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#' Calculate the phenotypes covariance matrix Sigma
#'
#' @param Vg d by d genetic covariance matrix for the d phenotypes
#' @param Ve d by d error covariance matrix for the d phenotypes
#' @param kinship optional n by n kinship matrix. if NULL, Vg is not used.
#' @param n_mouse number of subjects
#' @export
#' @return dn by dn covariance matrix
calc_Sigma <- function(Vg, Ve, kinship = NULL, n_mouse = nrow(kinship)) {
if (!is.null(kinship)){
out <- Vg %x% kinship + Ve %x% diag(n_mouse)
}
if (is.null(kinship)){
out <- Ve %x% diag(n_mouse) # n_mouse must be specified when kinship = NULL
}
return(out)
}
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