Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Improve two operators, and provide a starting tree generator #19

Open
wants to merge 8 commits into
base: master
Choose a base branch
from

Commits on Mar 23, 2021

  1. Move log computation earlier

    In linguistics, we tend to measure times in years, so heights are in the
    order of magnitude of 100s to 1000s, not the 0.1My often found in
    biology. In order to avoid overflow errors, the log should be taken
    ASAP, and in fact this does not make the computation more expensive.
    Anaphory committed Mar 23, 2021
    Configuration menu
    Copy the full SHA
    1b67e9a View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    5295a3a View commit details
    Browse the repository at this point in the history
  3. Fix initialization

    Gereon A. Kaiping committed Mar 23, 2021
    Configuration menu
    Copy the full SHA
    c1a3598 View commit details
    Browse the repository at this point in the history

Commits on Jul 21, 2021

  1. Modify tree, then set root.

    This should fix one of the symptoms of CompEvol/beast2#984 and also CompEvol#16
    Anaphory authored Jul 21, 2021
    Configuration menu
    Copy the full SHA
    5c93ce3 View commit details
    Browse the repository at this point in the history
  2. Add random tree that can start with sampled ancestors

    Gereon A. Kaiping committed Jul 21, 2021
    Configuration menu
    Copy the full SHA
    db0fe3a View commit details
    Browse the repository at this point in the history
  3. Fix to corner cases

    Gereon A. Kaiping committed Jul 21, 2021
    Configuration menu
    Copy the full SHA
    59e9583 View commit details
    Browse the repository at this point in the history
  4. Add default value that reduces RTwSA to RT

    Gereon A. Kaiping committed Jul 21, 2021
    Configuration menu
    Copy the full SHA
    6b2b5e1 View commit details
    Browse the repository at this point in the history

Commits on Jul 22, 2021

  1. Keep Sampled Ancestors as such.

    The SAWilsonBalding operator was permitted to turn sampled ancestors
    into normal tips. For an analysis where certain tips should be kept
    sampled ancestors, add a Boolean input (default: false) that aborts the
    operator proposal when it is about to do this change.
    Gereon A. Kaiping committed Jul 22, 2021
    Configuration menu
    Copy the full SHA
    0b2d58e View commit details
    Browse the repository at this point in the history