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The C++ code works for rooted trees, but not unrooted ones. Possibly a bug in my implementation, more testing needed.
Some datasets still produce divergent values. Likely a bug in my implementation.
Bringing the assay into C++ was using rowTree tip labels for the observation ids, causing nonsense results when they were in different order from the actual rownames. Also added a check for cladewise tree ordering.
However, speed is slower than current implementation
Unweighted is now significantly faster and less memory intensive than the existing implementation
Merge remote-tracking branch 'upstream/devel' into fastunifrac # Conflicts: # DESCRIPTION # NAMESPACE # R/RcppExports.R # R/addAlpha.R # src/.gitignore # src/RcppExports.cpp # src/assay.cpp # src/assay.h # src/propmap.cpp # src/propmap.h # src/tree.h
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Hey!
Just opening the PR earlier to share the progress. Will use this for the benchmark and refine it later on, but feel free to check it already if you like.