rm(list=ls()) #clear workspace
library(raster)
library(raster)
library(sp)
library(rgdal)
library(rgeos)
library(dplyr)
library(igraph)

rm(list=ls()) 
setwd("C:/Users/aradhik/Google Drive/Kutzu/from Gehendra")

###Kudzu Infestation in Oklahoma
set.seed(95) # set random number seed

#### kudzu grid ####
#read in raster of OK grid
OK.rast16<-raster("OK_raster_timberland_500m.tif")
sim.yr0<-OK.rast16
#vectorized code 
#on average takes less than 10 seconds for each simulation
fun.one.ann.sim<-function(raster_in){
rasterl<-raster_in
#create a raster layer with value 1 for kudzu cells otherwise 2
rasterl[!is.na(raster_in) & raster_in==1]<-1
rasterl[!is.na(raster_in) & raster_in==0]<-2
#minimum distance from kudzu cells to other cells
d <- gridDistance(rasterl,origin=1)
#set outside values to NA
d[is.na(raster_in)]<-NA
prob <- exp(0.0369599-0.00474401*d)

#create raster with uniformly distributed random numbers
rannum<-rasterl
rannum[]<-runif(ncell(rannum))
rannum[is.na(raster_in)]<-NA #set outside values to NA
#table(getValues(prob>rannum)) # use it to see the numbers of 1
return(prob>rannum) # raster with binary values
}
# matrices to store the cumulative results of the simulations  
blanklayer<-OK.rast16
blanklayer[]<-0

sim.yr1.tally <- blanklayer # tally spread after the 1st year
sim.yr2.tally <- blanklayer # tally spread after the 2nd year
sim.yr3.tally <- blanklayer # tally spread after the 3rd year
sim.yr4.tally <- blanklayer # tally spread after the 4th year
sim.yr5.tally <- blanklayer # tally spread after the 5th year

# apply the above function to do 10 5-year simulations

for (i in 1:6000){
  start_time <- Sys.time() 
  sim.yr1 <- fun.one.ann.sim(sim.yr0) # spread after the 1st year
  sim.yr2 <- fun.one.ann.sim(sim.yr1) # spread after the 2nd year
  sim.yr3 <- fun.one.ann.sim(sim.yr2) # spread after the 3rd year
  sim.yr4 <- fun.one.ann.sim(sim.yr3) # spread after the 4th year
  sim.yr5 <- fun.one.ann.sim(sim.yr4) # spread after the 5th year

  sim.yr1.tally <- sim.yr1.tally + sim.yr1
  sim.yr2.tally <- sim.yr2.tally + sim.yr2
  sim.yr3.tally <- sim.yr3.tally + sim.yr3
  sim.yr4.tally <- sim.yr4.tally + sim.yr4
  sim.yr5.tally <- sim.yr5.tally + sim.yr5
  cat(i, print(Sys.time() - start_time))
}

# save Raster
writeRaster(sim.yr1,file="sim.yr1.tif", overwrite=TRUE)
writeRaster(sim.yr2,file="sim.yr2.tif", overwrite=TRUE)
writeRaster(sim.yr3,file="sim.yr3.tif", overwrite=TRUE)
writeRaster(sim.yr4,file="sim.yr4.tif", overwrite=TRUE)
writeRaster(sim.yr5,file="sim.yr5.tif", overwrite=TRUE)

writeRaster(sim.yr1.tally,file="sim.yr1.tally.tif", overwrite=TRUE)
writeRaster(sim.yr2.tally,file="sim.yr2.tally.tif", overwrite=TRUE)
writeRaster(sim.yr3.tally,file="sim.yr3.tally.tif", overwrite=TRUE)
writeRaster(sim.yr4.tally,file="sim.yr4.tally.tif", overwrite=TRUE)
writeRaster(sim.yr5.tally,file="sim.yr5.tally.tif", overwrite=TRUE)