Using R: the best thing I’ve changed about my code in years

Hopefully, one’s coding habits are constantly improving. If you feel any doubt about yourself, I suggest looking back at something you wrote 2011.

One thing I’ve changed recently that made my life so much better is a simple silly thing: meaningful name for index and counter variables.

Take a look at these pieces of fake code, that both loop over a matrix of hypothetical data (say: genotypes) to pass each value to a function (that does something):

## First attempt
for (i in 1:ncol(geno)) {
   for (j in 1:nrow(geno)) {
        output[i,j] <- do_something(geno[j, i])
   }
}

## Second attempt
n_markers <- ncol(geno)
n_ind <- nrow(geno)
for (marker_ix in 1:n_markers) {
   for (individual_ix in 1:n_ind) {
        output[individual_ix, marker_ix] <-
            do_something(geno[individual_ix, marker_ix])
   }
}

Isn’t that much nicer? The second version explicitly states what is what: we are iterating over markers and individuals, where each row is an individual and each column a marker. It even helps us spot errors such as the one in the first version. You would marvel at how many years it took me to realise that there is now law that says that the loop variable must be called i .

(Yes, nested for loops and hard bracket indexing looks uglier than a split-apply-combine solution, and using an apply family function would do away with any risk of mixing up the indices. However, loops do look less arcane to the uninitiated, and sometimes in more complicated cases, we really need that loop variable for something else.)