So I want to apply a function over a matrix in R. This works really intuitively for simple functions:
> (function(x)x*x)(matrix(1:10, nrow=2))
[,1] [,2] [,3]
For this specific example you can just do something like this
> # Create some fake data
> mat <- matrix(1:16, 4, 4)
> # Set all elements divisible by 3 to NA
> mat[mat %% 3 == 0] <- NA
> # Add 1 to all non NA elements
> mat <- mat + 1
> mat
[,1] [,2] [,3] [,4]
[1,] 2 6 NA 14
[2,] 3 NA 11 15
[3,] NA 8 12 NA
[4,] 5 9 NA 17