Find second highest value on a raster stack in R

Question

In R I can easily compute the max/min value of each cell in a georeferenced raster stack using the max/min commands.

set.seed(42)
require(raster)
r1 <- r         


        

Answer 1

You'll probably want to use calc(), adapting the code below to your precise situation. Just to show that it works as advertised, I've separately plotted layers formed by taking the highest, second highest, third, and fourth highest values found in each cell of the 4-layer RasterStack object.

zz <- range(cellStats(rs, range))

par(mfcol=c(2,2))
plot(calc(rs, fun=function(X,na.rm) X[order(X,decreasing=T)[1]]), main="1st",zlim=zz)
plot(calc(rs, fun=function(X,na.rm) X[order(X,decreasing=T)[2]]), main="2nd",zlim=zz)
plot(calc(rs, fun=function(X,na.rm) X[order(X,decreasing=T)[3]]), main="3rd",zlim=zz)
plot(calc(rs, fun=function(X,na.rm) X[order(X,decreasing=T)[4]]), main="4th",zlim=zz)

Or, more compactly and efficiently, just construct a new raster stack holding the reordered values and then plot its layers:

zz <- range(cellStats(rs, range))
rs_ord <- calc(rs, fun=function(X,na.rm) X[order(X,decreasing=T)])

par(mfcol=c(2,2))
plot(rs_ord[[1]], main="1st", zlim=zz)
plot(rs_ord[[2]], main="2nd", zlim=zz)
plot(rs_ord[[3]], main="3rd", zlim=zz)
plot(rs_ord[[4]], main="4th", zlim=zz)