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Rate/time rescaling of posterior #364

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
This is a request for a feature that would take a posterior output (trees and 
logs) and rescale the rates/times. There are many reasons to want to do this:

(1) Change of units -- say from days to years
(2) Change to relative units -- say change so that all rates are relative to 
one of the genes, or to a mean across all genes of exactly 1, or exactly 
3.5e-6. Often the most convenient way to get mixing is to fix the ucld.mean of 
one gene and estimate the others, or constrain the ucld.means to average to 1, 
but this does not translate to an average meanRate statistic of 1, so a 
rescaling is necessary post-analysis.
(3) Rescale so that tree is height 1 for all samples.

et cetera...

Original issue reported on code.google.com by alexei.drummond on 17 Aug 2010 at 11:53

GoogleCodeExporter commented 9 years ago 
This would be a useful utility. Basically it could be based on LogCombiner - 
but you just select one Trees file and optionally a log file if you need the 
scaler from that. It would have various options - scale by a specified factor, 
rescale to a particular height, rescale by a statistic in the log file (or 
reciprocal of that). Also could add the ability to scale by an attribute 
attached to each branch (i.e., a rate).

Original comment by ramb...@gmail.com on 18 Aug 2010 at 9:29

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 10 Sep 2010 at 11:05

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 10 Sep 2010 at 11:05