sum non NA elements only, but if all NA then return NA

Following the suggestions from other users, I will post the answer to my question. The solution was provided by @sandipan in the comments above:

As noted in the question, if you need to sum the values of one column which contains NAs,there are two good approaches:

1) using ifelse:

A[, (ifelse(all(is.na(col2)), col2[NA_integer_], sum(col2, na.rm = T))), 
  by = .(col1)]

2) define a function as suggested by @Frank:

suma = function(x) if (all(is.na(x))) x[NA_integer_] else sum(x, na.rm = TRUE)

A[, suma(col2), by = .(col1)]

Note that I added NA_integer_ as @Frank pointed out because I kept getting errors about the types.

Using sum_ from hablar

library(hablar)
A[, as.numeric(sum_(col2)), .(col1)]
#   col1 V1
#1:    A NA
#2:    B  5
#3:    C  4