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Test for the LogRateSubstitutionModel
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<?xml version="1.0" encoding="utf-8"?> | ||
<beast> | ||
<taxa id="taxa"> | ||
<taxon id="taxon_1"> | ||
<attr name="loc"> | ||
A | ||
</attr> | ||
</taxon> | ||
<taxon id="taxon_2"> | ||
<attr name="loc"> | ||
A | ||
</attr> | ||
</taxon> | ||
<taxon id="taxon_3"> | ||
<attr name="loc"> | ||
A | ||
</attr> | ||
</taxon> | ||
<taxon id="taxon_4"> | ||
<attr name="loc"> | ||
B | ||
</attr> | ||
</taxon> | ||
<taxon id="taxon_5"> | ||
<attr name="loc"> | ||
B | ||
</attr> | ||
</taxon> | ||
<taxon id="taxon_6"> | ||
<attr name="loc"> | ||
B | ||
</attr> | ||
</taxon> | ||
<taxon id="taxon_7"> | ||
<attr name="loc"> | ||
B | ||
</attr> | ||
</taxon> | ||
<taxon id="taxon_8"> | ||
<attr name="loc"> | ||
B | ||
</attr> | ||
</taxon> | ||
<taxon id="taxon_9"> | ||
<attr name="loc"> | ||
B | ||
</attr> | ||
</taxon> | ||
<taxon id="taxon_10"> | ||
<attr name="loc"> | ||
A | ||
</attr> | ||
</taxon> | ||
</taxa> | ||
|
||
<generalDataType id="loc.dataType"> | ||
<state code="A"/> | ||
<state code="B"/> | ||
<state code="C"/> | ||
</generalDataType> | ||
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||
<attributePatterns id="loc.pattern" attribute="loc"> | ||
<taxa idref="taxa"/> | ||
<generalDataType idref="loc.dataType"/> | ||
</attributePatterns> | ||
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||
<newick id="startingTree" usingHeights="true" usingDates="false"> | ||
(taxon_6:1,((((taxon_8:1,taxon_4:1):1,taxon_7:1):1,taxon_10:1):1,((taxon_1:1,(taxon_2:1,taxon_5:1):1):1,(taxon_9:1,taxon_3:1):1):1):1); | ||
</newick> | ||
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||
<treeModel id="treeModel" fixHeights="true"> | ||
<tree idref="startingTree"/> | ||
<rootHeight> | ||
<parameter id="treeModel.rootHeight"/> | ||
</rootHeight> | ||
<nodeHeights internalNodes="true"> | ||
<parameter id="treeModel.internalNodeHeights"/> | ||
</nodeHeights> | ||
<nodeHeights internalNodes="true" rootNode="true"> | ||
<parameter id="treeModel.allInternalNodeHeights"/> | ||
</nodeHeights> | ||
</treeModel> | ||
|
||
<strictClockBranchRates id="loc.branchRates"> | ||
<rate> | ||
<parameter id="loc.clock.rate" value="1E-4" lower="0.0"/> | ||
</rate> | ||
</strictClockBranchRates> | ||
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||
<randomField id="test.field"> | ||
<data> | ||
<parameter id="loc.coefficients0" value="1 0 -1 0 0 0"/> | ||
</data> | ||
<distribution> | ||
<gaussianProcessField id="test.gp" dim="6"> | ||
<orderVariance> | ||
<parameter id="orderVariance" value="1.0"/> | ||
</orderVariance> | ||
<gaussianNoise> | ||
<parameter id="loc.noise" value="1"/> | ||
</gaussianNoise> | ||
<basis> | ||
<designMatrix id="loc.designMatrix0"> | ||
<parameter value="1 0 0 0 0 0"/> | ||
</designMatrix> | ||
<kernel type="dotProduct"/> | ||
</basis> | ||
<basis> | ||
<designMatrix id="loc.designMatrix1"> | ||
<parameter value="0 1 0 0 0 0"/> | ||
</designMatrix> | ||
<kernel type="dotProduct"/> | ||
</basis> | ||
</gaussianProcessField> | ||
</distribution> | ||
</randomField> | ||
<randomFieldGradient id="test.gradient"> | ||
<randomField idref="test.field"/> | ||
<parameter idref="loc.coefficients0"/> | ||
</randomFieldGradient> | ||
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||
<gaussianProcessPrediction id="test.prediction"> | ||
<parameter idref="loc.coefficients0"/> | ||
<additiveGaussianProcessDistribution idref="test.gp"/> | ||
<bases> | ||
<designMatrix id="loc.designMatrixPred0"> | ||
<parameter value="1 2"/> <!-- The dimension of this vector determines the dimension of the output--> | ||
</designMatrix> | ||
<designMatrix id="loc.designMatrixPred1"> | ||
<parameter value="2 1"/> | ||
</designMatrix> | ||
</bases> | ||
</gaussianProcessPrediction> | ||
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||
<report> | ||
<randomField idref="test.field"/> | ||
<randomFieldGradient idref="test.gradient"/> | ||
<gaussianProcessPrediction idref="test.prediction"/> | ||
</report> | ||
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||
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||
<logRateSubstitutionModel id="loc.model" normalize="true"> | ||
<generalDataType idref="loc.dataType"/> | ||
<rootFrequencies> | ||
<frequencyModel id="loc.frequencyModel" normalize="true"> | ||
