Issues

• Better confidence bounds for mutation ages from "exact" convolution

  tskit-dev/tsdate#514 · Filter by author nspope opened on Jun 4, 2026

• Collapse equivalent edges/blocks for EP

  tskit-dev/tsdate#513 · Filter by author nspope opened on May 12, 2026

• Assertion error in split_disjoint_nodes

  bug
  tskit-dev/tsdate#497 · Filter by author hyanwong opened on Mar 3, 2026
  5

• Support 3.14

  tskit-dev/tsdate#496 · Filter by author jeromekelleher opened on Mar 3, 2026
  1

  

• Scale exponential prior on roots using root spans

  tskit-dev/tsdate#484 · Filter by author hyanwong opened on Jan 20, 2026

• Use mutation rate map for missing data, etc

  tskit-dev/tsdate#482 · Filter by author nspope opened on Oct 14, 2025

• Revisit time discretization for path rescaling

  tskit-dev/tsdate#467 · Filter by author nspope opened on Jun 20, 2025
  2

• Can be hard to constrain root node to a fixed time on a large single tree

  tskit-dev/tsdate#466 · Filter by author hyanwong opened on Jun 10, 2025
  12

• Recommendations and exploration for match_segregating_sites rescaling parameter

  tskit-dev/tsdate#463 · Filter by author hyanwong opened on May 30, 2025

• tsdate.preprocess_ts() should split root nodes when their children change

  tskit-dev/tsdate#452 · Filter by author hyanwong opened on Jan 20, 2025

• Better error messages if smaller rescaling intervals needed

  numerical stability
  tskit-dev/tsdate#451 · Filter by author hyanwong opened on Jan 16, 2025

• Zero division error (with a putative solution)

  numerical stability
  tskit-dev/tsdate#450 · Filter by author hanbin973 opened on Jan 13, 2025

• API for singleton phasing

  tskit-dev/tsdate#446 · Filter by author hyanwong opened on Dec 13, 2024

• Node times remain biased after multiple EP rounds (and bias depends on number of nodes)

  tskit-dev/tsdate#444 · Filter by author hyanwong opened on Dec 11, 2024
  4

• Comparison to "Threads"

  tskit-dev/tsdate#430 · Filter by author hyanwong opened on Aug 25, 2024
  2

• Future work: time-variable split_disjoint_nodes routine

  tskit-dev/tsdate#402 · Filter by author hyanwong opened on Jun 5, 2024

• sample_as_parent in variational_gamma

  tskit-dev/tsdate#394 · Filter by author hyanwong opened on Jun 4, 2024
  3

• DeprecationWarning for scipy: quadpack

  tskit-dev/tsdate#384 · Filter by author hyanwong opened on Jun 4, 2024
  2

• Add some more evaluation scripts

  tskit-dev/tsdate#379 · Filter by author hyanwong opened on May 13, 2024

• Break tsinfer polytomies using mutational density

  tskit-dev/tsdate#363 · Filter by author hyanwong opened on Jan 11, 2024
  4

• Investigate effect of polytomies / topological uncertainty on posteriors

  tskit-dev/tsdate#359 · Filter by author hyanwong opened on Jan 8, 2024
  15

• Test ability to detect wrongly polarised ancestral states in tsinfer

  tskit-dev/tsdate#347 · Filter by author hyanwong opened on Dec 5, 2023

• Add iterative approach to the inside_outside method

  tskit-dev/tsdate#325 · Filter by author hyanwong opened on Oct 9, 2023

• Constraining multiple nodes to be at the same time?

  tskit-dev/tsdate#316 · Filter by author hyanwong opened on Sep 21, 2023
  3

• Adjust edge spans according to exclusion mask

  tskit-dev/tsdate#315 · Filter by author nspope opened on Sep 10, 2023