set the cmctScale prior as default for the trait.clock.rate in discrete trait analysis in BEAuti and include the estimation of root frequencies in the nonreversible model

evolvedmicrobe / beast-mcmc

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set the cmctScale prior as default for the trait.clock.rate in discrete trait analysis in BEAuti and include the estimation of root frequencies in the nonreversible model #702

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago

the ctmcScale prior avoids many issues with the default exp(1) prior on the 
overall rate scaler. the root frequency estimation avoids a dead-end state 
issue in the nonreversible model specifically. XML example (for both) attached

Original issue reported on code.google.com by philippe...@gmail.com on 7 Oct 2013 at 7:31

Attachments:

H5N1_HA_BSSVS.xml

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 8 Oct 2013 at 6:27

Added labels: BEAUti, Milestone-Release1.8, v1.7.5

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 11 Oct 2013 at 4:13

Changed state: Fixed