beast2-mcmc 2.4.4+dfsg-1 / usr / share / beast-mcmc2 / templates / ParametricDistributions.xml

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<beast version='2.0'
       namespace='beast.app.beauti:beast.core:beast.evolution.branchratemodel:beast.evolution.speciation:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood:beast.evolution:beast.math.distributions'>


    <mergewith point='parametricDistributions'>
        <!-- Parametric distributions, all without hyperpriors -->

        <!-- Uniform -->
        <subtemplate id='Uniform' class='beast.math.distributions.Uniform' mainid='[top]'>
            <![CDATA[
        <distr spec="beast.math.distributions.Uniform" lower='0' upper='Infinity'/>
]]>
        </subtemplate>

        <!-- Normal -->
        <subtemplate id='Normal' class='beast.math.distributions.Normal' mainid='[top]' suppressInputs='beast.math.distributions.Normal.tau'>
            <![CDATA[
    <distr offset="0.0" spec="beast.math.distributions.Normal">
        <parameter name='mean' value='0' estimate='false'/>
        <parameter name='sigma' value='1' estimate='false'/>
    </distr>
]]>
        </subtemplate>

        <!-- OneOnX -->
        <subtemplate id='1/X' class='beast.math.distributions.OneOnX' mainid='[top]'>
            <![CDATA[
        <distr spec="beast.math.distributions.OneOnX"/>
]]>
        </subtemplate>

        <!-- lognormal -->
        <subtemplate id='LogNormal' class='beast.math.distributions.LogNormalDistributionModel' mainid='[top]'>
            <![CDATA[
        <distr name='distr' spec="beast.math.distributions.LogNormalDistributionModel">
            <parameter name='M' value="1" estimate='false'/>
            <parameter name='S' value="1.25" lower="0" upper="5" estimate='false'/>
        </distr>
]]>
        </subtemplate>

        <!-- Exponential -->
        <subtemplate id='Exponential' class='beast.math.distributions.Exponential' mainid='[top]'>
            <![CDATA[
        <distr offset="0.0" spec="beast.math.distributions.Exponential">
            <parameter name='mean' value="1" estimate='false'/>
        </distr>
]]>
        </subtemplate>

        <!-- Gamma -->
        <subtemplate id='Gamma' class='beast.math.distributions.Gamma' mainid='[top]'>
            <![CDATA[
        <distr offset="0.0" spec="beast.math.distributions.Gamma">
            <parameter name='alpha' value="2" estimate='false'/>
            <parameter name='beta' value="2" estimate='false'/>
        </distr>
]]>
        </subtemplate>

        <!-- Beta -->
        <subtemplate id='Beta' class='beast.math.distributions.Beta' mainid='[top]'>
            <![CDATA[
        <distr offset="0.0" spec="beast.math.distributions.Beta">
            <parameter name='alpha' value="2" estimate='false'/>
            <parameter name='beta' value="2" estimate='false'/>
        </distr>
]]>
        </subtemplate>

        <!-- Laplace -->
        <subtemplate id='LaplaceDistribution' class='beast.math.distributions.LaplaceDistribution' mainid='[top]'>
            <![CDATA[
        <distr offset="0.0" spec="beast.math.distributions.LaplaceDistribution">
            <parameter name='mu' value="0" estimate='false'/>
            <parameter name='scale' value="1" estimate='false'/>
        </distr>
]]>
        </subtemplate>

        <!-- InverseGamma -->
        <subtemplate id='InverseGamma' class='beast.math.distributions.InverseGamma' mainid='[top]'>
            <![CDATA[
        <distr offset="0.0" spec="beast.math.distributions.InverseGamma">
            <parameter name='alpha' value="2" estimate='false'/>
            <parameter name='beta' value="2" estimate='false'/>
        </distr>
]]>
        </subtemplate>

        <!-- Poisson -->
        <subtemplate id='Poisson' class='beast.math.distributions.Poisson' mainid='[top]'>
            <![CDATA[
		<distr spec='beast.math.distributions.Poisson' offset="0.0">
			<parameter name="lambda" value="0.693"/>
		</distr>
]]>
        </subtemplate>


    </mergewith>


    <!-- Tree initialisation -->
    <!-- Random tree -->

    <subtemplate id='RandomTree' class='beast.evolution.tree.RandomTree' mainid='RandomTree.t:$(n)'>
        <![CDATA[
            <tree spec='beast.evolution.tree.RandomTree' id='RandomTree.t:$(n)' estimate='false' trait='@datetrait.$(n)'>
                <taxa spec='Alignment' idref='$(n)'/>
                <populationModel id='ConstantPopulation.t:$(n)' spec='ConstantPopulation'>
            		<popSize id='popSize.t:$(n)' spec='parameter.RealParameter' value='1'/>
	            </populationModel>
            </tree>
]]>
    </subtemplate>

    <!-- Cluster tree (for UPGMA) -->

    <subtemplate id='UPGMATree' class='beast.util.ClusterTree' mainid='UPGMATree.t:$(n)'>
        <![CDATA[
        <tree spec='beast.util.ClusterTree' id='UPGMATree.t:$(n)' clusterType='upgma' estimate='false'  trait='@datetrait.$(n)' taxa='@$(n)'/>
]]>
    </subtemplate>

    <!-- Newick tree -->
    <subtemplate id='NewickTree' class='beast.util.ClusterTree' mainid='NewickTree.t:$(n)'>
        <![CDATA[
        <tree spec='beast.util.TreeParser' id='NewickTree.t:$(n)' estimate='false'  trait='@datetrait.$(n)'  taxa='@$(n)' newick=""/>
]]>
    </subtemplate>


</beast>

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