birth-death-sampling-score-function-test.xml

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<beast version="2.0" namespace="beast:beast.core:beast.core.parameter:beast.evolution.tree:beast.evolution.speciation:beast.simulation:beast.validation:beast.validation.statistics:beast.validation.tests:master.model:master.conditions:master.postprocessors">
    <run spec="StochasticValidationTest" alpha="0.1" nSamples="10000" printEvery="1000">
        <sampler spec="TreeSamplerFromMaster" verbosity="0" reverseTime="false" simulationTime="3.0" id="masterTree">
            <model spec="Model">
                <population spec="Population" populationName="X" id="X"/>
                <population spec="Population" populationName="D" id="D"/>
                <reaction spec="Reaction" reactionName="Speciation" rate="0.5">
                    X -> 2X
                </reaction>
                <reaction spec="Reaction" reactionName="Extinction" rate="0.2">
                    X -> D
                </reaction>
            </model>

            <initialState spec="InitState">
                <lineageSeed spec="Individual" population="@X"/>
            </initialState>
            <inheritancePostProcessor spec="LineageFilter" populationName="X"/>
            <inheritancePostProcessor spec="LineageSampler" pSample="0.6" samplingTime="3.0"/>
            <postSimCondition spec="LeafCountPostSimCondition" nLeaves="4" exact="true" />
        </sampler>

        <statistic spec="NumericalScoreFunctionStatistics" state="@masterTree" id="grad">
            <parameter spec="RealParameter" id="birthDiffRate" value="0.3"/>
            <!-- Relative death rate excluded because of non-identifiability -->
            <parameter spec="RealParameter" id="sampleProbability" value="0.6"/>
            <likelihood spec="BirthDeathGernhard08Model" birthDiffRate="@birthDiffRate" relativeDeathRate="0.4" sampleProbability="@sampleProbability" originHeight="3.0" tree="@masterTree" />
        </statistic>

        <test spec="MultivariateNormalZeroMeanTest" id="test"/>

        <sampleLogger spec="Logger" fileName="birth-death-sampling-grad.txt" log="@grad"/>
        <resultLogger spec="Logger" fileName="birth-death-sampling-result.txt" log="@test"/>
        <sampleLogger spec="Logger" fileName="birth-death-sampling-tree.trees" log="@masterTree"/>
    </run>
</beast>