Add thorney beast support in Beauti #1211
Open
+7,219
−188
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This reverts commit 3661e10.
jtmccr1
commented
Dec 18, 2024
jtmccr1
commented
Dec 18, 2024
| } | ||
| } | ||
|
|
||
| //+++++++++++++++++ ThorneyBEAST / clock model Verification ++++++++++++++ |
Contributor
Author
There was a problem hiding this comment.
Warns the user about using a clock model for which gradients for tb are not implemented
jtmccr1
commented
Dec 18, 2024
| for (AbstractPartitionData partition : getDataPartitions()) { | ||
| if (partition.getPartitionClockModel() == model) { | ||
| substitutionModels.add(partition.getPartitionSubstitutionModel()); | ||
| PartitionSubstitutionModel substitutionModel = partition.getPartitionSubstitutionModel(); |
Contributor
Author
There was a problem hiding this comment.
DataType.Tree partitions don't have substitution models. This ensures we don't add 'null' substitution models t
jtmccr1
commented
Dec 18, 2024
|
|
||
| if (options.hasData()) { | ||
| if (getDataType().getType() != DataType.TREE) { | ||
| if (getDataType().getType() != DataType.TREE || getPartitionTreeModel().isUsingThorneyBEAST()) { |
Contributor
Author
There was a problem hiding this comment.
TB analyses have clock models
jtmccr1
commented
Dec 18, 2024
| private boolean hasNodeCalibrations = false; | ||
| public static List<ClockType> thorneyCompatibleClocks = Arrays.asList( ClockType.STRICT_CLOCK, ClockType.UNCORRELATED, | ||
| ClockType.FIXED_LOCAL_CLOCK, ClockType.RANDOM_LOCAL_CLOCK, ClockType.FIXED_LOCAL_CLOCK, | ||
| ClockType.MIXED_EFFECTS_CLOCK ); |
Contributor
Author
There was a problem hiding this comment.
List of TB compatible clocks (all others use gradients)
jtmccr1
commented
Dec 18, 2024
| abstract public boolean hasNodeTraits(); | ||
| abstract public void swapAllTraits(NodeRef node1, NodeRef node2); | ||
| abstract public boolean hasRates(); | ||
|
|
Contributor
Author
There was a problem hiding this comment.
Lifting these to the parent class to make it is easier to BigFastTrees and DefaultTrees interchangeably.
jtmccr1
commented
Dec 18, 2024
| * @author Xiang Ji | ||
| */ | ||
| public class NodeHeightProxyParameter extends Parameter.Proxy { | ||
| public class NodeHeightProxyParameter extends Parameter.Proxy implements Bounds<Double> { |
Contributor
Author
There was a problem hiding this comment.
Calculating bounds on the fly so we can use these proxy parameters in node heigh operators
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This is a smaller request than the previous one to add support for thorney beast to beauti.
This does not use BigFastIntervals in any way and so we don't wander into the breaking changes discussed elsewhere.
I will comment on other changes below but the two that stick out are: