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#' Variance-covariance of the estimates
#'
#' This function provides the variance-covariance matrix of the estimates. vcov
#' is an alias for it.
#'
#'
#' @param x an object of class \code{hlme}, \code{lcmm}, \code{multlcmm},
#' \code{Jointlcmm} or \code{mpjlcmm}
#' @return a matrix containing the variance-covariance of the estimates. For
#' the parameters of the matrix of variance-covariance of the random effects,
#' the Cholesky transformed parameters are considered so that VarCov provides
#' the covariance matrix of function \code{estimates} with cholesky=TRUE.
#' @author Cecile Proust-Lima, Viviane Philipps
#' @seealso \code{\link{estimates}}
#'
#' @export
#'
VarCov <- function(x)
{
if(missing(x)) stop("The argument x should be specified")
if (!inherits(x, c("hlme","lcmm","multlcmm","Jointlcmm","mpjlcmm","externX","externSurv"))) stop("use only with hlme, lcmm, multlcmm, Jointlcmm, mpjlcmm, externX or externSurv objects")
if(x$conv %in% c(1,2,3))
{
res <- matrix(0,length(x$best),length(x$best))
res[upper.tri(res,diag=TRUE)] <- x$V
res <- t(res)
res[upper.tri(res,diag=TRUE)] <- x$V
noms <- sub("varcov","cholesky",names(x$best))
colnames(res) <- noms
rownames(res) <- noms
}
else
{
res <- NA
cat("Output can not be produced since the program stopped abnormally. \n")
}
return(res)
}
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