linear_growth_test.xml

<!--  This simple input file just samples the distribution of ARGs conditional on a (constant)
 	population size and recombination rate. There's no alignment or input data, so this is basically
 	sampling from the prior distribution of ARGs -->
<ACG>

<!-- Still need a random number source -->
<RandomSource class="math.RandomSource" />


<!--  The Ancestral Recombination Graph (ARG) that is the central feature of the analysis -->
<arg class="arg.ARG" frequency="30.0" tips="10" theta="1.0" sites="1000">
	<modifiers class="list">
		<recombAddRemove class="modifier.RecombAddRemove"/>
		<rootHeight class="modifier.RootHeightModifier" />
		<nodeHeight class="modifier.NodeHeightModifier"/>
		<swapper class="modifier.SubtreeSwap" />
		<wideSwap class="modifier.WideSwap" />
		<shifter class="modifier.BreakpointShifter" />
		<bpSwap class="modifier.BreakpointSwapper" />
	</modifiers>
</arg>


<!-- ==========================   Coalescent model and likelihood  =========================== --> 

<!--  Parameter specifying population size that is growing at an exponential rate. We 
 want to estimate two parameters, the current size ("baseSize") as well as the growth 
 rate ("growthRate"). Don't forget to add these parameters to MCMC! -->
    <PopulationSize class="coalescent.LinearChangePop" frequency="1.0" value="1.0">
      <baseSize class="parameter.DoubleParameter" value="10">
	<baseSizeMod class="modifier.ScaleModifier" />
      </baseSize>
      <growthRate class="parameter.DoubleParameter" value="1">
	<growthRateMod class="modifier.SimpleModifier" />
      </growthRate>
    </PopulationSize>
<!-- 
   <constPopSize class="coalescent.ConstantPopSize" frequency="1.0" value="1" />
 -->

<!-- Simple, constant recombination rate across sites -->
<constantRecRate class="coalescent.ConstantRecombination" value="0.2" />

<!-- A likelihood object specifying the probability of observing the ARG  -->
<coalescentLikelihood class="coalescent.CoalescentLikelihood">
	<PopulationSize />
	<constantRecRate />
	<arg />
</coalescentLikelihood>





<!-- ===========================    Logging and output    =============================  --> 

<!-- A logger that tracks properties of the likelihoods and parameters in the MCMC -->
<statelogger class="logging.StateLogger" filename="priors.log" frequency="5000" echoToScreen="true" />

<!-- a logger that tracks the distribution of TMRCA (root height of marginal trees) along the sequence -->
<rootHeightLogger class="logging.RootHeightDensity" filename="priors_rootHeight.txt" frequency="5000" burnin="100000">
	<arg />
</rootHeightLogger>




<!-- ===========================     Markov chain  ============================== --> 

<mc class="mcmc.MCMC" length="3000000" run="true">
	<parameters class="list">
		<PopulationSize />
		<constantRecRate />
		<arg />  
	</parameters>
	<likelihoodComponents class="list">
		<coalescentLikelihood />
	</likelihoodComponents>
	<loggers class="list">
		<statelogger />
		<rootHeightLogger />
	</loggers>
</mc>

</ACG>