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Replacing values of raster in R to produce landuse-like raster map?
You must invert your order:
Z <- runif(100, 0, 2)
Z[Z>0.12]<-3
Z[Z==0.12]<-2
Z[Z<0.12]<-1
Your problem was due to in the first sentence (Z[Z<0.12]<-1) you made values become 1. Then in the last …