tskit-dev/tsdate issues and pull requests

#310 - Method for matching node sets across tree sequences

Pull Request - State: closed - Opened by nspope 11 months ago - 10 comments

#309 - Fix excess mutation count at last edge (closes #308)

Pull Request - State: closed - Opened by nspope 11 months ago - 1 comment

#308 - Example of incorrect mutation count in `Likelihoods`

Issue - State: closed - Opened by nspope 11 months ago - 2 comments

#307 - Update global prior via EM, use mixture of gammas

Pull Request - State: closed - Opened by nspope 11 months ago - 5 comments

#306 - Faster prior variance calculation

Pull Request - State: closed - Opened by nspope 11 months ago - 11 comments

#305 - Numeric fixes for extremely large shape parameters

Pull Request - State: closed - Opened by nspope 11 months ago - 7 comments

#304 - Add test case for Loopy ARG

Issue - State: open - Opened by hyanwong 12 months ago - 1 comment

#303 - Set metadata schemas

Pull Request - State: closed - Opened by hyanwong 12 months ago - 3 comments

#302 - "set_metadata" parameter

Issue - State: open - Opened by hyanwong 12 months ago - 1 comment

#301 - Comparing dates between simulated and inferred tree sequences

Issue - State: open - Opened by nspope 12 months ago - 4 comments

#300 - Make nicer progress bars for iteration

Pull Request - State: closed - Opened by hyanwong 12 months ago

#299 - New AssertionError for Jensen's inequality

Issue - State: closed - Opened by hyanwong 12 months ago - 5 comments

#298 - Nicer EP iteration progress bars

Issue - State: closed - Opened by hyanwong 12 months ago

#297 - Switch to auto tqdm

Pull Request - State: closed - Opened by hyanwong 12 months ago - 1 comment

#296 - Fix constrain_ages_topo bug

Pull Request - State: closed - Opened by hyanwong 12 months ago - 1 comment

#295 - Bug in constrain_ages_topo

Issue - State: closed - Opened by hyanwong 12 months ago
Labels: bug

#294 - Expose node spans not weights

Pull Request - State: closed - Opened by hyanwong 12 months ago - 1 comment

#293 - Numerical fixes (closes #286 and #289)

Pull Request - State: closed - Opened by nspope 12 months ago - 2 comments

#292 - Use of, and alternatives to, to a "global" (i.e. node-agnostic) prior

Issue - State: open - Opened by hyanwong 12 months ago - 13 comments

#291 - Documentation & API for tsdate.build_parameter_grid

Issue - State: closed - Opened by hyanwong 12 months ago - 2 comments

#290 - Example of Invalid2F1: Hypergeometric series did not converge

Issue - State: closed - Opened by hyanwong 12 months ago - 3 comments

#289 - AssertionError: kl-min: bad initial condition

Issue - State: closed - Opened by hyanwong 12 months ago - 3 comments

#288 - Revisit exclusion of unary regions

Issue - State: open - Opened by hyanwong 12 months ago - 9 comments

#287 - Test whether splitting the root node helps or hinders dating

Issue - State: open - Opened by hyanwong 12 months ago - 1 comment

#286 - "Invalid parent parameters" error using variational gamma

Issue - State: closed - Opened by hyanwong 12 months ago - 2 comments

#285 - Assess mixture prior problems by exhaustive simulation

Issue - State: closed - Opened by hyanwong 12 months ago - 4 comments

#284 - Allow a "control" dictionary to be passed to .date()

Issue - State: closed - Opened by hyanwong 12 months ago - 2 comments

#283 - Save PopulationSizeHistory params

Pull Request - State: closed - Opened by hyanwong about 1 year ago - 1 comment

#282 - Tidy a few test files

Pull Request - State: closed - Opened by hyanwong about 1 year ago

#281 - use root_threshold to check for multi-root trees

Pull Request - State: closed - Opened by hyanwong about 1 year ago

#280 - Avoid warnings for log(0)

