginal likelihood of the models}
##' \item{logPrior}{the log prior probabilities of the models}
##' }
##' Additionally, for each uncertain fixed form covariates a column with the inclusion
##' status, and for each fractional polynomial a column with the powers are returned.
##' @seealso \code{\link{glmBayesMfp}}
##' @keywords methods
##' @author Daniel Sabanes Bove \email{daniel.sabanesbove@@ifspm.uzh.ch}
##'
##' @export
as.data.frame.GlmBayesMfp <- function (x,
row.names = NULL,
...,
freq = FALSE
)
{
## posterior probabilites:
ret <- data.frame (posterior=
posteriors(x, type="normalized"))
if (! is.null(attr(x, "searchConfig")$chainlength) &&
freq)
ret$frequency <- posteriors (x, type="sampling")
## row names
row.names (ret) <-
if(! is.null(row.names))
row.names
else
names(x)
## log marginal likelihood and log prior
ret$logMargLik <- logMargLiks(x)
ret$logPrior <- logPriors(x)
## fixed form covariates:
for (i in seq_along (fixNames <- attr (x, "termNames")$fixed[-1]))
{
ret[[fixNames[i]]] <- sapply (x,
function(one)
i %in% one$configuration$fixTerms)
}
## uncertain fixed form covariates:
for (i in seq_along (ucNames <- attr (x, "termNames")$uc))
{
ret[[ucNames[i]]] <- sapply (x,
function(one)
i %in% one$configuration$ucTerms)
}
## fractional polynomial:
for (fpName in attr (x, "termNames")$bfp)
{
ret[[fpName]] <- sapply (x,
function(one)
paste(one$configuration$powers[[fpName]],
collapse = ", "))
}
ret
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.