search

phylotastic / datelife

R package containing datelife's core functionality
http://phylotastic.org/datelife/
13 stars 11 forks source link

Add taxa w/o brlen #13

Closed bomeara closed 6 years ago

bomeara commented 7 years ago

bladj, etc. BOLD scaling

arlin commented 7 years ago

The issue that concerned me was being able to send a topology and get back a scaled version of the topology, even if all the taxa cannot be matched. This would require some method of interpolation that (it seems to me) necessarily makes some substantive assumption about tree shapes.

Also, I was concerned that we previously had some trees in the portal with fake branch lengths, all set to 1. I don't know what is the algorithm being used at DateLife, but if you send (A, (B,C)) and (A:1, (B:1,C:1):1) you get different answers (not hugely different, but clearly different in proportion).

bomeara commented 7 years ago

Done with the GetBoldOToLTree function, but not exposed to users yet. Add option in EstimateDates() function to let users choose this.