Pull Request - State: closed - Opened by hyanwong about 1 year ago

#279 - Fix needed for JIT disabled tests

Pull Request - State: closed - Opened by nspope about 1 year ago - 1 comment

#278 - Disable JIT for coverage

Pull Request - State: closed - Opened by hyanwong about 1 year ago

#277 - More testing of prior classes and functions

Pull Request - State: closed - Opened by hyanwong about 1 year ago

#276 - Add a few variational tests

Pull Request - State: closed - Opened by hyanwong about 1 year ago

#275 - Provenance saving

Pull Request - State: closed - Opened by hyanwong about 1 year ago - 1 comment

#274 - Store PopulationSizeHistory as a json list

Issue - State: closed - Opened by hyanwong about 1 year ago - 5 comments

#273 - Raise errors not warnings if we can't convert a probability space

Pull Request - State: closed - Opened by hyanwong about 1 year ago - 1 comment

#272 - Remove unused code in cache.py

Pull Request - State: closed - Opened by hyanwong about 1 year ago

#271 - Change verbosity to a count

Pull Request - State: closed - Opened by hyanwong about 1 year ago

#270 - Cover main

Pull Request - State: closed - Opened by hyanwong about 1 year ago

#269 - Fix dblquad warnings

Pull Request - State: closed - Opened by hyanwong about 1 year ago

#268 - Remove versioning info at start of cache.py

Issue - State: closed - Opened by hyanwong about 1 year ago

#267 - Output number of iterations using EP

Pull Request - State: closed - Opened by hyanwong about 1 year ago - 1 comment

#266 - Increase coverage

Issue - State: closed - Opened by hyanwong about 1 year ago - 4 comments

#265 - Add variational method accuracy tests to `test_accuracy.py`

Issue - State: open - Opened by hyanwong about 1 year ago - 5 comments

#264 - Nicer progress bars for EP

Issue - State: closed - Opened by hyanwong about 1 year ago

#263 - Variational dating does not allow a null mutation rate

Issue - State: open - Opened by hyanwong about 1 year ago - 3 comments

#262 - Remove `ignore_oldest_root` option from CLI

Issue - State: closed - Opened by hyanwong about 1 year ago - 3 comments

#261 - Allow cli to work with variational_gamma

Pull Request - State: closed - Opened by hyanwong about 1 year ago - 1 comment

#260 - Some simpler functions

Pull Request - State: closed - Opened by hyanwong about 1 year ago - 2 comments

#259 - Simpler method for get_mut_edges

Issue - State: closed - Opened by hyanwong about 1 year ago

#258 - Fix codecov

Pull Request - State: closed - Opened by benjeffery about 1 year ago

#257 - Gamma-variational inference scheme

Pull Request - State: closed - Opened by nspope over 1 year ago - 30 comments

#256 - Switch to tqdm.autonotebook

Issue - State: closed - Opened by hyanwong over 1 year ago - 1 comment

#253 - Tidy tests and unpin numba

Pull Request - State: closed - Opened by hyanwong over 1 year ago

#252 - Fixup for #248, use generational scale for custom time grid

Pull Request - State: closed - Opened by nspope over 1 year ago - 1 comment

#251 - Return marginal likelihood from inside algorithm

Pull Request - State: closed - Opened by nspope over 1 year ago - 13 comments

#250 - Use moment constraints to choose timepoints for prior?

