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revert changes to test file
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@yucais
yucais committed Jul 31, 2023
1 parent c21fd5b commit a07ffb9
Showing 1 changed file with 196 additions and 4 deletions.
200 changes: 196 additions & 4 deletions ci/TestXML/testEssbdpGradient.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -57,10 +57,10 @@
<samplingRate>
<parameter id="bdss1.samplingRate" value ="3.42 2.95 1.21" lower="0.0"/>
</samplingRate>
<samplingProbability gradientFlag = "false">
<samplingProbability>
<parameter id="bdss1.samplingProbability" value ="0.2 0.8 0.6" lower="0.0" upper="1.0"/>
</samplingProbability>
<treatmentProbability gradientFlag = "false">
<treatmentProbability>
<parameter id="bdss1.treatmentProbability" value ="0.4 0.3 0.1" lower="0.0" upper="1.0"/>
</treatmentProbability>
<origin>
Expand Down Expand Up @@ -113,6 +113,9 @@
<speciationLikelihoodGradient idref="grad.birthRate1"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.deathRate1"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.samplingRate1"/>
Expand All @@ -134,10 +137,10 @@
<samplingRate>
<parameter id="bdss2.samplingRate" value ="3.42 2.95 1.21" lower="0.0"/>
</samplingRate>
<samplingProbability gradientFlag = "false">
<samplingProbability>
<parameter id="bdss2.samplingProbability" value ="0.07 0.22 0.18" lower="0.0" upper="1.0"/>
</samplingProbability>
<treatmentProbability gradientFlag = "false">
<treatmentProbability>
<parameter id="bdss2.treatmentProbability" value ="0.89 0.93 0.79" lower="0.0" upper="1.0"/>
</treatmentProbability>
<origin>
Expand Down Expand Up @@ -190,11 +193,200 @@
<speciationLikelihoodGradient idref="grad.birthRate2"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.deathRate2"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.samplingRate2"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.samplingProbability2"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.treatmentProbability2"/>
</report>

<!-- ########## -->
<!-- # CASE 3 # -->
<!-- ########## -->

<!-- macroevolution case -->

<newick id="startingTree2" usingHeights="true" usingDates="false">
((D:0.353,C:0.353):0.303,(B:0.471,A:0.471):0.185)
</newick>

<!-- Generate a tree model -->
<treeModel id="treeModel2">
<newick idref="startingTree2"/>
<rootHeight>
<parameter id="treeModel2.rootHeight"/>
</rootHeight>
<nodeHeights internalNodes="true">
<parameter id="treeModel2.internalNodeHeights"/>
</nodeHeights>
<nodeHeights internalNodes="true" rootNode="true">
<parameter id="treeModel2.allInternalNodeHeights"/>
</nodeHeights>
</treeModel>


<newBirthDeathSerialSampling id="bdss3" units="years" conditionOnSurvival="false">
<birthRate>
<parameter id="bdss3.birthRate" value ="8.47 4.66 1.82" lower="0.0"/>
</birthRate>
<deathRate>
<parameter id="bdss3.deathRate" value ="4.89 3.67 3.23" lower="0.0"/>
</deathRate>
<samplingRate>
<parameter id="bdss3.samplingRate" value ="3.42 2.95 1.21" lower="0.0"/>
</samplingRate>
<samplingProbability>
<parameter id="bdss3.samplingProbability" value ="1 0 0" lower="0.0" upper="1.0"/>
</samplingProbability>
<treatmentProbability>
<parameter id="bdss3.treatmentProbability" value ="0 0 0" lower="0.0" upper="1.0"/>
</treatmentProbability>
<origin>
<parameter id="bdss3.origin" value="0.656" lower="0.0"/>
</origin>
<cutOff>
<parameter value="0.656"/>
</cutOff>
<numGridPoints>
<parameter value="3"/>
</numGridPoints>
</newBirthDeathSerialSampling>

<!-- Generate a speciation likelihood for Yule or Birth Death -->
<speciationLikelihood id="speciation3" useNewLoop="true">
<model>
<newBirthDeathSerialSampling idref="bdss3"/>
</model>
<speciesTree>
<treeModel idref="treeModel2"/>
</speciesTree>
</speciationLikelihood>

