cov.wt <- function(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE) { if (is.data.frame(x)) x <- as.matrix(x) else if (!is.matrix(x)) stop("x must be a matrix or a data frame") if (!all(is.finite(x))) stop("x must contain finite values only") n <- nrow(x) if (with.wt <- !missing(wt)) { if (length(wt) != n) stop("length of wt must equal the number of rows in x") if (any(wt < 0) || (s <- sum(wt)) == 0) stop("weights must be non-negative and not all zero") wt <- wt / s } if (is.logical(center)) { center <- if (center) apply(wt * x, 2, sum) else 0 } else { if (length(center) != ncol(x)) stop("length of center must equal the number of columns in x") } x <- sqrt(wt) * sweep(x, 2, center) cov <- (t(x) %*% x) / (1 - sum(wt^2)) y <- list(cov = cov, center = center, n.obs = n) if (with.wt) y <- c(y, wt = wt) if (cor) { sdinv <- diag(1 / sqrt(diag(cov))) y <- c(y, cor = sdinv %*% cov %*% sdinv) } y }