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BEAST2-Dev / beast-classic

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Discrete trait phylogeography does not log posterior rate samples #1

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Run a discrete trait analysis

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

Expect that the log file will contain samples from the posterior for geographic 
transition rates.  Instead, the log file contains the rate and indicator 
variables used by BSSVS, and an additional step is required to transform this 
into the rate posteriors.

It's probably dangerous to expose users to the BSSVS rate and indicator 
variables, as this makes it possible for users to treat the BSSVS rate variable 
as the actual transition rate - which it is not.

What version of the product are you using? On what operating system?
BEAST_CLASSIC v1.1.8 on GNu/Linux.

Please provide any additional information below.

Original issue reported on code.google.com by tgvaughan on 15 May 2015 at 12:41

wangboioz commented 3 years ago

How to transform log file into the rate posteriors, please?