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evolvedmicrobe / beast-mcmc

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generation of multispecis xml in Beauti is incorrect for one locus #92

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
An unnecessary rate is generated

The non changing clock.rate is in the log

the "constant.popSize" parameter has an operator and is in the prior - wrong

bmPrior="true"  - no longer correct, default should be constantRoot="true"

Original issue reported on code.google.com by jhe...@gmail.com on 17 Jul 2009 at 4:44

GoogleCodeExporter commented 9 years ago 
In addition, an extra, incorrect '<coalescentLikelihood idref="coalescent"/>,
in the likelihood

    <speciesCoalescent idref="coalescent"/>
                <mixedDistributionLikelihood idref="spops"/>
                <speciationLikelihood idref="speciationlike"/>
                <oneOnXPrior>
                    <parameter idref="constant.popSize"/>
                </oneOnXPrior>
                <oneOnXPrior>
                    <parameter idref="species.popMean"/>
                </oneOnXPrior>
                <oneOnXPrior>
                    <parameter idref="kappa"/>
                </oneOnXPrior>
                <coalescentLikelihood idref="coalescent"/>

Original comment by jhe...@gmail.com on 17 Jul 2009 at 11:41

GoogleCodeExporter commented 9 years ago

Original comment by jhe...@gmail.com on 20 Jul 2009 at 2:33

GoogleCodeExporter commented 9 years ago

Original comment by dong.w.xie@gmail.com on 21 Jul 2009 at 11:28