deprecat spec/env_dist_method params hardly (e14f1f91) · Commits · github_fork / LinkET

R/mantel-test.R

+12 −13

Original line number	Diff line number	Diff line
		@@ -15,10 +15,9 @@
		#' @param spec_dist NULL (default) or \code{dist_func()}.
		#' @param env_dist NULL (default) or \code{dist_func()}.
		#' @param env_ctrl_dist NULL (default) or \code{dist_func()}.
		#' @param env_dist_method has been droped.
		#' @param seed a integer value.
		#' @param spec_dist_method has been droped.
		#' @param env_dist_method has been droped.
		## @param spec_dist_method has been droped.
		## @param env_dist_method has been droped.
		#' @param ... extra params passing to \code{mantel_fun}.
		#' @return a data.frame.
		#' @importFrom dplyr mutate
		@@ -64,8 +63,8 @@ mantel_test <- function(spec,
		env_dist = NULL,
		env_ctrl_dist = NULL,
		seed = 123,
		spec_dist_method,
		env_dist_method,
		# spec_dist_method,
		# env_dist_method,
		...)
		{
		if(!is.data.frame(spec))
		@@ -91,14 +90,14 @@ mantel_test <- function(spec,
		}
		}

		if(!missing(spec_dist_method)) {
		warning("'spec_dist_method' parameter has been deprecated,\n",
		"please use 'spec_dist' parameter instead.", call. = FALSE)
		}
		if(!missing(env_dist_method)) {
		warning("'env_dist_method' parameter has been deprecated,\n",
		"please use 'env_dist' parameter instead.", call. = FALSE)
		}
		# if(!missing(spec_dist_method)) {
		# warning("'spec_dist_method' parameter has been deprecated,\n",
		# "please use 'spec_dist' parameter instead.", call. = FALSE)
		# }
		# if(!missing(env_dist_method)) {
		# warning("'env_dist_method' parameter has been deprecated,\n",
		# "please use 'env_dist' parameter instead.", call. = FALSE)
		# }

		if(!is.null(group)) {
		# ## TODO: set group by regex

man/mantel_test.Rd

+0 −6

Original line number	Diff line number	Diff line
		@@ -17,8 +17,6 @@ mantel_test(
		env_dist = NULL,
		env_ctrl_dist = NULL,
		seed = 123,
		spec_dist_method,
		env_dist_method,
		...
		)
		}
		@@ -49,10 +47,6 @@ mantel_test(

		\item{seed}{a integer value.}

		\item{spec_dist_method}{has been droped.}

		\item{env_dist_method}{has been droped.}

		\item{...}{extra params passing to \code{mantel_fun}.}
		}
		\value{

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