-
Notifications
You must be signed in to change notification settings - Fork 73
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
1 changed file
with
191 additions
and
0 deletions.
There are no files selected for viewing
This file contains 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
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,191 @@ | ||
| <?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> | ||
|
|
||
| <attributePatterns id="loc.pattern" attribute="loc"> | ||
| <taxa idref="taxa"/> | ||
| <generalDataType idref="loc.dataType"/> | ||
| </attributePatterns> | ||
|
|
||
| <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> | ||
|
|
||
| <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> | ||
|
|
||
| <randomField id="test.field"> | ||
| <data> | ||
| <parameter id="loc.coefficients0" value="2 1 -1 1 -3 1"/> | ||
| </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> | ||
|
|
||
| <report> | ||
| <randomField idref="test.field"/> | ||
| <randomFieldGradient idref="test.gradient"/> | ||
| </report> | ||
|
|
||
| <transformedRateSubstitutionModel id="loc.model" | ||
| normalize="true" scaleRatesByFrequencies="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> | ||
| <transformedRates> | ||
| <parameter idref="loc.coefficients0"/> | ||
| <transform type="squared"/> | ||
| </transformedRates> | ||
| </transformedRateSubstitutionModel> | ||
|
|
||
| <!-- | ||
| <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> | ||
| --> | ||
|
|
||
| <siteModel id="loc.siteModel"> | ||
| <substitutionModel> | ||
| <logRateSubstitutionModel idref="loc.model"/> | ||
| </substitutionModel> | ||
| </siteModel> | ||
|
|
||
| <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> | ||
|
|
||
| <approximateTransformedCtmcRateGradient id="gradient1" traitName="loc"> | ||
| <treeDataLikelihood idref="treeLikelihood"/> | ||
| <transformedRateSubstitutionModel idref="loc.model"/> | ||
| </approximateTransformedCtmcRateGradient> | ||
|
|
||
| <report> | ||
| <approximateLogCtmcRateGradient idref="gradient1"/> | ||
| </report> | ||
|
|
||
| <jointGradient id="joint.gradient"> | ||
| <approximateTransformedCtmcRateGradient idref="gradient1"/> | ||
| <randomFieldGradient idref="test.gradient"/> | ||
| </jointGradient> | ||
|
|
||
| </beast> |