update document and fix bugs when use psych engine (18f05cde) · Commits · github_fork / LinkET

R/correlate.R

+14 −6

Original line number	Diff line number	Diff line
		@@ -27,15 +27,21 @@
		#' correlate(m1, m2)
		#'
		#' ## adjust p value
		#' correlate(m1, m2, cor.test = TRUE, adjust = TRUE)
		#' correlate(m1, m2, adjust = TRUE)
		#'
		#' ## fast compute correlation
		#' ## other package engine
		#' \dontrun{
		#' require(WGCNA)
		#' fast_correlate(m1, m2)
		#' ## use psych engine
		#' correlate(m1, engine = "psych")
		#'
		#' require(picante)
		#' fast_correlate2(m1)
		#' ## use Hmisc engine
		#' correlate(m1, engine = "Hmisc")
		#'
		#' ## use WGCNA engine
		#' correlate(m1, m2, engine = "WGCNA")
		#'
		#' ## use picante engine
		#' correlate(m1, engine = "picante")
		#' }
		#' @seealso \code{\link[stats]{cor}}, \code{\link[stats]{cor.test}}.
		#' @author Hou Yun
		@@ -100,6 +106,8 @@ correlate <- function(x,
		}
		} else {
		corr.test <- get_function("psych", "corr.test")
		x <- as.data.frame(x)
		y <- if (is.null(y)) y else as.data.frame(y)
		out <- as_correlate(corr.test(x = x,
		y = y,
		use = if (use == "everything") "complete" else "pairwise",

+12 −6

Original line number	Diff line number	Diff line
		@@ -71,15 +71,21 @@ m2 <- matrix(rnorm(60), nrow = 10)
		correlate(m1, m2)

		## adjust p value
		correlate(m1, m2, cor.test = TRUE, adjust = TRUE)
		correlate(m1, m2, adjust = TRUE)

		## fast compute correlation
		## other package engine
		\dontrun{
		require(WGCNA)
		fast_correlate(m1, m2)
		## use psych engine
		correlate(m1, engine = "psych")

		require(picante)
		fast_correlate2(m1)
		## use Hmisc engine
		correlate(m1, engine = "Hmisc")

		## use WGCNA engine
		correlate(m1, m2, engine = "WGCNA")

		## use picante engine
		correlate(m1, engine = "picante")
		}
		m <- correlate(mtcars, cor.test = TRUE)
		print(m)