Ghastly R code

My R package, R/qtl, contains about 33k lines of R code (and 21k lines of C code). Some of it is quite good; some of it is terrible. Here’s another example of the terrible.

I’ve long needed to revise the function scantwo, for performing a two-dimensional genome scan for pairs of loci. I was looking at the function today, and was aghast to find that it’s 1354 lines long. That’s 4% of the R code in the package!

And the R code is just moving data and results around; the actual calculations are in C (in a series of files that comprise 4725 lines — 20% of the C code in the package).

Yuck.

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