tskit-dev/tsdate issues and pull requests

#410 - Add `return_node_posteriors` argument.

Issue - State: open - Opened by hyanwong 21 days ago

#409 - Fill out more rescaling explanation

Pull Request - State: open - Opened by hyanwong 21 days ago

#408 - Vgamma default

Pull Request - State: closed - Opened by hyanwong 21 days ago

#407 - Start describing the rescaling step

Pull Request - State: closed - Opened by hyanwong 21 days ago

#406 - Add check for unary nodes

Pull Request - State: closed - Opened by nspope 24 days ago - 1 comment

#405 - Fix changelog

Pull Request - State: closed - Opened by benjeffery 24 days ago - 1 comment

#404 - Switch to ruff linting

Pull Request - State: open - Opened by benjeffery 25 days ago

#403 - Numpy 2 pinning

Issue - State: closed - Opened by benjeffery 25 days ago - 12 comments

#402 - Future work: time-variable `split_disjoint_nodes` routine

Issue - State: open - Opened by hyanwong 26 days ago

#401 - More docs tidying

Pull Request - State: closed - Opened by hyanwong 26 days ago

#400 - Italicise _tsdate_

Pull Request - State: closed - Opened by hyanwong 26 days ago

#399 - Add nice plot of inverse instantaneous coalescent rate to docs

Issue - State: closed - Opened by hyanwong 26 days ago - 5 comments

#398 - Inconsistent parameter naming for removing flanks vs tsinfer

Issue - State: open - Opened by hyanwong 26 days ago

#397 - Start tidying docs

Pull Request - State: closed - Opened by hyanwong 26 days ago

#396 - Make variational_gamma method the default, and document

Pull Request - State: closed - Opened by hyanwong 27 days ago - 1 comment

#395 - How to allow unary nodes in variational_gamma

Issue - State: open - Opened by hyanwong 27 days ago - 6 comments

#394 - sample_as_parent in variational_gamma

Issue - State: open - Opened by hyanwong 27 days ago - 3 comments

#393 - Remove need for tsinfer (and matplotlib?) from requirements.txt

Issue - State: open - Opened by hyanwong 27 days ago - 2 comments

#392 - Put constants at top level

Pull Request - State: closed - Opened by hyanwong 27 days ago

#391 - Fail vgamma if no mutations

Pull Request - State: closed - Opened by hyanwong 27 days ago

#390 - variational_gamma method fails on tree seq with no mutations

Issue - State: closed - Opened by hyanwong 27 days ago - 4 comments

#389 - Remove "ignore-oldest" option from the CLI

Pull Request - State: closed - Opened by hyanwong 27 days ago

#388 - variational_gamma does not seem to return posteriors

Issue - State: closed - Opened by hyanwong 27 days ago - 13 comments

#387 - Add split-disjoint to CLI preprocess

Pull Request - State: closed - Opened by hyanwong 27 days ago

#386 - Do not overwrite node metadata once tsinfer has set a schema

Issue - State: open - Opened by hyanwong 27 days ago

#385 - Document (and undocument) standard params & tidy calling conventions

Pull Request - State: closed - Opened by hyanwong 27 days ago - 1 comment

#384 - DeprecationWarning for scipy: quadpack

Issue - State: open - Opened by hyanwong 27 days ago - 2 comments

#383 - Set a new descriptive schema on mutations if none exists

Pull Request - State: closed - Opened by hyanwong 27 days ago - 3 comments

#382 - Save flags and metadata when splitting disjoint nodes

Pull Request - State: closed - Opened by hyanwong about 1 month ago - 7 comments

#381 - TODO before v-gamma release

Issue - State: open - Opened by hyanwong about 1 month ago - 12 comments

#380 - Allow compilation of wheels on mac

Pull Request - State: closed - Opened by hyanwong about 2 months ago

#379 - Add some more evaluation scripts

Issue - State: open - Opened by hyanwong about 2 months ago

#378 - Set sensible rescaling-intervals default value and save in provenance

Issue - State: closed - Opened by hyanwong about 2 months ago - 2 comments

#377 - CLI-use of variational_gamma specific params (e.g. max-shape, rescaling-intervals)

