NeighborJoining v0.2.0
Dev (v0.2) rewrite
Revise regNJ function:
It now only uses the memory space of a single distance matrix, and overwrites new nodes into one of the merged nodes. This does change the ordering of merges in the algorithm (i.e. the pseudoroot may change) but the unrooted tree is confirmed to be the same (i.e. patristic distances don't change).
Update testing framework:
followed SciML organization with safetestsets and made each testset a regular script
Update Docs:
added doctests, and new docstrings for heights and merges functions
Add benchmark suite:
I am now testing on matrices up to size 1024, with the revision regNJ seems much faster than before, but some of that seems to be testing on yuletree matrices rather than uniformly random matrices
Merged pull requests:
- Dev (v0.2) rewrite (#3) (@BenjaminDoran)
