R/plot_JAGSmask.R

In mikemeredith/makeJAGSmask: Construct a Habitat Matrix for Use with SECR Analysis in JAGS or BUGS

# Function to plot a JAGSmask object

plot.JAGSmask <- function(x, col, verify=TRUE, ...) {

  if(names(x)[1] == "habMat") {  # no covariate matrices
    if(missing(col))
      col <- c("grey", "white", "yellow")
    if(is.null(x$coreMat)) {
      toPlot <- x$habMat
    } else {
      toPlot <- x$habMat + x$coreMat
    }
    image(x=1:x$upperLimit[1],
          y=1:x$upperLimit[2],
          z=toPlot,
          ann=FALSE, axes=FALSE, col=col, asp=1, ...)
  } else {
    if(missing(col))
      col <- terrain.colors(100)
    image(x=1:x$upperLimit[1],
          y=1:x$upperLimit[2],
          z=x[[1]],
          ann=FALSE, axes=FALSE, col='black', asp=1)#, ...)
    tmp1 <- x[[1]]
    tmp1[x$habMat==0] <- NA
    image(x=1:x$upperLimit[1],
          y=1:x$upperLimit[2],
          z=tmp1, col=col, add=TRUE)#, ...)
    if(!is.null(x$coreMat)) {
      tmp2 <- x$coreMat
      tmp2 <- 1-tmp2
      tmp2[tmp2==0] <- NA
      tmp2[x$habMat==0] <- NA
      image(x=1:x$upperLimit[1],
            y=1:x$upperLimit[2],
            z=tmp2, col=adjustcolor('grey', 0.7), add=TRUE)
    }
  }

  bbox <- attr(x, "boundingbox")
  xlabels <- pretty(bbox[1:2, 1], n=5)
  xpos <- (xlabels - bbox[1, 1]) / diff(bbox[1:2, 1]) * nrow(x$habMat) + 1
  ylabels <- pretty(bbox[2:3, 2], n=5)
  ypos <- (ylabels - bbox[2, 2]) / diff(bbox[2:3, 2]) * ncol(x$habMat) + 1

  title(xlab="Easting", ylab="Northing")
  axis(1, at=xpos, labels = xlabels)
  axis(2, at=ypos, labels = ylabels)
  box()
  points(x$trapMat, pch=3, col='red', xpd=TRUE)

  if(verify) {
    # Check locations of traps
    trapcells <- floor(x$trapMat)
    ok <- numeric(nrow(trapcells))
    for(i in 1:nrow(trapcells))
      ok[i] <- x$habMat[trapcells[i,1], trapcells[i,2]]
    if(!all(ok == 1)) {
      cat("The following traps appear to be in bad habitat:\n", which(!ok), "\n")
      cat("They are circled in the plot.\n")
      cat("If on the edge, this is probably due to rasterization of the habitat polygon.\n")
    }
    if(!all(ok == 1))
      points(x=x$trapMat[!ok, 1], y=x$trapMat[!ok, 2], col='red', cex=2, xpd=TRUE)
  }
}