make param ID's unique

BEAST2-Dev · Jun 1, 2015 · 27e213b · 27e213b
1 parent e60108c
commit 27e213b
Showing 1 changed file with 34 additions and 34 deletions.
diff --git a/templates/BDSKY_serial.xml b/templates/BDSKY_serial.xml
@@ -32,36 +32,36 @@ suppressInputs='beast.evolution.speciation.BirthDeathSkylineModel.intervalTimes,
 <![CDATA[
 <!-- Sequential Birth Death Skyline model-->
 	<BirthDeathSkylineModel spec="beast.evolution.speciation.BirthDeathSkylineModel" id="BirthDeathSkySerial.t:$(n)" tree="@Tree.t:$(n)">
-		<parameter name="origin" id="origin.t:$(n)" value ="100" lower="0." upper="Infinity"/>  	
-		<parameter name="R0" id="R0.t:$(n)" value="2" lower="0." dimension ="10" upper="Infinity"/>
-		<parameter name="becomeUninfectiousRate" id="becomeUninfectiousRate.t:$(n)" value="1." lower="0." upper="Infinity" dimension ="1"/>
-		<parameter name="samplingProportion" id="samplingProportion.t:$(n)" value="0.01" lower="0." upper="1." dimension ="1"/> 
+		<parameter name="origin" id="origin.s.t:$(n)" value ="100" lower="0." upper="Infinity"/>  	
+		<parameter name="R0" id="R0.s.t:$(n)" value="2" lower="0." dimension ="10" upper="Infinity"/>
+		<parameter name="becomeUninfectiousRate" id="becomeUninfectiousRate.s.t:$(n)" value="1." lower="0." upper="Infinity" dimension ="1"/>
+		<parameter name="samplingProportion" id="samplingProportion.s.t:$(n)" value="0.01" lower="0." upper="1." dimension ="1"/> 
 	</BirthDeathSkylineModel>
 
-	<distribution  id='originPrior.t:$(n)' x="@origin.t:$(n)" spec='beast.math.distributions.Prior'>
+	<distribution  id='originPrior.s.t:$(n)' x="@origin.s.t:$(n)" spec='beast.math.distributions.Prior'>
 		<distr spec='beast.math.distributions.Uniform' lower="0." upper="Infinity"/>
 	</distribution>
-	<distribution id="samplingProportionPrior.t:$(n)" spec="beast.math.distributions.Prior" x="@samplingProportion.t:$(n)">
+	<distribution id="samplingProportionPrior.s.t:$(n)" spec="beast.math.distributions.Prior" x="@samplingProportion.s.t:$(n)">
 		<distr spec="beast.math.distributions.Beta" alpha="1." beta="1." offset="0."/>
 	</distribution>
-	<distribution id="becomeUninfectiousRatePrior.t:$(n)" spec="beast.math.distributions.Prior" x="@becomeUninfectiousRate.t:$(n)">
+	<distribution id="becomeUninfectiousRatePrior.s.t:$(n)" spec="beast.math.distributions.Prior" x="@becomeUninfectiousRate.s.t:$(n)">
 		<distr spec='beast.math.distributions.LogNormalDistributionModel' M="0." S="1." offset="0.0" meanInRealSpace="false"/>
 	</distribution>
-	<distribution id="RPrior.t:$(n)" spec="beast.math.distributions.Prior" x="@R0.t:$(n)">
+	<distribution id="RPrior.s.t:$(n)" spec="beast.math.distributions.Prior" x="@R0.s.t:$(n)">
 		<distr spec='beast.math.distributions.LogNormalDistributionModel' M="0." S="1." offset="0.0" meanInRealSpace="false"/>
 	</distribution>
 
