Skip to content

Support for time-dependent transcriptional relations in BEAST 2.7 outputs
Compare
Choose a tag to compare
@jjmccollum jjmccollum released this 24 Apr 13:55
· 26 commits to main since this release
v0.1.11
5724b9f
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Verified
Learn about vigilant mode.

The main change introduced in this release is support for tagging of potential transcriptional explanations with notBefore and notAfter attributes. If these attributes are present in a variation unit's transcriptional relations list, teiphy will now map the transcriptional relations to an EpochSubstitutionModel with a different substitution model for different slices of time. This feature is only supported for BEAST 2.7 XML outputs. This means that BEAST users can now model time-dependent transcriptional changes (like assimilation to later popular texts, paleographic confusions possible only for earlier or later scripts, etc.) more accurately.

A related change is the addition of more comprehensive rules for updating witness date ranges based on the date range of the work's composition (and vice-versa). This change affects age/date calibrations for NEXUS and BEAST 2.7 XML formats (including the MrBayes NEXUS input format).

This release also fixes an error that prevented the --verbose flag from working correctly.

Assets 2
Loading