R/adjacencyFromTransition.R

In gdistance: Distances and Routes on Geographical Grids

#' Adjacent cells
#'
#' Identify pairs of cells that are adjacent.
#'
#' @aliases adjacencyFromTransition
#' @param x TransitionLayer
#' @return A two column matrix with each row containing
#'  a pair of adjacent cells.
#' @details
#' Extracts the indices of those cells that are connected
#'  (e.g. cells i,j that have a non-zero value in the transition
#'  matrix).
#'
#' Cell numbers are unique indices of cells in the original grid.
#'  By convention, cell numbers start with 1 in the upper-left
#'  corner of the grid and increase from left to right and from top
#'  to bottom.
#'
#' @author Jacob van Etten
#'
#' @seealso \code{\link[raster]{adjacent}}
#' @examples
#' library("raster")
#' r <- raster(nrows = 6, ncols = 7,
#'             xmn = 0, xmx = 7,
#'             ymn = 0, ymx = 6,
#'             crs = "+proj=utm +units=m")
#' r[] <- runif(6 * 7)
#' tr <- transition(r, function(x) 1 / mean(x), 8)
#'
#' aft <- adjacencyFromTransition(tr)
#'
#' head(aft)
#'
#' @export
adjacencyFromTransition <- function(x) {
	tc <- transitionCells(x)
	x <- transitionMatrix(x)
	transition.dgT <- as(as(x, "generalMatrix"), "TsparseMatrix")
	adj <- cbind(transition.dgT@i + 1, transition.dgT@j + 1)
	adj <- cbind(tc[adj[, 1]], tc[adj[, 2]])
	return(adj)
}