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beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees
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Debug dump doesn't work with skygrid+covariates+BSSVS #992

Open GuyBaele opened 6 years ago

GuyBaele commented 6 years ago

Currently, performing BSSVS on a skygrid+covariates model involves defining a productParameter first:

<productParameter id="skygrid.beta.withindicator.1">
    <parameter id="skygrid.beta.noindicator.1" value="0.01" lower="-1000.0" upper="1000.0"/>
    <parameter id="indicator.1" value="1"/>         
</productParameter>

However, it's not possible to set the value of a productPatameter as there's no telling what the values of each parameter in the product would be; hence the following error is generated: Exception in thread "Thread-1" java.lang.RuntimeException: Not implemented at dr.inference.model.ProductParameter.setParameterValue(ProductParameter.java:77) at dr.app.checkpoint.BeastCheckpointer.readStateFromFile(BeastCheckpointer.java:415) at dr.app.checkpoint.BeastCheckpointer.loadState(BeastCheckpointer.java:124) at dr.inference.mcmc.MCMC.chain(MCMC.java:169) at dr.inference.mcmc.MCMC.run(MCMC.java:137) at java.lang.Thread.run(Thread.java:745)

Would suggest to modify the XML structure (and update the syntax rules) to mimic that of a GLM, if that's possible.