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

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walterxie opened this issue May 2, 2023 · 5 comments
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Update standard operators to Bactrian operators used in BEAST 2.7.x #109

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

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@walterxie
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walterxie commented May 2, 2023 •
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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
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walterxie added a commit that referenced this issue Dec 18, 2023
@walterxie
create new TreeOperatorStrategy for Bactrian operators #109
c1078aa
walterxie added a commit that referenced this issue Dec 19, 2023
@walterxie
rewrite the OperatorStrategy and update to Bactrian operators, but ne…
10da1e7 
…ed AdaptableOperatorSampler and AdaptableVarianceMultivariateNormalOperator #109
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TODO: AdaptableOperatorSampler and AdaptableVarianceMultivariateNormalOperator

walterxie added a commit that referenced this issue Jan 15, 2024
@walterxie
update to BactrianUpDownOperator #109
dbc1cf6
walterxie added a commit that referenced this issue Jan 15, 2024
@walterxie
move addUpDownOperator to the same class creating all operators #109
8ac4505
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walterxie commented Jan 15, 2024 •
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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
first version to create XML with new operators #109
2d2aaaf
walterxie added a commit that referenced this issue Jan 16, 2024
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save TODO #109
52ae3fe
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walterxie commented Jan 17, 2024 •
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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
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pass the test of RSV2

@walterxie walterxie unpinned this issue Jan 17, 2024
@walterxie walterxie reopened this Jan 17, 2024
walterxie added a commit that referenced this issue Jan 17, 2024
@walterxie
move addDeltaExchangeOperator to the same class creating all operators …
e6b7cce 
…#109
walterxie added a commit that referenced this issue Jan 17, 2024
@walterxie
fix unit tests #109 #112
bdf24a3
walterxie added a commit that referenced this issue Jan 17, 2024
@walterxie
fix build, strange github workflow #109 #112
2e769fa
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