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.

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

Update standard operators to Bactrian operators used in BEAST 2.7.x #109

Closed
walterxie opened this issue May 2, 2023 · 5 comments
Closed
Labels
critical change the bug fix or new feature will significant change the code enhancement New feature or request

Comments

@walterxie
Copy link
Collaborator

walterxie commented May 2, 2023

Most of operators in BEAST 2.7.x have been different to 2.6, which are more effective.

In addition, the relaxed clock model has new operators to optimise the sampling between rates and trees. It'd better to replace the old ones.

@walterxie walterxie added the enhancement New feature or request label May 2, 2023
@walterxie walterxie pinned this issue Aug 16, 2023
@walterxie walterxie added the critical change the bug fix or new feature will significant change the code label Sep 20, 2023
walterxie added a commit that referenced this issue Dec 19, 2023
…ed AdaptableOperatorSampler and AdaptableVarianceMultivariateNormalOperator #109
@walterxie
Copy link
Collaborator Author

TODO: AdaptableOperatorSampler and AdaptableVarianceMultivariateNormalOperator

@walterxie
Copy link
Collaborator Author

walterxie commented Jan 15, 2024

The BEAST AdaptableOperatorSampler, especially AdaptableVarianceMultivariateNormalOperator, have to know the specific type of parameters, such as frequencies, site and substitution model parameters, and trees. So it requires to create these operators in GeneratorToBEAST. In addition, it may add another list in BEASTContext to store these operators.

walterxie added a commit that referenced this issue Jan 16, 2024
@walterxie
Copy link
Collaborator Author

walterxie commented Jan 17, 2024

AdaptableOperatorSampler and AdaptableVarianceMultivariateNormalOperator are very complex, leave them in #128. This release will cut off at the commit 8ac4505.

@walterxie walterxie changed the title Update all operators to BEAST 2.7.x Update standard operators to Bactrian operators used in BEAST 2.7.x Jan 17, 2024
@walterxie
Copy link
Collaborator Author

pass the test of RSV2

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
critical change the bug fix or new feature will significant change the code enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

1 participant