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not working - will ask AR
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@GuyBaele
GuyBaele committed Oct 10, 2024
1 parent 54aeb8b commit 38e2b7d
Showing 1 changed file with 82 additions and 74 deletions.
156 changes: 82 additions & 74 deletions src/dr/app/beauti/generator/ClockModelGenerator.java
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Expand Up @@ -28,11 +28,9 @@
package dr.app.beauti.generator;

import dr.app.beauti.components.ComponentFactory;
import dr.app.beauti.options.BeautiOptions;
import dr.app.beauti.options.Parameter;
import dr.app.beauti.options.PartitionClockModel;
import dr.app.beauti.options.PartitionTreeModel;
import dr.app.beauti.options.*;
import dr.app.beauti.types.ClockType;
import dr.app.beauti.types.OperatorType;
import dr.app.beauti.util.XMLWriter;
import dr.evolution.util.Taxa;
import dr.evomodel.branchratemodel.ArbitraryBranchRates;
Expand Down Expand Up @@ -301,78 +299,88 @@ public void writeBranchRatesModel(PartitionClockModel clockModel, XMLWriter writ

writeCovarianceStatistic(writer, tag, prefix, treePrefix);

//scale prior
writer.writeOpenTag(DistributionLikelihood.DISTRIBUTION_LIKELIHOOD,
new Attribute.Default<>(XMLParser.ID,
prefix + BranchSpecificFixedEffects.SCALE_PRIOR));
writeParameterRef(MixedDistributionLikelihoodParser.DATA, prefix + ClockType.HMCLN_SCALE, writer);
writer.writeOpenTag(DistributionLikelihoodParser.DISTRIBUTION);
writer.writeOpenTag(ExponentialDistributionModel.EXPONENTIAL_DISTRIBUTION_MODEL);
writer.writeOpenTag(ExponentialDistributionModelParser.MEAN);
writeParameter(null, 1, 1.0, 0.0, Double.NaN, writer);
writer.writeCloseTag(ExponentialDistributionModelParser.MEAN);
writer.writeCloseTag(ExponentialDistributionModel.EXPONENTIAL_DISTRIBUTION_MODEL);
writer.writeCloseTag(DistributionLikelihoodParser.DISTRIBUTION);
writer.writeCloseTag(DistributionLikelihood.DISTRIBUTION_LIKELIHOOD);
//TODO put this in an IF statement depending on choice in BEAUti
boolean generateScaleGradient = false;
if (options.getOperator("HMC relaxed clock location and scale").isUsed()) {
generateScaleGradient = true;
}

//compound parameter
writer.writeOpenTag(CompoundParameterParser.COMPOUND_PARAMETER, new Attribute.Default<>(XMLParser.ID, prefix + LocationScaleGradientParser.LOCATION_SCALE));
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMC_CLOCK_LOCATION);
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMCLN_SCALE);
writer.writeCloseTag(CompoundParameterParser.COMPOUND_PARAMETER);
if (generateScaleGradient) {

//CTMC scale prior
writer.writeOpenTag(CTMCScalePriorParser.MODEL_NAME, new Attribute.Default<>(XMLParser.ID, prefix + BranchSpecificFixedEffects.LOCATION_PRIOR));
writer.writeOpenTag(CTMCScalePriorParser.SCALEPARAMETER);
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMC_CLOCK_LOCATION);
writer.writeCloseTag(CTMCScalePriorParser.SCALEPARAMETER);
writer.writeIDref(DefaultTreeModel.TREE_MODEL, treePrefix + DefaultTreeModel.TREE_MODEL);
writer.writeCloseTag(CTMCScalePriorParser.MODEL_NAME);

//location gradient
writer.writeOpenTag(LocationScaleGradientParser.NAME, new Attribute[] {
new Attribute.Default<>(XMLParser.ID, prefix + LocationGradient.LOCATION_GRADIENT),
new Attribute.Default<>("traitName", "Sequence"),
new Attribute.Default<>(LocationScaleGradientParser.USE_HESSIAN, "false")
});
writer.writeIDref(TreeDataLikelihoodParser.TREE_DATA_LIKELIHOOD, treePrefix + "treeLikelihood");
writer.writeOpenTag(LocationScaleGradientParser.LOCATION);
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMC_CLOCK_LOCATION);
writer.writeCloseTag(LocationScaleGradientParser.LOCATION);
writer.writeCloseTag(LocationScaleGradientParser.NAME);

