Fill the gaps in raster stack using subsequent layers

0
votes

Suppose I have a raster stack that each layer has data gap in. I want to use the next two layers in the stack to fill the gaps of each layer:

library(raster)
r1 <- raster(ncol=20,nrow=20, xmn=0, xmx=20, ymn=0,ymx=20)
r1[] <- 1:20
r2 <- r3 <- r4 <- r5 <- r1
set.seed(0)
r1[sample(1:ncell(r1), size = 20)] <- NA
r2[sample(1:ncell(r2), size = 30)] <- NA
r3[sample(1:ncell(r3), size = 10)] <- NA
r4[sample(1:ncell(r4), size = 18)] <- NA
r5[sample(1:ncell(r5), size = 18)] <- NA

s <- stack(r1, r2, r3, r4, r5)

In this case r2 and r3 will be used to fill the gaps in r1 and so forth.

2
rraster

2 Answers

2
votes

Not sure if this is what you want, but it will give you a start. I'm still new to R, so there is probably another way to do it.

library(raster)
r1 <- raster(ncol=20,nrow=20, xmn=0, xmx=20, ymn=0,ymx=20)
r1[] <- 1:20
r2 <- r3 <- r4 <- r5 <- r1
set.seed(0)
r1[sample(1:ncell(r1), size = 20)] <- NA
r2[sample(1:ncell(r2), size = 30)] <- NA
r3[sample(1:ncell(r3), size = 10)] <- NA
r4[sample(1:ncell(r4), size = 18)] <- NA
r5[sample(1:ncell(r5), size = 18)] <- NA

s <- stack(r1, r2, r3, r4, r5)

for(i in 1:(nlayers(s) - 2) ){
    s[[i]] <- merge( s[[i]], mask( s[[(i+1)]], s[[i]], inverse = TRUE))
    s[[i]] <- merge( s[[i]], mask( s[[(i+2)]], s[[i]], inverse = TRUE))
}
1
votes

MikeJewski's solution might work, but the cover function is designed for this and more direct. It is not clear how you want to use the next two layers. The mean:

for(i in 1:(nlayers(s) - 2) ){
    s[[i]] <- cover( s[[i]], mean( s[[(i+1):(i+2)]], na.rm=TRUE))
}

Or first the closest (as MikeJewski assumed):

for(i in 1:(nlayers(s) - 2) ){
    s[[i]] <- cover( s[[i]], s[[(i+1)]])
    s[[i]] <- cover( s[[i]], s[[(i+2)]])
}

This would be another, but probably inefficient, approach:

f <- function(x) {
    for(i in 1:((ncol(x)-2)) ){
        x[is.na(x[,i]),i]  <- x[is.na(x[,i]),i+1]  
        x[is.na(x[,i]),i]  <- x[is.na(x[,i]),i+2]  
    }
    x
}

ss <- calc(s, f)