-	<RPNcalculator spec="beast.math.statistic.RPNcalculator" id="birth.t:$(n)" expression="R0.t:$(n) becomeUninfectiousRate.t:$(n) *"> <!-- s/(d+s) -->
-		<parameter idref="becomeUninfectiousRate.t:$(n)"/>
-		<parameter idref="R0.t:$(n)"/>        
+	<RPNcalculator spec="beast.math.statistic.RPNcalculator" id="birth.t:$(n)" expression="R0.s.t:$(n) becomeUninfectiousRate.s.t:$(n) *"> <!-- s/(d+s) -->
+		<parameter idref="becomeUninfectiousRate.s.t:$(n)"/>
+		<parameter idref="R0.s.t:$(n)"/>        
 	</RPNcalculator>
-	<RPNcalculator spec="beast.math.statistic.RPNcalculator" id="sampling.t:$(n)" expression="becomeUninfectiousRate.t:$(n) samplingProportion.t:$(n) *"> 
-		<parameter idref="becomeUninfectiousRate.t:$(n)"/>
-		<parameter idref="samplingProportion.t:$(n)"/>        
+	<RPNcalculator spec="beast.math.statistic.RPNcalculator" id="sampling.t:$(n)" expression="becomeUninfectiousRate.s.t:$(n) samplingProportion.s.t:$(n) *"> 
+		<parameter idref="becomeUninfectiousRate.s.t:$(n)"/>
+		<parameter idref="samplingProportion.s.t:$(n)"/>        
 	</RPNcalculator>
-	<RPNcalculator spec="beast.math.statistic.RPNcalculator" id="death.t:$(n)" expression="becomeUninfectiousRate.t:$(n) 1 samplingProportion.t:$(n) - *"> <!-- b*S0/(d+s) -->
-		<parameter idref="becomeUninfectiousRate.t:$(n)"/>
-		<parameter idref="samplingProportion.t:$(n)"/>        
+	<RPNcalculator spec="beast.math.statistic.RPNcalculator" id="death.t:$(n)" expression="becomeUninfectiousRate.s.t:$(n) 1 samplingProportion.s.t:$(n) - *"> <!-- b*S0/(d+s) -->
+		<parameter idref="becomeUninfectiousRate.s.t:$(n)"/>
+		<parameter idref="samplingProportion.s.t:$(n)"/>        
 	</RPNcalculator>
 
 	<!-- tree operators -->	
@@ -74,24 +74,24 @@ suppressInputs='beast.evolution.speciation.BirthDeathSkylineModel.intervalTimes,
 	<operator id='BDSKY_serialWilsonBalding.t:$(n)' spec='WilsonBalding' weight="3" tree="@Tree.t:$(n)"/>
 
 	<!-- BDSKY operators -->
-	<operator id='becomeUninfectiousRateScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@becomeUninfectiousRate.t:$(n)"/>
-	<operator id='samplingScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@samplingProportion.t:$(n)"/>
-	<operator id='RScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="10" parameter="@R0.t:$(n)"/>
+	<operator id='becomeUninfectiousRateScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@becomeUninfectiousRate.s.t:$(n)"/>
+	<operator id='samplingScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@samplingProportion.s.t:$(n)"/>
+	<operator id='RScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="10" parameter="@R0.s.t:$(n)"/>
 
 	<operator id="updownBD.t:$(n)" spec="UpDownOperator" scaleFactor=".75" weight="2">
-		<up idref="R0.t:$(n)"/>
-		<down idref="becomeUninfectiousRate.t:$(n)"/>
+		<up idref="R0.s.t:$(n)"/>
+		<down idref="becomeUninfectiousRate.s.t:$(n)"/>
 	</operator>
 
-	<operator id='origScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="1" parameter="@origin.t:$(n)"/>
+	<operator id='origScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="1" parameter="@origin.s.t:$(n)"/>
 ]]>
             <connect srcID='BirthDeathSkySerial.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerial.t:$(n)) and inlikelihood(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'/>
             <connect srcID='RandomTree.t:$(n)'                targetID='BirthDeathSkySerial.t:$(n)' inputName='init'   if='inposterior(Tree.t:$(n))'/>
 
