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@benjeffery benjeffery released this 10 Jun 14:21
· 93 commits to main since this release
0.2.0
0c5ccf2
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Learn about vigilant mode.

Bugfixes

  • Variational gamma uses a rescaling approach which helps considerably if e.g.
    population sizes vary over time

  • Variational gamma does not use mutational area of branches, but average path
    length, which reduces bias in tree sequences containing polytomies

Breaking changes

  • The default method has been changed to variational_gamma.

  • Variational gamma uses an improper (flat) prior, and therefore
    no longer needs population_size specifying.

  • The standalone preprocess_ts function also applies the split_disjoint_nodes
    method, which creates extra nodes but improves dating accuracy.

  • Json metadata for mean time and variance in the mutation and node tables is now saved
    with a suitable schema. This means json.loads() is no longer needed to read it.

  • The mutation_rate and population_size parameters are now keyword-only, and
    therefore these parameter names need to be explicitly typed out.

  • The ignore-oldest option has been removed from the command-line interface,
    as it is no longer very helpful with new tsinfer output, which has the root
    node split. The option is still accessible from the Python API.

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