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cov.mnp <- function(object, subset = NULL, ...) {
if (is.null(subset))
subset <- 1:nrow(object$param)
else if (max(subset) > nrow(object$param))
stop(paste("invalid input for `subset.' only", nrow(param), "draws are stored."))
p <- object$n.alt
n <- length(subset)
Sigma <- array(0, c(p-1, p-1, n))
param <- object$param
n.cov <- ncol(param) - p*(p-1)/2
cov <- param[,(n.cov+1):ncol(param)]
for (i in 1:n) {
count <- 1
for (j in 1:(p-1)) {
Sigma[j,j:(p-1),i] <- cov[subset[i],count:(count+p-j-1)]
count <- count + p - j
}
diag(Sigma[,,i]) <- diag(Sigma[,,i]/2)
Sigma[,,i] <- Sigma[,,i] + t(Sigma[,,i])
}
tmp <- list()
tmp[[1]] <- tmp[[2]] <- object$alt[-pmatch(object$base, object$alt)]
tmp[[3]] <- as.character(subset)
dimnames(Sigma) <- tmp
if (n > 1)
return(Sigma)
else
return(Sigma[,,1])
}
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