Why is the code duplicated 3 times?

[nsheff]

Can you consolidate the C code so that the R and python packages use the same C codebase? otherwise you have to maintain 3 versions of the code, which doesn't make sense.

[jf2016GH]

Not completely possible for any complex code especially for the R version. Because the languages are quite different on the basic data structures and the R-internals is limited. To be efficient, the code for R has to be redesign and re-coded. It is basically a new project.

And the C version has to include data structures and functions that can fairly compare with Giggle results, which is not necessary in the future, so it should not appear in the R or Python version;

Also IGD is not yet completely finished. I am still developing new algorithms/new functionalities.
I am currently implementing the seqpare metric in IGD, almost finished.