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Just change some values of parameters #56
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@zjzxiaohei
zjzxiaohei committed Oct 14, 2024
1 parent 093f420 commit 29f8739
Showing 1 changed file with 40 additions and 21 deletions.
61 changes: 40 additions & 21 deletions examples/test_read_count_model.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,8 @@
<sequence id="Sequence5" spec="Sequence" taxon="5" totalcount="6" value="b1a103561b"/>
</data>



read counts
<readCount id="readcount" spec="phylonco.beast.evolution.datatype.ReadCount">
0,0,3,12; 9,0,0,0; 14,0,4,0; 15,1,0,0; 16,0,0,0; 13,0,0,11; 1,2,0,7; 0,8,10,0; 7,0,10,0; 0,0,16,8;
Expand All @@ -60,41 +62,58 @@
<state id="state" spec="State">
<parameter id="epsilon" lower="0.0" upper="1.0" dimension="1" name="stateNode">0.1</parameter>
<parameter id="delta" lower="0.0" upper="1.0" dimension="1" name="stateNode">0.2</parameter>
<parameter id="t" lower="1.0" upper="10.0" dimension="1" name="stateNode">9.510591534058255</parameter>
<parameter id="v" lower="0.0" upper="10.0" dimension="1" name="stateNode">1.1699892891308206</parameter>
<parameter id="s" lower="0.5" upper="1.5" dimension="6" name="stateNode">1.039915 1.042499 1.039479 1.040432 1.042806 1.042825</parameter>
<parameter id="w" lower="0.0" dimension="1" name="stateNode">10.0</parameter>
<parameter id="t" dimension="1" name="stateNode">9.510591534058255</parameter>
<parameter id="v" dimension="1" name="stateNode">1.1699892891308206</parameter>
<parameter id="s" dimension="6" name="stateNode">1.039915 1.042499 1.039479 1.040432 1.042806 1.042825</parameter>
<parameter id="w" dimension="1" name="stateNode">10.0</parameter>
</state>



<distribution spec='CompoundDistribution' id='posterior'>
<distribution id="prior" spec="CompoundDistribution">
<prior id='epsilonPrior' name='distribution' x='@epsilon'>
<Beta id="BetaDistributionModel.0" name="distr">
<parameter estimate="false" id="RealParameter.0" name="alpha" value="10.0"/>
<parameter estimate="false" id="RealParameter.1" name="beta" value="100.0"/>
</Beta>
</prior>
<prior id='deltaPrior' name='distribution' x='@delta'>
<Beta id="BetaDistributionModel.1" name="distr">
<parameter estimate="false" id="RealParameter.2" name="alpha" value="25.0"/>
<parameter estimate="false" id="RealParameter.3" name="beta" value="100.0"/>
</Beta>
</prior>
<prior id='tPrior' name='distribution' x='@t'>
<LogNormal id="LogNormalDistributionModel.0" name="distr">
<parameter estimate="false" id="RealParameter.0" name="M" value="0.1"/>
<parameter estimate="false" id="RealParameter.1" lower="0.0" name="S" upper="5.0"
value="1.25"/>
<parameter estimate="false" id="RealParameter.4" name="M" value="1.702"/>
<parameter estimate="false" id="RealParameter.5" name="S" value="0.8671"/>
</LogNormal>
</prior>
<prior id='vPrior' name='distribution' x='@v'>
<LogNormal id="LogNormalDistributionModel.1" name="distr">
<parameter estimate="false" id="RealParameter.2" name="M" value="0.1"/>
<parameter estimate="false" id="RealParameter.3" lower="0.0" name="S" upper="5.0"
value="1.25"/>
<parameter estimate="false" id="RealParameter.6" name="M" value="0.8"/>
<parameter estimate="false" id="RealParameter.7" name="S" value="0.475"/>
</LogNormal>
</prior>
<prior id='sPrior' name='distribution' x='@s'>
<LogNormal id="NormalDistributionModel.2" name="distr">
<parameter estimate="false" id="RealParameter.8" name="M" value="0.2"/>
<parameter estimate="false" id="RealParameter.9" name="S" value="0.75"/>
</LogNormal>
</prior>
<prior id='wPrior' name='distribution' x='@w'>
<LogNormal id="LogNormalDistributionModel.2" name="distr">
<parameter estimate="false" id="RealParameter.4" name="M" value="0.1"/>
<parameter estimate="false" id="RealParameter.5" lower="0.0" name="S" upper="5.0"
value="1.25"/>
<parameter estimate="false" id="RealParameter.10" name="M" value="2.5"/>
<parameter estimate="false" id="RealParameter.11" name="S" value="1.0"/>
</LogNormal>
</prior>
</distribution>

<distribution id="likelihood" spec="CompoundDistribution">
<!-- The read count model -->
<!-- read count model -->
<distribution spec='phylonco.beast.evolution.readcountmodel.ReadCountModel' id='readcountmodel'>
<distribution spec='phylonco.beast.evolution.readcountmodel.LikelihoodReadCountModel' id='readcountmodel'>
<delta idref="delta"/>
<epsilon idref="epsilon"/>
<t idref="t"/>
Expand All @@ -109,18 +128,18 @@
</distribution>

<!-- Read count model operators -->
<operator id='deltaScaler' spec='ScaleOperator' scaleFactor='0.05' weight='1' parameter='@delta'/>
<operator id='epsilonScaler' spec='ScaleOperator' scaleFactor='0.05' weight='1' parameter='@epsilon'/>
<operator id='tScaler' spec='ScaleOperator' scaleFactor='0.1' weight='1' parameter='@t'/>
<operator id='vScaler' spec='ScaleOperator' scaleFactor='0.01' weight='1' parameter='@v'/>
<operator id='sScaler' spec='ScaleOperator' scaleFactor='0.01' weight='1' parameter='@s'/>
<operator id='wScaler' spec='ScaleOperator' scaleFactor='0.2' weight='1' parameter='@w'/>
<operator id='deltaScaler' spec='ScaleOperator' scaleFactor='0.5' weight='1' parameter='@delta'/>
<operator id='epsilonScaler' spec='ScaleOperator' scaleFactor='0.5' weight='1' parameter='@epsilon'/>
<operator id='tScaler' spec='ScaleOperator' scaleFactor='0.75' weight='1' parameter='@t'/>
<operator id='vScaler' spec='ScaleOperator' scaleFactor='0.75' weight='1' parameter='@v'/>
<operator id='sScaler' spec='ScaleOperator' scaleFactor='0.75' weight='1' parameter='@s'/>
<operator id='wScaler' spec='ScaleOperator' scaleFactor='0.9' weight='1' parameter='@w'/>

<!-- RandomWalk or Scale operator for your parameters -->



<logger logEvery="1000" fileName="test_read_count.log">
<logger logEvery="1000" fileName="test_read_count.$(seed).log">
<!-- <model idref='likelihood'/>-->
<!-- <log idref="likelihood"/>-->
<log idref='delta'/>
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