SA v2.2.0

What's Changed

• expand access to tree with offset by @bjoelle in #22
• Mostly cleanup and fixing of build.xml by @Lars-B in #23
• Eliminate BEASTLabs dependency and fix automated testing by @tgvaughan in #24
• Migrate sampled-ancestors to BEAST 3 by @alexeid in #25

New Contributors

• @Lars-B made their first contribution in #23
• @alexeid made their first contribution in #25

Full Changelog: v2.1.1...v2.2.0

SA v2.1.1

Improved BEAUti support: tip sampled dates will result in adding the appropriate operator for sampled ancestor analyses

Compatibility with BEAST 2.7

This release should be BEAST v2.7 compatible

Compatibility with BEAST 2.6.

This release should be compatible with BEAST 2.6.0.

Condition on sampling when condition on the root corrected

When conditioning on the root, the tree likelihood function should condition on sampling at least one extant individual on both sides of the root. It was previously conditioned on sampling at least one individual on just one side of the root.

Milestone for Beast 2.5 release

1. update classes to use BEAST 2.5;
2. use Function instead of RealParameter for turnover;
3. more tests.

Minor bug fixes

Wilson Baldwin fixed to not stuck. ZeroBranch classes deprecated.

Minor bug fixes.

This release fix an issue with origin input.

Update for Beast 2.4 release

Method's signature change. New parameterisations for SA birth death model.

Update for Beast 2.3 release

Beuati template update for tree operators.