plot_mcmc_fix

# EDITED FROM:
# https://rdrr.io/github/cjcarlson/embarcadero/src/R/plot_mcmc.R
# fixes problem for rasters containing NA pixels (e.g. masked rasters)

plot.mcmc <- function(object, inputstack, iter=100, wait=0.1, quiet=FALSE) {

warning("This function is no longer maintained. Instead, use the one at https://raw.githubusercontent.com/AMBarbosa/embarcadero/master/R/plot_mcmc.R")
  
  xnames <- attr(object$fit$data@x, "term.labels")
  if(all(xnames %in% names(inputstack))) {
    inputstack <- inputstack[[xnames]]
  } else {
    stop("Variable names of RasterStack don't match the requested names")
  }
  input.matrix <- as.matrix(getValues(inputstack))
  
  whichvals <- which(complete.cases(input.matrix))
  #input.matrix <- input.matrix[complete.cases(input.matrix),]  # my edit (disabled so raster pixels don't get disorganized)
  
  cat('\n Generating the posterior predictions (takes a second) \n')
  pred <- dbarts:::predict.bart(object, input.matrix)
  
  cat('\n Generating plots \n')
  if(!quiet){pb <- txtProgressBar(min = 0, max = iter, style = 3)}
  for (i in 1:iter){
    output.m <- t(matrix(pred[i,],
                         nrow = ncol(inputstack),
                         ncol = nrow(inputstack)))
    r <- raster(output.m,
                xmn=xmin(inputstack[[1]]), xmx=xmax(inputstack[[1]]),
                ymn=ymin(inputstack[[1]]), ymx=ymax(inputstack[[1]]),
                crs=inputstack[[1]]@crs)

    r <- mask(r, inputstack[[1]])  # add suggested by @RS-eco to remove values outside initial mask

    if(i==1){r1 <- r} else {r1 <- sum(r1, r)}
    par(mfrow=c(1,2))
    par(mar=c(2,1,2,5))
    plot(r, box=F, axes=F, zlim=c(0,1), main=paste('Iter',i))
    plot(r1/i, box=F, axes=F, zlim=c(0,1), main='Mean')
    Sys.sleep(0.1)
    if(!quiet){setTxtProgressBar(pb, i)}
  }
}