How to write rasters after stacking them?

Question

There are several raster files that I want to manipulate and then write them again.

rasterfiles   <- list.files("C:\\data", "*.envi", full.names = TRUE)
d1 <-  overlay(stack(rasterfiles ), 
               fun=function(x) movingFun(x, fun=mean, n=3, na.rm=TRUE))
d2=unstack(d1)

I am grateful to any idea on how we write d2 (rasters)

Answer 1

 writeRaster(d1, file="d1.nc") #other file formats such as .envi work as well

works since d1 is one single raster and not a list of rasters: indeed the result of overlay is one single raster (see ?overlay).
Additionally the concept of stack is precisely to take several rasters having one layer and produce one raster with several layer.
Eventually if you really want to save each layer separately, you can unstack your raster prior to writing.
In which case:

d2 <- unstack(d1)
outputnames <- paste(seq_along(d2), ".nc",sep="")
for(i in seq_along(d2)){writeRaster(d2[[i]], file=outputnames[i])}

Answer 2

Plannapus solution should work. Alternatively, you can either write to a single file in one step:

 rasterfiles   <- list.files("C:\\data", "*.envi", full.names = TRUE)
 d1 <-  overlay(stack(rasterfiles ), 
           fun=function(x) movingFun(x, fun=mean, n=3, na.rm=TRUE), 
           filename='output.tif' )

Or to multiple files in two steps

 rasterfiles   <- list.files("C:\\data", "*.envi", full.names = TRUE)
 d1 <-  overlay(stack(rasterfiles ), 
           fun=function(x) movingFun(x, fun=mean, n=3, na.rm=TRUE))
 d2 <- writeRaster(d1, 'out.tif', bylayer=TRUE)