R/extract.data.R

In SDMTools: Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises

#' Spatial Join of Points with Raster Grids
#' 
#' \code{extract.data} extracts data from raster object of class 'asc' (this
#' and the adehabitat package), 'RasterLayer' (raster package) or
#' 'SpatialGridDataFrame' (sp package) at specified locations. This represents
#' a faster version of 'join.asc' of the adehabitat package that assumes all
#' locations are within the map extents. \cr \cr \bold{Note:} there is no
#' interpolation done here. The values reported are simply the values of the
#' raster cell the point falls into.
#' 
#' Implements a faster version of 'join.asc' from the adehabitat package. \cr
#' \cr \bold{NOTE:} this assumes all locations are within the extent of the
#' raster map. Values outside the extent will be given a value of NA.
#' 
#' @param pts a two-column data frame or matrix with the x and y coordinates of
#' the locations of interest.
#' @param x a raster matrix of class 'asc' (this and the adehabitat package),
#' 'RasterLayer' (raster package) or 'SpatialGridDataFrame' (sp package)
#' @return Returns a vector equal in length to the number of locations in pnts.
#' @author Jeremy VanDerWal \email{jjvanderwal@@gmail.com}
#' @examples
#' 
#' 
#' #create a simple object of class 'asc'
#' tasc = as.asc(matrix(1:50,nr=50,nc=50)); print(tasc)
#' 
#' #define some point locations
#' points = data.frame(x=runif(25,1,50),y=runif(25,1,50))
#' 
#' #extract the data
#' points$values = extract.data(points,tasc)
#' 
#' #show the data
#' print(points)
#' 
#' 
#' @export extract.data
extract.data <- function(pts, x) {
	#check if raster from sp or raster package and convert if necessary
	if (any(class(x) %in% 'RasterLayer')) x = asc.from.raster(x)
	if (any(class(x) == 'SpatialGridDataFrame')) x = asc.from.sp(x)
	if (class(x) != 'asc') stop('matrix must be of class "asc"') #check to ensure x is of class asc
	xy <- getXYcoords(x)
	xy$x <- xy$x + attr(x, "cellsize")/2
	xy$x <- c(xy$x[1] - attr(x, "cellsize"),xy$x)
	xy$y <- xy$y + attr(x, "cellsize")/2
	xy$y <- c(xy$y[1] - attr(x, "cellsize"),xy$y)
	xf <- as.numeric(cut(pts[, 1], xy$x))
	yf <- as.numeric(cut(pts[, 2], xy$y))
	return(x[cbind(xf,yf)])
}