Ancestral state reconstruction for multiple MRCAs with datatype-awareness

[Anaphory]

I have written and tested an AncestralStatesLogger extension, which allows the reconstruction at multiple MRCA nodes, each specified by a taxonset, and which logs the original representation of the value instead of the internal one (eg. covarion logs as 01ab instead of 0123 – The code for that was taken from the AncestralStateTreeLikelihood class in beast-classics).

That class should be backward compatible with AncestralStateLogger and I would be happy to create a pull-request to it for this directory, if you like.

[Anaphory]

Do you want that contribution here, or what would be a good place to provide that functionality to the wider BEAST users community?

[biozj-tz]

Hi Anaphory,

I am trying to investigate the state distributions of each site in the genetic sequences, for the interested internal node of the phylogenitic tree, during the MCMC samples. When the interested internal node being the root of the tree, I have successflly obtained the states distributions. But when the interested internal node becoming the root of a branch of the tree, an error message occured as below:
java.lang.RuntimeException: Gamma rate heterogeneity or proportion invariant is not supported yet
      at beastlabs.evolution.likelihood.AncestralStateLogger.sample(Unknown Source)
      at beastlabs.evolution.likelihood.AncestralStateLogger.log(Unknown Source)
      at beast.base.inference.Logger.log(Unknown Source)
      at beast.base.inference.MCMC.log(Unknown Source)
      at beast.base.inference.MCMC.propagateState(Unknown Source)
      at beast.base.inference.MCMC.doLoop(Unknown Source)
      at beast.base.inference.MCMC.run(Unknown Source)
      at beastfx.app.beast.BeastMCMC.run(Unknown Source)
      at beastfx.app.beast.Controller$2.run(Unknown Source)
java.lang.RuntimeException: Gamma rate heterogeneity or proportion invariant is not supported yet
      at beastlabs.evolution.likelihood.AncestralStateLogger.sample(Unknown Source)
      at beastlabs.evolution.likelihood.AncestralStateLogger.log(Unknown Source)
      at beast.base.inference.Logger.log(Unknown Source)
      at beast.base.inference.MCMC.log(Unknown Source)/
      at beast.base.inference.MCMC.propagateState(Unknown Source)
      at beast.base.inference.MCMC.doLoop(Unknown Source)
      at beast.base.inference.MCMC.run(Unknown Source)
      at beastfx.app.beast.BeastMCMC.run(Unknown Source)
      at beastfx.app.beast.Controller$2.run(Unknown Source)

I used BEAST v2.7.8 with the BEASTLabs v 2.0.3.

I attached the succesful and failure xml file for you check the source of the error.

Successful.xml

failure.xml

Best,

Jie