Issue - State: closed - Opened by nspope over 1 year ago - 1 comment

#249 - Return marginal likelihood from inside pass

Issue - State: closed - Opened by nspope over 1 year ago - 2 comments

#248 - Priors with piecewise demographic histories

Pull Request - State: closed - Opened by nspope over 1 year ago - 18 comments

#247 - Optimize likelihood cache

Issue - State: open - Opened by hyanwong over 1 year ago - 1 comment

#246 - Implement lightweight benchmarks

Issue - State: open - Opened by hyanwong over 1 year ago

#245 - Rename "reduce" to "ratio"

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 1 comment

#244 - Change "normalize" to "standardize"

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 3 comments

#243 - Just a bit of code tidying

Pull Request - State: closed - Opened by hyanwong over 1 year ago

#242 - Reinstate unary node tests

Pull Request - State: closed - Opened by hyanwong over 1 year ago

#241 - Branch length distribution between parent and child nodes within the same timeslice

Issue - State: open - Opened by hyanwong over 1 year ago - 19 comments

#240 - Mean time in discretised distribution

Issue - State: open - Opened by hyanwong over 1 year ago - 12 comments

#239 - Allow easy conversion from generations to calendar time

Issue - State: open - Opened by hyanwong over 1 year ago

#238 - Separate out the grid creating and filling step

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 13 comments

#237 - Iterative approach to variable Ne

Issue - State: open - Opened by hyanwong over 1 year ago - 11 comments

#236 - More accuracy tests

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 1 comment

#235 - Correct docstring for create_timepoints

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 1 comment

#234 - Shifting copyright for altered files to Tskit Developers

Issue - State: closed - Opened by hyanwong over 1 year ago - 4 comments

#233 - Better timeslices

Pull Request - State: open - Opened by hyanwong over 1 year ago - 7 comments

#232 - Fix unit test and posteriors

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 3 comments

#231 - Allow ConditionalCoalescentTimes displayed as str

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 2 comments

#230 - Returned posteriors incorrect for 2 tip tree with mutation_rate=None

Issue - State: open - Opened by hyanwong over 1 year ago - 6 comments

#229 - Bias due to timepoint selection

Issue - State: open - Opened by hyanwong over 1 year ago

#228 - Allow scaling function for Ne

Issue - State: closed - Opened by hyanwong over 1 year ago - 3 comments

#227 - Require newer tsinfer version

Pull Request - State: closed - Opened by hyanwong over 1 year ago

#226 - Don't warn when we expect np.log(0) to occur

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 1 comment

#225 - Fix nested loop var and remove duplicate class name

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 1 comment

#224 - Describe the actual time values

Pull Request - State: closed - Opened by hyanwong over 1 year ago - 1 comment

#223 - Mask out more regions of genome using `preprocess_ts`

Issue - State: open - Opened by hyanwong over 1 year ago

#222 - New tsinfer edge trimming may bias tsdate

Issue - State: open - Opened by hyanwong over 1 year ago - 3 comments

#221 - Readthedocs "latest" version not updating

Issue - State: closed - Opened by hyanwong almost 2 years ago - 4 comments

#220 - Accuracy test

Pull Request - State: closed - Opened by hyanwong almost 2 years ago - 1 comment

#219 - Add a simple / trivial QC method to the test suite?

Issue - State: closed - Opened by hyanwong almost 2 years ago

#218 - No need to pass timepoints to posterior_mean_var

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#217 - Revisit numba pinning

Issue - State: closed - Opened by hyanwong almost 2 years ago - 1 comment

#216 - constrain_ages_topo assumes nodes are in time order

Issue - State: closed - Opened by hyanwong almost 2 years ago - 10 comments

#215 - Remove noop

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#214 - Allow historical samples

Pull Request - State: open - Opened by hyanwong almost 2 years ago - 8 comments

#213 - New logo

Pull Request - State: closed - Opened by benjeffery almost 2 years ago

#212 - Allow unary nodes (not default) when creating prior

Pull Request - State: closed - Opened by hyanwong almost 2 years ago - 1 comment

#211 - Fix git issue in wheel building

Pull Request - State: closed - Opened by benjeffery about 2 years ago

#210 - Release 0.1.5?

Issue - State: closed - Opened by benjeffery about 2 years ago - 3 comments

#209 - Build wheel on python 3.10

Pull Request - State: closed - Opened by benjeffery about 2 years ago

GitHub / tskit-dev/tsdate issues and pull requests