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Release v1.2.3

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@github-actions github-actions released this 26 Apr 15:35
v1.2.3
002dc64

Changes

  • Setting collapseSampledAncestors=true is now ignored -- use fnCollapseSA(tree).
  • Temporarily disable FBD-Range models (#449).
  • Refactor PhyloOrnsteinUhlenbeckREML (#426)

Features

  • Allow mnFile and mnModel to write JSON output if given format="json" (#377)
  • Refactor dnBDSTP, dnFBDP, and dnPhylodynamicBDP (#386, #440)
  • Compute average distance matrices more efficiently (#454).
  • Compute ExponentialError probability densities more efficiently (#432, #434).
  • Add member procedure to set node age (#380).
  • Add member procedures to remove invariant and gap sites (#379, #392).
  • Be less picky about initial tree ages matching ages from taxon files (#455).
  • Make mvCollapseExpandFossilBranch complain if r=1 (no fossil sampling) (#440).
  • Make power posterior analyses more flexible (#397).

Bug fixes

  • Stop BD simulations from hanging in situations with many constraints (#453).
  • Stop moving fossil tip nodes in mvRootTimeSlideUniform (#447).
  • Fix consensusTree (#441).
  • Fix crash reading trees with bad indices (#403, #395).
  • Fix ancestral state reconstruction with missing data (#396)
  • Fix the uniform topology prior (#442).
  • Fix vectorFlatten (#445, #389).
  • Fix a memory leak in reversible jump mixtures (#430).
  • Fix BDSTP segfault (#367)
  • Fix updating phylogenetic likelihood when site mixture probability changes (#437).
  • Fix interaction of multiple stopping rules (#458).
  • Fix crash with tuning on mvScale (#452).
  • Fix writing delimited character data (#362)
  • Fix representation of sampled ancestors in tensorphylo functions (#369).
  • Fix offset for the read tree trace function (#381).
  • Fix Probability(-1) and Probability(2) (#410).
  • Don't flatten arrays of stochastic variables in checkpoint files (#448).
Assets 7