thorney_beast.xml

<?xml version="1.0" standalone="yes"?>

<!-- Generated by BEAUTi v1.10.4 Prerelease #bc6cbd9                         -->
<!--       by Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard         -->
<!--       Department of Computer Science, University of Auckland and        -->
<!--       Institute of Evolutionary Biology, University of Edinburgh        -->
<!--       David Geffen School of Medicine, University of California, Los Angeles-->
<!--       http://beast.community/                                           -->
<beast version="1.10.4">


	<!-- The list of taxa to be analysed (can also include dates/ages).          -->
	<!-- ntaXX                                                              -->
	<taxa id="taxa">
	
	<!-- taxon block here -->
	
	</taxa>
	

	
	<!-- This is a simple constant population size coalescent model              -->
	<!-- that is used to generate an initial tree for the chain.                 -->
	<constantSize id="constant" units="years">
		<populationSize>
			<parameter id="popSize" value="0.1"/>
		</populationSize>
	</constantSize>
	
	<newick id="startingTree" usingDates="true">
<!-- newick string of time-scaled tree from treetime. Used to reduce burn-in, not compulsory but advised -->
<!-- it's best to have resolved polytomies here [mostly applicable for SARS-CoV-2] -->
	</newick>
	<newick id="dataTree" usingDates="false" usingHeights="true">
<!-- ML tree of topology that will be scaled here. MUST be same topology as above. -->
<!-- If you provide treetime with the alignment, it will re-estimate parameters so could result in slightly different topogies to IQTree. See SOP for further info-->
	</newick>
	
	<!-- NEW  This treemodel wraps a treemodel and provides access to subtrees defined by the constraints tree-->
	<!-- This model would throw an error if its topology was changed directly, but its subtrees can be operated on-->
	<constrainedTreeModel id = "treeModel">
		<tree idref="startingTree"/>
		<constraintsTree>
			<tree idref="dataTree"/>
		</constraintsTree>
	</constrainedTreeModel>
	
		<!-- Statistic for root height of the tree       -->
	<treeHeightStatistic id="treeModel.rootHeight">
		<treeModel idref="treeModel"/>
	</treeHeightStatistic>
	<!-- Statistic for sum of the branch lengths of the tree (tree length)       -->
	<treeLengthStatistic id="treeLength">
		<treeModel idref="treeModel"/>
	</treeLengthStatistic>
	<!-- Statistic for time of most recent common ancestor of tree               -->
	<tmrcaStatistic id="age(root)" absolute="true">
		<treeModel idref="treeModel"/>
	</tmrcaStatistic>
	
	<gmrfSkyGridLikelihood id="skygrid">
		<populationSizes>

			<!-- skygrid.logPopSize is in log units unlike other popSize                 -->
			<parameter id="skygrid.logPopSize" dimension="24" value="0"/>
		</populationSizes>
		<precisionParameter>
			<parameter id="skygrid.precision" value="0.1" lower="0.0"/>
		</precisionParameter>
		<numGridPoints>
			<parameter id="skygrid.numGridPoints" value="23.0"/> 
		</numGridPoints>
		<cutOff>
			<parameter id="skygrid.cutOff" value="0.5"/>
		</cutOff>

		<intervals>
			<bigFastTreeIntervals>
				<treeModel idref="treeModel"/>
			</bigFastTreeIntervals>
		</intervals>

	</gmrfSkyGridLikelihood>
	
	
	
	<thorneyTreeLikelihood id="treeLikelihood">
		
		<treeModel idref="treeModel"/>
		
		<strictClockBranchLengthLikelihood id="branchLengthLikelihood" scale="29903.0">
			<parameter id="clock.rate" value="0.0008" lower="0.0"/>
		</strictClockBranchLengthLikelihood>
		
		<constrainedBranchLengthProvider scale="29903.0" discrete="true" minBranchlength="0.0">
			<treeModel idref="treeModel"/>
			<dataTree>
				<tree idref="dataTree"/>
			</dataTree>
		</constrainedBranchLengthProvider>
	</thorneyTreeLikelihood>
	
	<!-- Define operators                                                        -->
	<operators id="operators" optimizationSchedule="log">