<generalDataType idref="loc.dataType"/> | ||
<frequencies> | ||
<parameter id="loc.frequencies" dimension="3"/> | ||
</frequencies> | ||
</frequencyModel> | ||
</rootFrequencies> | ||
<logRates> | ||
<parameter idref="loc.coefficients0"/> | ||
</logRates> | ||
</logRateSubstitutionModel> | ||
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||
<siteModel id="loc.siteModel"> | ||
<substitutionModel> | ||
<logRateSubstitutionModel idref="loc.model"/> | ||
</substitutionModel> | ||
</siteModel> | ||
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||
<treeDataLikelihood id="treeLikelihood" useAmbiguities="true" usePreOrder="true" | ||
branchInfinitesimalDerivative="true" | ||
scalingScheme="never" delayScaling="false"> | ||
<patterns idref="loc.pattern"/> | ||
<treeModel idref="treeModel"/> | ||
<siteModel idref="loc.siteModel"/> | ||
<strictClockBranchRates idref="loc.branchRates"/> | ||
</treeDataLikelihood> | ||
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||
<!-- <report>--> | ||
<!-- <treeDataLikelihood idref="treeLikelihood"/>--> | ||
<!-- </report>--> | ||
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||
<approximateLogCtmcRateGradient id="gradient1" traitName="loc"> | ||
<treeDataLikelihood idref="treeLikelihood"/> | ||
<logRateSubstitutionModel idref="loc.model"/> | ||
</approximateLogCtmcRateGradient> | ||
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||
<!-- <report>--> | ||
<!-- <approximateLogCtmcRateGradient idref="gradient1"/>--> | ||
<!-- </report>--> | ||
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||
<jointGradient id="joint.gradient"> | ||
<approximateLogCtmcRateGradient idref="gradient1"/> | ||
<randomFieldGradient idref="test.gradient"/> | ||
</jointGradient> | ||
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<!-- <report>--> | ||
<!-- <jointGradient idref="joint.gradient"/>--> | ||
<!-- </report>--> | ||
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||
<operators id="operators" optimizationSchedule="log"> | ||
<randomWalkOperator windowSize="0.1" weight="1"> | ||
<parameter idref="loc.coefficients0"/> | ||
</randomWalkOperator> | ||
<!-- <scaleOperator scaleFactor="0.75" weight="1">--> | ||
<!-- <parameter idref="loc.kernel"/>--> | ||
<!-- </scaleOperator>--> | ||
</operators> | ||
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||
<!-- check values predictive mean --> | ||
<assertEqual tolerance="1e-3" verbose="true" charactersToStrip="\[\],"> | ||
<message> | ||
Check GP prediction: mean | ||
</message> | ||
<actual regex="mean: (.*?)\n"> | ||
<gaussianProcessPrediction idref="test.prediction"/> | ||
</actual> | ||
<expected> | ||
0.5 1 | ||
</expected> | ||
</assertEqual> | ||
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<!-- check values predictive variance --> | ||
<assertEqual tolerance="1e-3" verbose="true" charactersToStrip="\[\],"> | ||
<message> | ||
Check GP prediction: variance | ||
</message> | ||
<actual regex="variance: (.*?)\n"> | ||
<gaussianProcessPrediction idref="test.prediction"/> | ||
</actual> | ||
<expected> | ||
2.5 2 2 2.5 | ||
</expected> | ||
</assertEqual> | ||
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<!-- check values Gradients--> | ||
<assertEqual tolerance="1e-3" verbose="true" charactersToStrip="\[\],"> | ||
<message> | ||
Check values for gradient | ||
</message> | ||
<actual regex="analytic:(.*?)\n"> | ||
<randomFieldGradient idref="test.gradient"/> | ||
</actual> | ||
<expected> | ||
-0.5 0 1 0 0 0 | ||
</expected> | ||
</assertEqual> | ||
|
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|
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<report id = "report.prediction"> | ||
<gaussianProcessPrediction idref="test.prediction"/> | ||
</report> | ||
|
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|
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<!-- <!– check value log-likelihood–>--> | ||
<!-- <assertEqual tolerance="1e-3" verbose="true" charactersToStrip="\[\],">--> | ||
<!-- <message>--> | ||
<!-- Check GP prior values (for an MCMC chain of length 0)--> | ||
<!-- </message>--> | ||
<!-- <actual regex="likelihood:(.*?)\n">--> | ||
<!-- <prior idref="prior"/>--> | ||
<!-- </actual>--> | ||
<!-- <expected>--> | ||
<!-- -6.956778--> | ||
<!-- </expected>--> | ||
<!-- </assertEqual>--> | ||
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</beast> |