ordered characters in BEAST2

[Mike Lee]

Hello all -

I am trying to implement ordered characters in BEAST2 (transferring datasets across from BEAST1) and failing miserably.

I've used the attached penguin dataset (from Gavryshkina et al) to illustrate my issue.  The original file runs fine on BEAST2; just for the sake of example, I've made some edits (annotated) to the site model for the 3-state character to change it from a Lewis (unordered) character to an ordered character, where changes from 0 to 2 have to pass through state 1.  This kills the likelihoods of 3-state characters and subsequent character classes:

P(likelihood) = -Infinity (was -Infinity)
        P(morphTreeLikelihood.penguins2) = -1746.9993787881644 (was -1746.9993787881644)
        P(morphTreeLikelihood.penguins3) = -Infinity (was -Infinity)
        P(morphTreeLikelihood.penguins4) = NaN (was NaN)  **
        P(morphTreeLikelihood.penguins5) = NaN (was NaN)  **
        P(morphTreeLikelihood.penguins6) = NaN (was NaN)  **


Any pointers as to how to fix this would be greatly appreciated!

Cheers, Mike Lee

[Remco Bouckaert]

Hi Mike,

You might want to try to run the analysis with the -java option so that it does not use BEAGLE. With the Java TreeLikelihood a different way of exponentiating the rate matrix is used, which sometimes solves problems, especially when some of the rates are zero (as they are in the example you posted).

Cheers,

Remco

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<Penguins8.xml>

[Mike Lee]

Thanks as always - the above example runs fine with that option!  Mike