###Mixing Polygon Simulation (2 isotopes); v1.1, 22.7.2013, R version 3.0.1
###J.A.Smith et. al. 2013 (The University of NSW)###
###For updates and instructions, visit http://www.famer.unsw.edu.au/downloads.html
###New in v1.1: added black and white plot of mixing region

  install.packages("sp")  #for point-in-polygon (P-I-P) calculations
  install.packages("splancs") #to calculate polygon area
  sources <- read.table("Sources_example.csv",header=T,sep=",") #always put 13C(x) before 15N(y)
  mixture <- read.table("Mixture_example.csv",header=T,sep=",") #some error is required for every value
  TEF <-  read.table("TEF_example.csv", header=T,sep=",")
  its <- 1500  #specify the number of iterations ("its")
  min_C <- -50  #specifiy the dimensions and resolution for the mixing region figure
  max_C <- -20    #choose values outside the 95% mixing region
  min_N <- -2  
  max_N <- 10
  res <- 250 #resolution of the mixing region figure; reducing this improves performance
 ##Now RUN the simulation 
  step_C <- (max_C - min_C)/(res - 1)
  step_N <- (max_N - min_N)/(res - 1)   
  C_g <- seq(min_C,max_C,by=step_C) #values must be in ascending order
  N_g <- seq(min_N,max_N,by=step_N) #values must be in ascending order
  mgrid <- function(a,b) {  #create a grid of values to test for P-I-P
  m <- mgrid(C_g,N_g)
  Par_values <- array(0, c(its,(nrow(sources)*4+3)))  #create files to store data
  p <- array(0, c(its,(nrow(mixture))))
  mix_reg <- array(0, c(res,res))
  for (i in 1:its) {    #run loops to generate source isotopic signatures, for iterations = 'its'
    v <- array(0, c(nrow(sources),2))
    f <- array(0, c(nrow(TEF),2))
        for (j in 1:nrow(sources)) {
        v[j,1] <- rnorm(1, mean=sources[j,1], sd=sources[j,2])  #generate values from norm. dist. for d13C
        v[j,2] <- rnorm(1, mean=sources[j,3], sd=sources[j,4])  #generate values from norm. dist. for d15N
        f[j,1] <- rnorm(1, mean=TEF[j,1], sd=TEF[j,2])  #generate values from norm. dist. for d13C enrichment
        f[j,2] <- rnorm(1, mean=TEF[j,3], sd=TEF[j,4])  #generate values from norm. dist. for d15N enrichment
    V <- v+f
    hull <- chull(V)  #create a 2D convex hull from the enriched sources
    hull_a <- append(hull,hull[1])  #closes the polygon
    P <- point.in.polygon(mixture[,1], mixture[,2], V[hull_a,1], V[hull_a,2]) #calculate P_I_P 
    P_n <- as.numeric(P)                        
    p[i,] <- P_n
    poly_a <- areapl(V[hull_a,])  #calculate polygon area, for evaluating the quantity of iterations
    m$y_f <- m$y[res:1,]  #flip y grid data to resemble axes (d13C=x, d15N=y) 
    m_r <- point.in.polygon(m$x, m$y_f, V[hull_a,1], V[hull_a,2]) #calculate P-I-P for the mixing region
    m_r_s <- matrix(m_r,nrow=res,byrow=F)  #convert vector into square matrix
    m_r_s[m_r_s > 1] <- 1  #point.in.polygon can return '2' or '3'
    mix_reg <- mix_reg + m_r_s
    vals <- c(v[,1],v[,2],f[,1],f[,2],0,0,0)  #concatenate values for this iteration
    Par_values[i,] <- vals  #store values
    Par_values[i,ncol(Par_values)-2] <- poly_a
    Par_values[i,ncol(Par_values)-1] <- i
    Par_values[i,ncol(Par_values)] <- var(Par_values[1:i,ncol(Par_values)-2])
    if (i %% 10 ==0) cat(paste("iteration", i, "n")) 
 ##FIGURE 1: variance of polygon area during simulation
   Iterations <- Par_values[,ncol(Par_values)-1]
   Variance <- Par_values[,ncol(Par_values)]
   plot(Iterations, Variance, type="n")  #plots 
   lines(Iterations, Variance, lty=1, lwd=1.5, col="blue")
 ##FIGURE 2: proportion of iterations that each consumer was inside mixing polygon
   p[p > 1] <- 1   #point.in.polygon can return '2' or '3'
   Probabilities <- colSums(p)/its
   barplot(Probabilities, xlab="Consumer", ylab="Probability consumer is within mixing polygon", 
           ylim=c(0,1), names.arg=seq(1,nrow(mixture),by=1))
 ##FIGURE 3: mixing region, consumers, average enriched source signatures
   mix_reg <- mix_reg/its  #convert to 0-1 scale
   mix_reg[mix_reg==0] <- NA #make the zeros white
   mix_regt <- t(mix_reg[ncol(mix_reg):1,])  #transpose matrix for use with 'image'
   image(C_g, N_g, mix_regt, col=colorRampPalette(c("blue", "light blue", "green", "light green", 
          "yellow", "red"))(100), xlab="d13C", ylab="d15N", useRaster=TRUE)
   cont <- c(0.05, seq(0.1, 1, by=0.1))
   contour(C_g, N_g, mix_regt, levels=cont, add=TRUE, drawlabels=FALSE, lwd=1.9)
   sources_TEF <- sources + TEF
   points(sources_TEF[,1], sources_TEF[,3], col="white", pch=4, lwd=2, cex=1.5)
   points(mixture, pch=19, cex=1.3)
   windows()  #create colour bar for figure 3
   cust_color <- colorRampPalette(c("blue", "light blue", "green", "light green", "yellow", "red"))
   z <- matrix(1:100, nrow=1)
   x <- 1
   y <- seq(0,1,len=100)
   image(x,y,z,col=colorRampPalette(c("blue", "light blue", "green", "light green", "yellow", "red"))(100), 
          xaxt="n", xlab="", ylab="", useRaster=TRUE, bty="n", las=1)
  ##FIGURE 4: Same as Fig. 3, but black and white
  plot(C_g, N_g, type = "n")
  cont <- c(0.05, seq(0.1, 1, by=0.1))
  contour(C_g, N_g, mix_regt, levels=cont, add=TRUE, drawlabels=FALSE, lwd=1.9)
  sources_TEF <- sources + TEF
  points(sources_TEF[,1], sources_TEF[,3], col="black", pch=4, lwd=2, cex=1.5)
  points(mixture, pch=19, cex=1.3)
 ##Write data to files
   p_a <- rbind(p,Probabilities)
   write.table(p_a, file = "Consumer_Probabilities.csv", sep = ",", row.names=FALSE)
   col_names <- c(rep("d13C",nrow(sources)),rep("d15N",nrow(sources)),
   col_nums <- c(rep(1:nrow(sources),4),0,0,0)
   col_n <- paste(col_names, col_nums)
   write.table(Par_values, file = "Parameter_Values.csv", sep = ",", row.names=FALSE, col.names=col_n)