Phylobayes, Tracecomp Output Interpretation
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Entering edit mode
7.4 years ago
5heikki 9.7k

How does one interpret the output of the tracecomp function of PhyloBayes, e.g.:

    $ tracecomp -x 100 2 chain1 chain2

    initialising random
    seed was : 896505

    setting upper limit to : 2129
    name                effsize    rel_diff

    loglik              9        0.524245
    length              35        0.183442
    alpha               119        0.253582
    nocc                25        0.340367
    stat                19        0.25722
    statalpha           1426        0.185346
    kappa               50        0.250689
    allocent            6        0.433294

The manual states:

tracecomp -x 100 2 rnapol1 rnapol2
will produce an output summarizing the discrepancies and the effective sizes estimated for each column of the trace file. The discrepancy is defined as D=2|m1 - m2| / (s1 + s2), where mi is the mean and si the standard deviation associated with a particular column, and i runs over the chains. The effective size is evaluated using the method of Geyer (1992). The guidelines are:
- maximum discrepancy < 0.1 and minimum effective size > 100 : good run,
- maximum discrepancy < 0.3 and minimum effective size > 50 : acceptable run.

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Entering edit mode
25 days ago

Hello! I still have the same question. I am running molecular dating analyses with Phylobayes and some of the parameters have converged but others have not. Any thoughts on this issue?

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