#This script is R code for “RandPtsLandcover”

#This script is designed to generate 100 sets of spatially random points within a non-continuous raster
# representing certain landcover types. In this example, we are looking at 3563 farms in the county of Clwyd, UK,
# for which we wish to retain attributes of the number of animals for future simulations.
#Due to the specific use of this script, there may be information generated that is superfluous in other applications.

##This script was generated and written in collaboration with Jim Regetz (regetz@nceas.ucsb.edu)
#at the National Center for Ecological Analysis and Synthesis (NCEAS), Santa Barbara, CA.
#Script annotated for publication August 10, 2012, by Sadie J. Ryan (sjryan@esf.edu).

##This function "generatePoints" takes a raster (of type SpatialPixelsDataFrame) and distributes 
# random points on it, using the spsample routine from R. Since the spsample function
# doesn't always get the exact number of points, this function further checks the number
# of points and adds 10 until the number is exceeded, then returns the first n of points.

library(sp)
generatePoints <- function(raster, n) {
   pts <- spsample(raster, n=n, type = "random")
   while (length(pts) < n) {
      pts <- rbind(pts, spsample(raster, n=10, type="random"))
   }
   return(pts[seq_len(n)])
}

## Here, we are importing the landcover ascii files (generated from ArcGIS layers) and turning them into the right kind of raster
# to run through the generatePoints function

library(maptools)
gpclibPermit()
clwyd6n <- as(readAsciiGrid("clwyd_6n.asc"), "SpatialPixelsDataFrame") #modify this for each of 24 scenarios
acps <- read.table ("clwydacps.txt") #reads in the attributes of farms - modify this for each county
county <- rep (56, times = 3563) #creates the county number vector - modify this for each county (aber: 66, 3086; cumbria: 8, 8035; clwyd: 56, 3563; devon: 10, 11167)

t=c(1:100)
	for (i in 1:length(t)) {
		w <- generatePoints(clwyd6n, 3563)
		alcrnd <- cbind(county, w, acps) 
		suff <- sprintf("%02d", i-1)
		write.table(alcrnd, file=sprintf("cl6n_lcrnd.%s.txt", suff), row.names=FALSE, col.names=FALSE)
	}