As is stands you probably have an array with three dimensions. If you wanted to have a list you would have added simplify=FALSE. Try this:
do.call( rbind, replicate(5, my.fun(), simplify=FALSE ) )
Or you can use aperm
in the case where "final" is still an array:
fun <- function() matrix(1:10, 2,5)
final <- replicate( 2, fun() )
> final
, , 1
[,1] [,2] [,3] [,4] [,5]
[1,] 1 3 5 7 9
[2,] 2 4 6 8 10
, , 2
[,1] [,2] [,3] [,4] [,5]
[1,] 1 3 5 7 9
[2,] 2 4 6 8 10
> t( matrix(aperm(final, c(2,1,3)), 5,4) )
[,1] [,2] [,3] [,4] [,5]
[1,] 1 3 5 7 9
[2,] 2 4 6 8 10
[3,] 1 3 5 7 9
[4,] 2 4 6 8 10
There may be more economical matrix operations. I just haven't discovered one yet.