-            <connect srcID='originPrior.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerial.t:$(n)) and origin.t:$(n)/estimate=true'>prior on origin.t:$(n)</connect>
-            <connect srcID='samplingProportionPrior.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerial.t:$(n)) and samplingProportion.t:$(n)/estimate=true'>prior on sampling proportion t:$(n)</connect>
-            <connect srcID='becomeUninfectiousRatePrior.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerial.t:$(n)) and becomeUninfectiousRate.t:$(n)/estimate=true'>prior on becomeUninfectiousRate.t:$(n)</connect>
-            <connect srcID='RPrior.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerial.t:$(n)) and R0.t:$(n)/estimate=true'>prior on R0.t:$(n)</connect>
+            <connect srcID='originPrior.s.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerial.t:$(n)) and origin.s.t:$(n)/estimate=true'>prior on origin.s.t:$(n)</connect>
+            <connect srcID='samplingProportionPrior.s.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerial.t:$(n)) and samplingProportion.s.t:$(n)/estimate=true'>prior on sampling proportion t:$(n)</connect>
+            <connect srcID='becomeUninfectiousRatePrior.s.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerial.t:$(n)) and becomeUninfectiousRate.s.t:$(n)/estimate=true'>prior on becomeUninfectiousRate.s.t:$(n)</connect>
+            <connect srcID='RPrior.s.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkySerial.t:$(n)) and R0.s.t:$(n)/estimate=true'>prior on R0.s.t:$(n)</connect>
 
             <connect srcID='BDSKY_serialtreeScaler.t:$(n)'                targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerial.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Scales all internal nodes for tree t:$(n)</connect>
             <connect srcID='BDSKY_serialtreeRootScaler.t:$(n)'            targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerial.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Scales root node for tree t:$(n)</connect>
@@ -101,18 +101,18 @@ suppressInputs='beast.evolution.speciation.BirthDeathSkylineModel.intervalTimes,
             <connect srcID='BDSKY_serialwide.t:$(n)'                      targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerial.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Wide exchange performs global rearrangement of tree t:$(n)</connect>
             <connect srcID='BDSKY_serialWilsonBalding.t:$(n)'             targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkySerial.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Performs Wilson-Balding global rearrangement of tree t:$(n)</connect>
 
-            <connect srcID='becomeUninfectiousRateScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and becomeUninfectiousRate.t:$(n)/estimate=true'/>
-            <connect srcID='samplingScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and samplingProportion.t:$(n)/estimate=true'/>
-            <connect srcID='RScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and R0.t:$(n)/estimate=true'/>
-            <connect srcID='updownBD.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and R0.t:$(n)/estimate=true and becomeUninfectiousRate.t:$(n)/estimate=true'/>
-            <connect srcID='origScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and origin.t:$(n)/estimate=true'/>
+            <connect srcID='becomeUninfectiousRateScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and becomeUninfectiousRate.s.t:$(n)/estimate=true'/>
+            <connect srcID='samplingScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and samplingProportion.s.t:$(n)/estimate=true'/>
+            <connect srcID='RScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and R0.s.t:$(n)/estimate=true'/>
+            <connect srcID='updownBD.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and R0.s.t:$(n)/estimate=true and becomeUninfectiousRate.s.t:$(n)/estimate=true'/>
+            <connect srcID='origScaler.t:$(n)' targetID='mcmc' inputName='operator'     if='inposterior(BirthDeathSkySerial.t:$(n)) and origin.s.t:$(n)/estimate=true'/>
 
 
 
             <connect srcID='BirthDeathSkySerial.t:$(n)' targetID='tracelog' inputName='log' if='inposterior(BirthDeathSkySerial.t:$(n))'/>
             <plate var='p' range='origin,samplingProportion,becomeUninfectiousRate,R0'>
-                    <connect srcID='$(p).t:$(n)' targetID='state' inputName='stateNode' if='inposterior(BirthDeathSkySerial.t:$(n)) and $(p).t:$(n)/estimate=true'/>
-                    <connect srcID='$(p).t:$(n)' targetID='tracelog' inputName='log' if='inposterior(BirthDeathSkySerial.t:$(n)) and $(p).t:$(n)/estimate=true'/>
+                    <connect srcID='$(p).s.t:$(n)' targetID='state' inputName='stateNode' if='inposterior(BirthDeathSkySerial.t:$(n)) and $(p).s.t:$(n)/estimate=true'/>
+                    <connect srcID='$(p).s.t:$(n)' targetID='tracelog' inputName='log' if='inposterior(BirthDeathSkySerial.t:$(n)) and $(p).s.t:$(n)/estimate=true'/>
             </plate>
             <plate var='p' range='birth,death,sampling'>
 	            <connect srcID='$(p).t:$(n)' targetID='tracelog' inputName='log' if='inposterior(BirthDeathSkySerial.t:$(n))'/>