r - Index values from a matrix using row, col indices

Question

I have a 2D matrix mat with 500 rows × 335 columns, and a data.frame dat with 120425 rows. The data.frame dat has two columns I and J, which are integers to index the row, column from mat. I would like to add the values from mat to the rows of dat.

Here is my conceptual fail:

> dat$matval <- mat[dat$I, dat$J]
Error: cannot allocate vector of length 1617278737

(I am using R 2.13.1 on Win32). Digging a bit deeper, I see that I'm misusing matrix indexing, as it appears that I'm only getting a sub-matrix of mat, and not a single-dimension array of values as I expected, i.e.:

> str(mat[dat$I[1:100], dat$J[1:100]])
 int [1:100, 1:100] 20 1 1 1 20 1 1 1 1 1 ...

I was expecting something like int [1:100] 20 1 1 1 20 1 1 1 1 1 .... What is the correct way to index a 2D matrix using indices of row, column to get the values?

Answer 1

Almost. Needs to be offered to "[" as a two column matrix:

dat$matval <- mat[ cbind(dat$I, dat$J) ] # should do it.

There is a caveat: Although this also works for dataframes, they are first coerced to matrix-class and if any are non-numeric, the entire matrix becomes the "lowest denominator" class.