can missing parameter (5b063d4f) · Commits · github_fork / LinkET

R/network.R

+7 −5

Original line number	Diff line number	Diff line
		@@ -135,6 +135,7 @@ as_tbl_graph.corr.test <- function(x, ...) {
		#' @param type one of "full", "upper" or "lower", used to extract upper or lower
		#' triangular part of a adjacency matrix.
		#' @param diag if FALSE (default), self-edges will be removed.
		#' @param missing numeric, used to fill in missing values.
		#' @return a matrix object.
		#' @author Hou Yun
		#' @rdname adjacency_matrix
		@@ -142,7 +143,8 @@ as_tbl_graph.corr.test <- function(x, ...) {
		adjacency_matrix <- function(x,
		...,
		type = "full",
		diag = FALSE) {
		diag = FALSE,
		missing = 0) {
		type <- match.arg(type, c("full", "upper", "lower"))
		if (!inherits(x, "cor_md_tbl") && !inherits(x, "correlate")) {
		clss <- class(x)[1]
		@@ -165,7 +167,7 @@ adjacency_matrix <- function(x,
		}
		x <- dplyr::filter(x, ...)
		out <- df_to_matrix(x, "r", row_id = ".rownames", col_id = ".colnames",
		row_names = rnm, col_names = cnm, missing = 0)
		row_names = rnm, col_names = cnm, missing = missing)
		} else {
		out <- x$r
		params <- rlang::enquos(...)
		@@ -177,18 +179,18 @@ adjacency_matrix <- function(x,
		id <- id & rlang::eval_tidy(params[[ii]], x)
		}
		}
		out[!id] <- 0
		out[!id] <- missing
		}

		if (isFALSE(diag) && identical(rownames(out), colnames(out))) {
		diag(out) <- 0
		diag(out) <- missing
		}
		if (!identical(type, "full") && identical(rownames(out), colnames(out))) {
		.f <- switch (type,
		"upper" = "lower.tri",
		"lower" = "upper.tri"
		)
		out[do.call(.f, list(x = out))] <- 0
		out[do.call(.f, list(x = out))] <- missing
		}
		}
		out

+3 −1

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@
		\alias{adjacency_matrix}
		\title{Generate adjacency matrix}
		\usage{
		adjacency_matrix(x, ..., type = "full", diag = FALSE)
		adjacency_matrix(x, ..., type = "full", diag = FALSE, missing = 0)
		}
		\arguments{
		\item{x}{a correlation object (\code{correlate}, \code{md_tbl}, and so on).}
		@@ -15,6 +15,8 @@ adjacency_matrix(x, ..., type = "full", diag = FALSE)
		triangular part of a adjacency matrix.}

		\item{diag}{if FALSE (default), self-edges will be removed.}

		\item{missing}{numeric, used to fill in missing values.}
		}
		\value{
		a matrix object.