Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Piecewise uniform prior for timescale #371

Merged
merged 3 commits into from
May 13, 2024
Merged

Piecewise uniform prior for timescale #371

merged 3 commits into from
May 13, 2024

Conversation

nspope
Copy link
Contributor

@nspope nspope commented Feb 17, 2024 •
edited
Loading

Overhaul of variational dating, in particular re-estimating the timescale after expectation propagation

@nspope nspope marked this pull request as ready for review May 2, 2024 00:50
@nspope
Copy link
Contributor Author

nspope commented May 2, 2024

@hyanwong I think we should get this in, and add unit tests for normalisation.py in a followup (once that algorithm stabilizes). Testing is a bit of mess at the moment because of the different algorithms / options / CLI, and needs a cleanup overall.

@hyanwong hyanwong self-requested a review May 13, 2024 12:43
hyanwong
hyanwong approved these changes May 13, 2024
View reviewed changes
Copy link
Member

@hyanwong hyanwong left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

All LGTM. You can ignore as many comments as you like @nspope, or open an issue and we can address anything later. Let me know if you would like me to merge?

evaluation/evaluate_accuracy.py Show resolved Hide resolved
tests/test_cli.py Show resolved Hide resolved
tests/test_functions.py Outdated Show resolved Hide resolved
tests/test_inference.py Show resolved Hide resolved
tests/test_inference.py Show resolved Hide resolved
tests/test_inference.py Outdated Show resolved Hide resolved
tsdate/core.py Show resolved Hide resolved
tsdate/core.py Show resolved Hide resolved
tsdate/variational.py Show resolved Hide resolved
@nspope
Copy link
Contributor Author

nspope commented May 13, 2024

Thanks for looking @hyanwong, let's merge this in

@hyanwong hyanwong merged commit 110a09b into tskit-dev:main May 13, 2024
3 checks passed
@hyanwong
Copy link
Member

Done!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@hyanwong hyanwong hyanwong approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@nspope @hyanwong