UncertaintyPlot.R

##' Plots the uncertainty analysis
##'
##'@param param.ci Parameter confidence intervals from uncertainty_anal
##'@param out.mat2 Model predictions at t = 1-16
##'@export
plot_uncertainty <- function(param.ci, out.mat2) {
  t1=1988:2003
  t2=2004:2016
  t=1988:2016
  trans=1 #transparency
  
  N.det = as.array(param.ci[[1]])
  N.I.ci = as.array(param.ci[[2]])
  N.IP.ci = as.array(param.ci[[3]])
  N.IPD.ci = as.array(param.ci[[4]])
  N.IPDE.ci = as.array(param.ci[[5]])
  N.IPDEA.ci = as.array(param.ci[[6]])
  
  loc=c("Lower Keys","Middle Keys","Upper Keys","Biscayne Bay","Dry Tortugas")
  for(r in 1:5) {
    col=seq(0, 79, by=5)
    col=col+r
    bp=out.mat2[,col]
    bp.ci=apply(bp, 2,quantile,c(0.025,0.5,0.975))
    plot(t1, bp.ci[2,], xlim=c(1988, 2016), ylim=c(.05, .95),
         xlab="year", ylab="percent bleaching", main=(paste(loc[r], "Uncertainty", sep=" ")))
    ecoforecastR::ciEnvelope(t1,bp.ci[1,],bp.ci[3,],col=col.alpha("lightBlue", .6))
    lines(t1, bp.ci[2,], col="blue")
    ecoforecastR::ciEnvelope(t2,N.IPDEA.ci[r,,1],N.IPDEA.ci[r,,3],col=col.alpha("orange",trans))
    ecoforecastR::ciEnvelope(t2,N.IPDE.ci[r,,1],N.IPDE.ci[r,,3],col=col.alpha("blue",trans))
    ecoforecastR::ciEnvelope(t2,N.IPD.ci[r,,1],N.IPD.ci[r,,3],col=col.alpha("green",trans))
    ecoforecastR::ciEnvelope(t2,N.IP.ci[r,,1],N.IP.ci[r,,3],col=col.alpha("red",trans))
    ecoforecastR::ciEnvelope(t2,N.I.ci[r,,1],N.I.ci[r,,3],col=col.alpha("black",trans))
    lines(t2,N.det[r,,1],lwd=0.5, col="purple")
    #legend("bottomleft", legend=c("IC", "Param", "Driver", "Process", "Random"), 
    #fill=c('black','red','green','blue','orange'))
  }
}