Add thorney beast support in Beauti #1211
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This reverts commit 3661e10.
jtmccr1
commented
Dec 18, 2024
jtmccr1
commented
Dec 18, 2024
| @@ -239,6 +239,23 @@ public void checkOptions() throws GeneratorException { | |||
| } | |||
| } | |||
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| //+++++++++++++++++ ThorneyBEAST / clock model Verification ++++++++++++++ | |||
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Warns the user about using a clock model for which gradients for tb are not implemented
jtmccr1
commented
Dec 18, 2024
| @@ -254,7 +254,11 @@ public List<Parameter> selectParameters(List<Parameter> parameters) { | |||
| Set<PartitionSubstitutionModel> substitutionModels = new LinkedHashSet<>(); | |||
| for (AbstractPartitionData partition : getDataPartitions()) { | |||
| if (partition.getPartitionClockModel() == model) { | |||
| substitutionModels.add(partition.getPartitionSubstitutionModel()); | |||
| PartitionSubstitutionModel substitutionModel = partition.getPartitionSubstitutionModel(); | |||
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DataType.Tree partitions don't have substitution models. This ensures we don't add 'null' substitution models t
jtmccr1
commented
Dec 18, 2024
| @@ -557,8 +557,9 @@ public List<Operator> selectOperators(List<Operator> operators) { | |||
| List<Operator> ops = new ArrayList<Operator>(); | |||
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| if (options.hasData()) { | |||
| if (getDataType().getType() != DataType.TREE) { | |||
| if (getDataType().getType() != DataType.TREE || getPartitionTreeModel().isUsingThorneyBEAST()) { | |||
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TB analyses have clock models
jtmccr1
commented
Dec 18, 2024
| private boolean isNewick = true; | ||
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| private boolean hasTipCalibrations = false; | ||
| 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 ); |
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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(); | ||
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Lifting these to the parent class to make it is easier to BigFastTrees and DefaultTrees interchangeably.
jtmccr1
commented
Dec 18, 2024
| @@ -38,7 +39,7 @@ | |||
| * @author Marc A. Suchard | |||
| * @author Xiang Ji | |||
| */ | |||
| public class NodeHeightProxyParameter extends Parameter.Proxy { | |||
| public class NodeHeightProxyParameter extends Parameter.Proxy implements Bounds<Double> { | |||
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Calculating bounds on the fly so we can use these proxy parameters in node heigh operators
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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: