HARD/CleanCoordinates/UrbanCoordinates.R

In AshwinAgrawal16/BiodiversityGSoC17: Integrating biodiversity data curation functionality.

library(sp)
library(raster)
library(rgeos)
library(rgbif)

UrbanCoordinates <- function(x, ref = NULL) {
  pts <- SpatialPoints(x)
  limits <- extent(pts) + 1
  
  if (is.null(ref)) {
    stop("No referencepolygons found. Set 'urban.ref'")
  }
  
  ref <- crop(ref, limits)
  
  urban <- over(x = pts, y = ref)[, 1]
  out <- is.na(urban)
  
  return(out)
}

#Driver script
#Urban and verbose by defalut true
if (urban) {
      if (verbose) {
        cat("running urban test\n")
      }
      urb <-UrbanCoordinates(x, poly = urban.ref)
      if (verbose) {
        cat(sprintf("flagged %s records \n", sum(!urb)))
      }
    } else {
      urb <- rep(NA, dim(x)[1])
    }
#urb contains flagged records