If partitions are unlinked then the base frequencies should be calculated from each partition separately

xhyccc / beast-mcmc

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If partitions are unlinked then the base frequencies should be calculated from each partition separately #38

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago

What steps will reproduce the problem?
1. Choose the codon-partitioned model and unlink the substitution model in 
BEAUti
2. Generate a BEAST file

What is the expected output? What do you see instead?

The hky1.frequencies and hky2.frequencies should be different values but they 
are the same (when 
the BEAST XML is run). They should be calculated from the individual partitions 
rather than from the 
overall alignment.

Original issue reported on code.google.com by alexei.drummond on 14 Nov 2007 at 9:03

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 31 Jan 2008 at 2:03

Added labels: v1.5

GoogleCodeExporter commented 9 years ago

It seems new BEAUTi has fixed this bug, but it needs more tests.

Original comment by dong.w.xie@gmail.com on 2 Aug 2009 at 11:35

Changed state: Started
Added labels: BEAUTi1.5
Removed labels: v1.5

GoogleCodeExporter commented 9 years ago

not fixed, and also generator has wrong method to create only 1 frequency when
linking substitution model but unlinking frequencies.

Original comment by dong.w.xie@gmail.com on 31 Aug 2009 at 12:38

Changed state: Accepted

GoogleCodeExporter commented 9 years ago

fixed by adding mergedPartten ref

Original comment by dong.w.xie@gmail.com on 31 Aug 2009 at 9:55

Changed state: Fixed