//scale gradient
writer.writeOpenTag(LocationScaleGradientParser.NAME, new Attribute[] {
new Attribute.Default<>(XMLParser.ID, prefix + ScaleGradient.SCALE_GRADIENT),
new Attribute.Default<>("traitName", "Sequence"),
new Attribute.Default<>(LocationScaleGradientParser.USE_HESSIAN, "false")
});
writer.writeIDref(TreeDataLikelihoodParser.TREE_DATA_LIKELIHOOD, treePrefix + "treeLikelihood");
writer.writeOpenTag(LocationScaleGradientParser.SCALE);
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMCLN_SCALE);
writer.writeCloseTag(LocationScaleGradientParser.SCALE);
writer.writeCloseTag(LocationScaleGradientParser.NAME);

//location scale (compound) gradient
writer.writeOpenTag(CompoundGradientParser.COMPOUND_GRADIENT, new Attribute.Default<>(XMLParser.ID, prefix + LocationScaleGradientParser.NAME));
writer.writeIDref(LocationScaleGradientParser.NAME, prefix + LocationGradient.LOCATION_GRADIENT);
writer.writeIDref(LocationScaleGradientParser.NAME, prefix + ScaleGradient.SCALE_GRADIENT);
writer.writeCloseTag(CompoundGradientParser.COMPOUND_GRADIENT);

//location scale (compound) prior gradient
writer.writeOpenTag(CompoundGradientParser.COMPOUND_GRADIENT, new Attribute.Default<>(XMLParser.ID, prefix + LocationScaleGradientParser.LOCATION_SCALE_PRIOR_GRADIENT));
writer.writeIDref(CTMCScalePriorParser.MODEL_NAME, prefix + BranchSpecificFixedEffects.LOCATION_PRIOR);
writer.writeOpenTag(HessianWrapperParser.NAME);
writer.writeIDref(DistributionLikelihood.DISTRIBUTION_LIKELIHOOD, BranchSpecificFixedEffects.SCALE_PRIOR);
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMCLN_SCALE);
writer.writeCloseTag(HessianWrapperParser.NAME);
writer.writeCloseTag(CompoundGradientParser.COMPOUND_GRADIENT);

//location scale joint gradient
writer.writeOpenTag(JointGradientParser.JOINT_GRADIENT, new Attribute.Default<>(XMLParser.ID, prefix + LocationScaleGradientParser.LOCATION_SCALE_JOINT_GRADIENT));
writer.writeIDref(CompoundGradientParser.COMPOUND_GRADIENT, prefix + LocationScaleGradientParser.LOCATION_SCALE_PRIOR_GRADIENT);
writer.writeIDref(CompoundGradientParser.COMPOUND_GRADIENT, prefix + LocationScaleGradientParser.NAME);
writer.writeCloseTag(JointGradientParser.JOINT_GRADIENT);
//scale prior
writer.writeOpenTag(DistributionLikelihood.DISTRIBUTION_LIKELIHOOD,
new Attribute.Default<>(XMLParser.ID,
prefix + BranchSpecificFixedEffects.SCALE_PRIOR));
writeParameterRef(MixedDistributionLikelihoodParser.DATA, prefix + ClockType.HMCLN_SCALE, writer);
writer.writeOpenTag(DistributionLikelihoodParser.DISTRIBUTION);
writer.writeOpenTag(ExponentialDistributionModel.EXPONENTIAL_DISTRIBUTION_MODEL);
writer.writeOpenTag(ExponentialDistributionModelParser.MEAN);
writeParameter(null, 1, 1.0, 0.0, Double.NaN, writer);
writer.writeCloseTag(ExponentialDistributionModelParser.MEAN);
writer.writeCloseTag(ExponentialDistributionModel.EXPONENTIAL_DISTRIBUTION_MODEL);
writer.writeCloseTag(DistributionLikelihoodParser.DISTRIBUTION);
writer.writeCloseTag(DistributionLikelihood.DISTRIBUTION_LIKELIHOOD);

//compound parameter
writer.writeOpenTag(CompoundParameterParser.COMPOUND_PARAMETER, new Attribute.Default<>(XMLParser.ID, prefix + LocationScaleGradientParser.LOCATION_SCALE));
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMC_CLOCK_LOCATION);
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMCLN_SCALE);
writer.writeCloseTag(CompoundParameterParser.COMPOUND_PARAMETER);