<speciationLikelihoodGradient id="grad.birthRate3" wrtParameter="birthRate" useNewLoop="true">
<speciationLikelihood idref="speciation3"/>
<treeModel idref="treeModel2"/>
</speciationLikelihoodGradient>


<speciationLikelihoodGradient id="grad.deathRate3" wrtParameter="deathRate" useNewLoop="true">
<speciationLikelihood idref="speciation3"/>
<treeModel idref="treeModel2"/>
</speciationLikelihoodGradient>

<speciationLikelihoodGradient id="grad.samplingRate3" wrtParameter="samplingRate" useNewLoop="true">
<speciationLikelihood idref="speciation3"/>
<treeModel idref="treeModel2"/>
</speciationLikelihoodGradient>



<report>
<speciationLikelihoodGradient idref="grad.birthRate3"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.deathRate3"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.samplingRate3"/>
</report>


<!-- ########## -->
<!-- # CASE 4 # -->
<!-- ########## -->

<!-- Origin is in different interval from rest of tree -->
<newBirthDeathSerialSampling id="new.bdss4" units="years" hasFinalSample="false" conditionOnSurvival="false">
<birthRate>
<parameter id="bdss4.birthRate" value ="8.47 2.88 1.82" lower="0.0"/>
</birthRate>
<deathRate>
<parameter id="bdss4.deathRate" value ="4.89 2.67 3.23" lower="0.0"/>
</deathRate>
<samplingRate>
<parameter id="bdss4.samplingRate" value ="3.42 2.95 1.21" lower="0.0"/>
</samplingRate>
<samplingProbability>
<parameter id="bdss4.samplingProbability" value ="0.07 0.22 0.18" lower="0.0" upper="1.0"/>
</samplingProbability>
<treatmentProbability>
<parameter id="bdss4.treatmentProbability" value ="0.89 0.93 0.79" lower="0.0" upper="1.0"/>
</treatmentProbability>
<origin>
<parameter id="bdss4.origin" value="20.0" lower="0.0"/>
</origin>
<cutOff>
<parameter value="18.0"/>
</cutOff>
<numGridPoints>
<parameter value="3"/>
</numGridPoints>
</newBirthDeathSerialSampling>

<speciationLikelihood id="speciation4" useNewLoop="true">
<model>
<newBirthDeathSerialSampling idref="new.bdss4"/>
</model>
<speciesTree>
<treeModel idref="treeModel"/>
</speciesTree>
</speciationLikelihood>

<speciationLikelihoodGradient id="grad.birthRate4" wrtParameter="birthRate" useNewLoop="true">
<speciationLikelihood idref="speciation4"/>
<treeModel idref="treeModel"/>
</speciationLikelihoodGradient>

<speciationLikelihoodGradient id="grad.deathRate4" wrtParameter="deathRate" useNewLoop="true">
<speciationLikelihood idref="speciation4"/>
<treeModel idref="treeModel"/>
</speciationLikelihoodGradient>

<speciationLikelihoodGradient id="grad.samplingRate4" wrtParameter="samplingRate" useNewLoop="true">
<speciationLikelihood idref="speciation4"/>
<treeModel idref="treeModel"/>
</speciationLikelihoodGradient>

<speciationLikelihoodGradient id="grad.samplingProbability4" wrtParameter="samplingProbability" useNewLoop="true">
<speciationLikelihood idref="speciation4"/>
<treeModel idref="treeModel"/>
</speciationLikelihoodGradient>

<speciationLikelihoodGradient id="grad.treatmentProbability4" wrtParameter="treatmentProbability" useNewLoop="true">
<speciationLikelihood idref="speciation4"/>
<treeModel idref="treeModel"/>
</speciationLikelihoodGradient>


<report>
<speciationLikelihoodGradient idref="grad.birthRate4"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.deathRate4"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.samplingRate4"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.samplingProbability4"/>
</report>

<report>
<speciationLikelihoodGradient idref="grad.treatmentProbability4"/>
</report>

</beast>

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