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version 1.9-alpha

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@bayesiancook bayesiancook released this 24 Apr 10:42
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v1.9
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The main new feature of version 1.9 is the availability of improved methods for computing the fit of models. A detailed analysis and presentation of the methods is given in Lartillot (2022).

More specifically:

  • the old cross-validation approach has numerical inaccuracies and is not recommended anymore
  • a new routine has been implemented for measuring the fit by leave-one-out cross-validation (loo-cv) and using the widely applicable (or Watanabe-Akaike) information criterion (wAIC).
  • a method is also available for computing the marginal likelihood by sequential importance sampling; however, it is computationally intensive.

additional minor points:

  • improved implementation and MCMC mixing for finite mixture models (-ncat option).
  • bug corrected for restarting / reading finite poisson mixture models.
  • bug corrected in old cross-validation under Poisson models.
  • the number of components of truncated stick-breaking process is now set to 1000 -- and tunable on demand (backward compatibility implemented).

Lartillot, Nicolas. 2022. Identifying the best approximating model in Bayesian phylogenet-
ics: Bayes factors, cross-validation or wAIC? bioRxiv https://biorxiv.org/cgi/content/short/2022.04.22.489153v1

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