Defines functions impute_na

Documented in impute_na

#'@name impute_na
#'@title Impute NA cells according to nearest neighbor
#'@description The spatstat package is used to impute NA values in the intermediate irregular landscape graph output from acc_path 
#'@importFrom spatstat as.ppp nncross
#'@importFrom raster xyFromCell cellFromXY
#'@param csurf Raster cost surface
#'@param result Raster output from acc_path
#'@param warn logical print warnings?
#'@param graph igraph object

impute_na <- function(result, csurf, graph, warn = TRUE){
  cells <- graph$cells
  infcells <- cells[which(result[cells] == Inf)]
  nonnullcells <- (1:length(csurf))[!(1:length(csurf) %in% graph$cells)]
  nonnullcells <- nonnullcells[!(nonnullcells %in% graph$nullcells)]
  nonnullcells <- c(nonnullcells, infcells)
  cells <- cells[!cells %in% nonnullcells]
  cellcoords <- raster::xyFromCell(csurf, cells)
  nonnullcellcoords <- raster::xyFromCell(csurf, nonnullcells)
  fcells <- spatstat::as.ppp(cellcoords,c(0,dim(csurf)[1],0,dim(csurf)[2]))
  icells <- spatstat::as.ppp(nonnullcellcoords,c(0,dim(csurf)[1],0,dim(csurf)[2]))
  ncross <- spatstat::nncross(icells, fcells, what = "which")
  if(length(ncross) < 2){
    if(warn == TRUE){
      warning("No cells found needing to impute. Check that scoords exist in graph and re-run.")
    result[nonnullcells] <- result[raster::cellFromXY(csurf, cellcoords[ncross,])]
jsta/irlgraph documentation built on May 18, 2017, 10:45 a.m.