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matsen / pplacer

Phylogenetic placement and downstream analysis
http://matsen.fredhutch.org/pplacer/
GNU General Public License v3.0
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unweighted edge PCA #146

Closed matsen closed 12 years ago

matsen commented 13 years ago

Add an --unweighted flag to the splitify cmdobject, such that instead of using the usual Guppy_splitify.splitify command, it uses an "unweighted_splitify` command.

That command returns +1 if x -. (1. -. x) is strictly positive, -1 if negative, and 0 otherwise.

Note that we may later want to have a user-specifiable cutoff such that this function returns zero if the absolute value of x -. (1. -. x) is less than some cutoff.

Everything else with eg PCA would then continue as before but with this vector.

habnabit commented 13 years ago

There's already an --unweighted flag on splitify which deals with placements. Should this use a different flag name?

matsen commented 13 years ago

If I was going to start over, I would replace "unweighted" with "point" and "weighted" with "spread" everywhere in the code. Then --unweighted would take the meaning described here.

On Wed, Nov 2, 2011 at 4:56 PM, Aaron Gallagher reply@reply.github.com wrote:

There's already an --unweighted flag on splitify which deals with placements. Should this use a different flag name?

Reply to this email directly or view it on GitHub: https://github.com/matsen/pplacer/issues/146#issuecomment-2611664

Frederick "Erick" Matsen, Assistant Member Fred Hutchinson Cancer Research Center http://matsen.fhcrc.org/

matsen commented 13 years ago

Note that the above commit fixes this naming conflict.