Tutorial 3

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BEAST Documentation->Tutorials->Tutorial 3

Placing an upper limit on the root height

This can now be done using the Priors tab in BEAUti, by selecting a Uniform Prior on the rootHeight parameter.

Alternatively, to do this by manually editing the BEAST XML simply add a uniformPrior element in to the mcmc element:

<mcmc id="mcmc1" chainLength="100000" autoOptimize="true">
	<posterior id="posterior">
		<prior id="prior">
			<uniformPrior lower="0" upper="100">
				<parameter idref="treeModel.rootHeight"/>
			</uniformPrior >
			...
		</prior>
		<likelihood id="likelihood">
			<treeLikelihood idref="treeLikelihood"/>
		</likelihood>
	</posterior>
	...
</mcmc>

Now the prior probability will be NEGATIVE INFINITY whenever the root height is above 100. Thus any operator moves that propose that the root height should be greater than 100 will not be accepted. The final trick is to ensure that the starting tree does not have a root height larger than 100. This can be achieved either by providing a user defined starting tree, creating a starting tree using the coalescentTree element with a very small population size (for example 1.0) or by scaling the starting tree with the rootHeight attribute:

	<coalescentTree id="startingTree" rootHeight="50.0">
		...
	</coalescentTree>

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Alexei Drummond and Andrew Rambaut
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