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##' @title Variance-covariance matrix of the estimated parameters for joint models
##' @name vcov
##' @aliases vcov.JMMLSM
##' @description Extract variance-covariance matrix for joint models.
##' @param object an object inheriting from class \code{JMMLSM}.
##' @param ... further arguments passed to or from other methods.
##' @return a matrix of variance covariance of all parameter estimates.
##' @author Shanpeng Li \email{lishanpeng0913@ucla.edu}
##' @seealso \code{\link{JMMLSM}}
##' @export
##'
vcov.JMMLSM <- function(object, ...) {
if (!inherits(object, "JMMLSM"))
stop("Use only with 'JMMLSM' objects.\n")
variance.formula <- as.formula(paste("", object$LongitudinalSubmodelvariance[3], sep = "~"))
getdum <- getdummy(long.formula = object$LongitudinalSubmodelmean,
surv.formula = object$SurvivalSubmodel,
variance.formula = variance.formula,
random = object$random, ydata = object$ydata, cdata = object$cdata)
random <- all.vars(object$random)
vcov <- as.data.frame(object$vcov)
long <- names(object$beta)
tau <- names(object$tau)
survival <- names(object$gamma1)
survival1 <- paste0("T.", survival)
long <- paste0("Ymean.", long)
tau <- paste0("Yvariance.", tau)
p1a <- length(object$alpha1) + 1
alpha1 <- rep("T.asso:", p1a-1)
nu1 <- "T.asso.Residual_1:"
sig <- "Sig"
sig <- rep(sig, p1a*(p1a+1)/2)
for (i in 1:p1a) sig[i] <- paste0(sig[i], i, i)
if (p1a == 2) {
sig[p1a+1] <- paste0(sig[p1a+1], "12")
alpha1 <- paste0(alpha1, "(Intercept)_1")
} else {
sig[p1a+1] <- paste0(sig[p1a+1], "12")
sig[p1a+2] <- paste0(sig[p1a+2], "23")
sig[p1a+3] <- paste0(sig[p1a+3], "13")
alpha1[1] <- paste0(alpha1[1], "(Intercept)_1")
alpha1[2] <- paste0(alpha1[2], random[1], "_1")
}
if (object$CompetingRisk) {
survival <- names(object$gamma2)
survival2 <- paste0("T.", survival)
alpha2 <- rep("T.asso:", p1a-1)
nu2 <- "T.asso.Residual_2:"
if (p1a == 2) {
alpha2 <- paste0(alpha2, "(Intercept)_2")
} else {
alpha2[1] <- paste0(alpha2[1], "(Intercept)_2")
alpha2[2] <- paste0(alpha2[2], random[1], "_2")
}
colnames(vcov) <- c(long, tau, survival1, survival2, alpha1, alpha2, nu1, nu2, sig)
rownames(vcov) <- c(long, tau, survival1, survival2, alpha1, alpha2, nu1, nu2, sig)
} else {
colnames(vcov) <- c(long, tau, survival1, alpha1, nu1, sig)
rownames(vcov) <- c(long, tau, survival1, alpha1, nu1, sig)
}
vcov
}
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