	
		<nodeHeightOperator type="uniform" weight="1000">
			<treeModel idref="treeModel"/>
		</nodeHeightOperator>
		
		<nodeHeightOperator type="scaleRoot" weight="100" scaleFactor="0.75" >
			<treeModel idref="treeModel"/>
		</nodeHeightOperator>
		
		<uniformSubtreePruneRegraft weight="500">
			<treeModel idref="treeModel"/>
		</uniformSubtreePruneRegraft>
		
		<narrowExchange weight="500">
			<treeModel idref="treeModel"/>
		</narrowExchange>
		
		<wideExchange weight="500">
			<treeModel idref="treeModel"/>
		</wideExchange>
		
		<wilsonBalding weight="500">
			<treeModel idref="treeModel"/>
		</wilsonBalding>

		<gmrfSkygridBlockUpdateOperator scaleFactor="1.1" weight="100">
			<gmrfSkygridLikelihood idref="skygrid"/>
		</gmrfSkygridBlockUpdateOperator>
		<scaleOperator scaleFactor="0.75" weight="1">
			<parameter idref="skygrid.precision"/>
		</scaleOperator>
		<randomWalkOperator windowSize="1.0" weight="1">
			<parameter idref="skygrid.logPopSize"/>
		</randomWalkOperator>

	</operators>

	<!-- Define MCMC                                                             -->
	<mcmc id="mcmc" chainLength="100000000" autoOptimize="true" operatorAnalysis="thorney.ops">
		<joint id="joint">
			<prior id="prior">
				
				<gammaPrior shape="0.001" scale="1000.0" offset="0.0">
					<parameter idref="skygrid.precision"/>
				</gammaPrior>
				<!-- 
<gammaPrior shape="0.001" scale="1000.0" offset="0.0">
					<parameter idref="clock.rate"/>
				</gammaPrior>
 -->
				<gmrfSkyGridLikelihood idref="skygrid"/>
			</prior>
			<likelihood id="likelihood">
				<thorneyTreeLikelihood idref="treeLikelihood"/>
			</likelihood>
			
			
		</joint>
		<operators idref="operators"/>
	
		<!-- write log to screen                                                     -->
		<log id="screenLog" logEvery="10000">
			<column label="Joint" dp="4" width="12">
				<joint idref="joint"/>
			</column>
			<column label="Prior" dp="4" width="12">
				<prior idref="prior"/>
			</column>
			<column label="Likelihood" dp="4" width="12">
				<likelihood idref="likelihood"/>
			</column>
			<column label="age(root)" sf="6" width="12">
				<tmrcaStatistic idref="age(root)"/>
			</column>
<!-- 
			<column label="clock.rate" sf="6" width="12">
				<parameter idref="clock.rate"/>
			</column>
 -->
			<column label="tree_len" sf='6' width='12'>
				<parameter idref="treeLength"/>
			</column>
			
		</log>
	
	
		<!-- write log to file                                                       -->
		<log id="fileLog" logEvery="10000" fileName="thorney.log" overwrite="false">
	
			<joint idref="joint"/>
			<prior idref="prior"/>
			<likelihood idref="likelihood"/>
			<parameter idref="treeModel.rootHeight"/>
			<tmrcaStatistic idref="age(root)"/>
			<treeLengthStatistic idref="treeLength"/>
			<parameter idref="skygrid.precision"/>
			<parameter idref="skygrid.logPopSize"/>
			<parameter idref="skygrid.cutOff"/>
			
<!-- 
			<parameter idref="clock.rate"/>
 -->

			<thorneyTreeLikelihood idref="treeLikelihood"/>
			<gmrfSkyGridLikelihood idref="skygrid"/>
		</log>
	
	
		<!-- write tree log to file                                                  -->
		<logTree id="treeFileLog" logEvery="10000" nexusFormat="true" fileName="thorney.trees" sortTranslationTable="true">
			<treeModel idref="treeModel"/>

			<joint idref="joint"/>
		</logTree>
	</mcmc>
	

	<report>
		<property name="timer">
			<mcmc idref="mcmc"/>
		</property>
	</report>
	
</beast>