How to overlay more than 2 files in r?

Question

We can compute the mean of corresponding layers from 2 stacks like this.

library(raster)
s1 <- stack(system.file("external/rlogo.grd", package="raster")) 
s2 <- sqrt(s1)
m4 <- overlay(s1, s2, fun=function(x) mean(x, na.rm=TRUE))

I have several files in a folder:

 data<- list.files ("C:data\\", ".nc", full.names = TRUE)
 for (i in 1:length(data)){
     nn=stack(dff[i])
     res=nn[[1:8]]
     ...............}

How can I apply the overlay function to all res

Answer 1

It is easier to do this with "terra" (the replacement of "raster"),

Example data

library(terra)
s1 <- rast(system.file("ex/logo.tif", package="terra"))   
s2 <- sqrt(s1)

Solutions to get the "parallel" mean with two SpatRasters:

mean(s1, s2)

#class       : SpatRaster 
#dimensions  : 77, 101, 3  (nrow, ncol, nlyr)
#resolution  : 1, 1  (x, y)
#extent      : 0, 101, 0, 77  (xmin, xmax, ymin, ymax)
#coord. ref. : Cartesian (Meter) 
#source(s)   : memory
#names       :      red,    green,     blue 
#min values  :   0.0000,   0.0000,   0.0000 
#max values  : 135.4844, 135.4844, 135.4844 

Or like this

app(sds(s1, s2), mean)

If you have many files (SpatRasters) you can do:

f <- system.file("ex/logo.tif", package="terra")
ff <- rep(f, 5)

s <- sds(ff)
app(s, mean)

# or 
x <- lapply(ff, rast)
do.call(mean, x)

# or
x <- lapply(ff, rast)
app(sds(x), mean)

To subset each SpatRaster before the computations, you can do

x <- lapply(ff, \(f) rast(f)[[1:2]])
do.call(mean, x)

Or (but this is currently broken)

s <- sds(ff)
s <- s[, 1:2,drop=FALSE]
app(s, mean)

You can, of course, also subset the output with [[1:2]]

---

Note that to get the mean of all layers you could do this instead

mean(c(s1, s2))
# or
app(c(s1, s2), mean)