//CTMC scale prior
writer.writeOpenTag(CTMCScalePriorParser.MODEL_NAME, new Attribute.Default<>(XMLParser.ID, prefix + BranchSpecificFixedEffects.LOCATION_PRIOR));
writer.writeOpenTag(CTMCScalePriorParser.SCALEPARAMETER);
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMC_CLOCK_LOCATION);
writer.writeCloseTag(CTMCScalePriorParser.SCALEPARAMETER);
writer.writeIDref(DefaultTreeModel.TREE_MODEL, treePrefix + DefaultTreeModel.TREE_MODEL);
writer.writeCloseTag(CTMCScalePriorParser.MODEL_NAME);

//location gradient
writer.writeOpenTag(LocationScaleGradientParser.NAME, new Attribute[]{
new Attribute.Default<>(XMLParser.ID, prefix + LocationGradient.LOCATION_GRADIENT),
new Attribute.Default<>("traitName", "Sequence"),
new Attribute.Default<>(LocationScaleGradientParser.USE_HESSIAN, "false")
});
writer.writeIDref(TreeDataLikelihoodParser.TREE_DATA_LIKELIHOOD, treePrefix + "treeLikelihood");
writer.writeOpenTag(LocationScaleGradientParser.LOCATION);
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMC_CLOCK_LOCATION);
writer.writeCloseTag(LocationScaleGradientParser.LOCATION);
writer.writeCloseTag(LocationScaleGradientParser.NAME);

//scale gradient
writer.writeOpenTag(LocationScaleGradientParser.NAME, new Attribute[]{
new Attribute.Default<>(XMLParser.ID, prefix + ScaleGradient.SCALE_GRADIENT),
new Attribute.Default<>("traitName", "Sequence"),
new Attribute.Default<>(LocationScaleGradientParser.USE_HESSIAN, "false")
});
writer.writeIDref(TreeDataLikelihoodParser.TREE_DATA_LIKELIHOOD, treePrefix + "treeLikelihood");
writer.writeOpenTag(LocationScaleGradientParser.SCALE);
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMCLN_SCALE);
writer.writeCloseTag(LocationScaleGradientParser.SCALE);
writer.writeCloseTag(LocationScaleGradientParser.NAME);

//location scale (compound) gradient
writer.writeOpenTag(CompoundGradientParser.COMPOUND_GRADIENT, new Attribute.Default<>(XMLParser.ID, prefix + LocationScaleGradientParser.NAME));
writer.writeIDref(LocationScaleGradientParser.NAME, prefix + LocationGradient.LOCATION_GRADIENT);
writer.writeIDref(LocationScaleGradientParser.NAME, prefix + ScaleGradient.SCALE_GRADIENT);
writer.writeCloseTag(CompoundGradientParser.COMPOUND_GRADIENT);

//location scale (compound) prior gradient
writer.writeOpenTag(CompoundGradientParser.COMPOUND_GRADIENT, new Attribute.Default<>(XMLParser.ID, prefix + LocationScaleGradientParser.LOCATION_SCALE_PRIOR_GRADIENT));
writer.writeIDref(CTMCScalePriorParser.MODEL_NAME, prefix + BranchSpecificFixedEffects.LOCATION_PRIOR);
writer.writeOpenTag(HessianWrapperParser.NAME);
writer.writeIDref(DistributionLikelihood.DISTRIBUTION_LIKELIHOOD, BranchSpecificFixedEffects.SCALE_PRIOR);
writer.writeIDref(ParameterParser.PARAMETER, prefix + ClockType.HMCLN_SCALE);
writer.writeCloseTag(HessianWrapperParser.NAME);
writer.writeCloseTag(CompoundGradientParser.COMPOUND_GRADIENT);

//location scale joint gradient
writer.writeOpenTag(JointGradientParser.JOINT_GRADIENT, new Attribute.Default<>(XMLParser.ID, prefix + LocationScaleGradientParser.LOCATION_SCALE_JOINT_GRADIENT));
writer.writeIDref(CompoundGradientParser.COMPOUND_GRADIENT, prefix + LocationScaleGradientParser.LOCATION_SCALE_PRIOR_GRADIENT);
writer.writeIDref(CompoundGradientParser.COMPOUND_GRADIENT, prefix + LocationScaleGradientParser.NAME);
writer.writeCloseTag(JointGradientParser.JOINT_GRADIENT);

}

break;

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