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Support for non-contemporaneous samples, preprocessing tree sequences
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@awohns awohns released this 16 Feb 00:51
· 483 commits to main since this release
0.1.3
31b6f79
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Learn about vigilant mode.

Features

  • Two new methods, tsdate.sites_time_from_ts and tsdate.add_sampledata_times,
    support inference of tree sequences from non-contemporaneous samples.
  • New tutorial on inferring tree sequences from modern and historic/ancient samples
    explains how to use these functions in conjunction with tsinfer.
  • tsdate.preprocess_ts supports dating inferred tree sequences which include large,
    uninformative stretches (i.e. centromeres and telomeres). Simply run this function
    on the tree sequence before dating it.
  • ignore_outside is a new parameter in the outside pass which tells tsdate to
    ignore edges from oldest root (these edges are often of low quality in tsinfer
    inferred tree sequences)
  • Development environment is now equivalent to other tskit-dev projects
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