delete upper and lower CI (9ba5d5e1) · Commits · github_fork / LinkET

R/correlate.R

+2 −27

Original line number	Diff line number	Diff line
		@@ -175,43 +175,21 @@ correlate <- function(x,
		m <- ncol(y)
		r <- cor(x, y, use = use, method = method)

		p <- lower_ci <- upper_ci <- matrix(NA, ncol = m, nrow = n)
		p <- matrix(NA, ncol = m, nrow = n, dimnames = list(rownames(r), colnames(r)))
		id <- expand.grid(1:n, 1:m)
		if (y_is_null) {
		id <- id[id$Var1 > id$Var2, , drop = FALSE]
		purrr::walk2(id$Var1, id$Var2, function(.idx, .idy) {
		tmp <- cor.test(x = x[ , .idx], y = y[ , .idy], method = method, ...)
		p[c(.idx, .idy), c(.idy, .idx)] <<- tmp$p.value
		if (method == "pearson") {
		if (nrow(x) > 3) {
		lower_ci[c(.idx, .idy), c(.idy, .idx)] <<- tmp$conf.int[1]
		upper_ci[c(.idx, .idy), c(.idy, .idx)] <<- tmp$conf.int[2]
		} else {
		warning("correlation test interval needs 4 observations at least.", call. = FALSE)
		}
		}
		})
		diag(p) <- 0
		if (method == "pearson") {
		diag(lower_ci) <- diag(upper_ci) <- 1
		}
		} else {
		purrr::walk2(id$Var1, id$Var2, function(.idx, .idy) {
		tmp <- cor.test(x = x[ , .idx], y = y[ , .idy], method = method, ...)
		p[.idx, .idy] <<- tmp$p.value
		if (method == "pearson") {
		if (nrow(x) > 3) {
		lower_ci[.idx, .idy] <<- tmp$conf.int[1]
		upper_ci[.idx, .idy] <<- tmp$conf.int[2]
		} else {
		warning("correlation test interval needs 4 observations at least.", call. = FALSE)
		}
		}
		})
		}

		lower_ci <- if (method == "pearson") lower_ci else NULL
		upper_ci <- if (method == "pearson") upper_ci else NULL
		if (isTRUE(adjust)) {
		adjust_method <- match.arg(adjust_method, p.adjust.methods)
		p[] <- p.adjust(p, adjust_method)
		@@ -220,10 +198,7 @@ correlate <- function(x,
		structure(
		.Data = list(
		r = r,
		p = p,
		lower_ci = lower_ci,
		upper_ci = upper_ci
		), class = "correlate"
		p = p), class = "correlate"
		)
		}

R/random-forest.R

+4 −4

File changed.

Contains only whitespace changes.

Admin message