Issue - State: closed - Opened by hyanwong about 2 months ago - 1 comment

#376 - Move population_size and priors out of .date() method

Issue - State: closed - Opened by hyanwong about 2 months ago - 1 comment

#375 - Bump tqdm from 4.65.0 to 4.66.3 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 2 months ago
Labels: dependencies

#374 - Phasing singletons with expectation propagation

Issue - State: open - Opened by nspope about 2 months ago - 10 comments

#373 - Add `split_disjoint_nodes` to preprocess routine

Issue - State: closed - Opened by hyanwong 3 months ago

#372 - unpin numba version

Issue - State: closed - Opened by alxsimon 4 months ago - 6 comments

#371 - Piecewise uniform prior for timescale

Pull Request - State: closed - Opened by nspope 4 months ago - 3 comments

#370 - Branch/site statistic mismatch and inferred tree sequences

Issue - State: open - Opened by nspope 5 months ago - 8 comments

#369 - Extend jupyterbook timeout

Pull Request - State: closed - Opened by benjeffery 5 months ago

#368 - Cache JIT compiled code

Issue - State: closed - Opened by nspope 5 months ago - 5 comments

#367 - Add links to github from the docs

Pull Request - State: closed - Opened by hyanwong 5 months ago

#366 - Mismatch between site and branch diversity calculations

Issue - State: closed - Opened by hyanwong 5 months ago - 5 comments

#365 - Make the doc example smaller

Pull Request - State: closed - Opened by hyanwong 5 months ago

#364 - Non-contemporary samples

Pull Request - State: closed - Opened by nspope 6 months ago - 4 comments

#363 - Break tsinfer polytomies using mutational density

Issue - State: open - Opened by hyanwong 6 months ago - 4 comments

#362 - Change URL to docs

Pull Request - State: closed - Opened by hyanwong 6 months ago

#361 - Document bugfix

Pull Request - State: closed - Opened by hyanwong 6 months ago

#360 - Rescale messages at end of each iteration

Pull Request - State: closed - Opened by nspope 6 months ago - 2 comments

#359 - Investigate effect of polytomies / topological uncertainty on posteriors

Issue - State: open - Opened by hyanwong 6 months ago - 15 comments

#358 - Update docs for posterior

Pull Request - State: closed - Opened by hyanwong 6 months ago

#357 - Remove readthedocs status from readme

Pull Request - State: closed - Opened by benjeffery 6 months ago

#356 - Use direct memory access for checks

Pull Request - State: closed - Opened by hyanwong 6 months ago

#355 - Speed up pre-algorithm steps

Issue - State: closed - Opened by nspope 6 months ago - 4 comments

#354 - Tidy CHANGELOG for 0.1.6

Pull Request - State: closed - Opened by hyanwong 6 months ago

#353 - Tidy the documentation and default values

Pull Request - State: closed - Opened by hyanwong 6 months ago

#352 - Pass epsilon explicitly

Pull Request - State: closed - Opened by hyanwong 6 months ago

#351 - Api extras

Pull Request - State: closed - Opened by hyanwong 6 months ago - 2 comments

#350 - Refactor/redocument API

Pull Request - State: closed - Opened by nspope 6 months ago - 1 comment

#349 - Add mixture-of-gammas global prior, updated by EM

Pull Request - State: closed - Opened by nspope 7 months ago - 12 comments

#348 - Fix provenance

Pull Request - State: closed - Opened by hyanwong 7 months ago - 1 comment

#347 - Test ability to detect wrongly polarised ancestral states in tsinfer

Issue - State: open - Opened by hyanwong 7 months ago

#346 - Minor fixes for central moment matching

Pull Request - State: closed - Opened by nspope 7 months ago - 9 comments

#345 - Fix numerical issues via damping

Pull Request - State: closed - Opened by nspope 7 months ago - 7 comments