joey711/phyloseq — Issue #66: Bug in old unweighted-unifrac
Author: joey711
Created: 2012-02-03 19:30:21+00:00
State: open
Labels: Bug

Certain combinations of small trees fail, while in other cases pairwise distances are consistently inflated, slightly (between 0.01 and 0.1).

THIS IS NOT THE CASE for the new fast-UniFrac implementation, which does not seem to have any discrepancies with reference values at all. It is also faster, simpler, and easier to maintain. It is therefore unclear if the original implementation of UniFrac in this package will remain. There are some historical reasons for leaving it in the package, albeit with a default choice of "fast" (for fast-UniFrac) and a caveat in the documentation that there are very few instances in which you would want to use the original algorithm, other than out of interest and to compare the performance boost.

Nevertheless, this slight bug in unweighted UniFrac should be fixed as long as the original UniFrac algorithm is going to remain included in the package.

The error message occurring from small datasets looks like this:
Error in { : task 79 failed - "incorrect number of dimensions"