<?xml version="1.0" standalone="yes"?>
<!--
  ~ testTransposedMatrixParameter.xml
  ~
  ~ Copyright (c) 2002-2012 Alexei Drummond, Andrew Rambaut and Marc Suchard
  ~
  ~ This file is part of BEAST.
  ~ See the NOTICE file distributed with this work for additional
  ~ information regarding copyright ownership and licensing.
  ~
  ~ BEAST is free software; you can redistribute it and/or modify
  ~ it under the terms of the GNU Lesser General Public License as
  ~ published by the Free Software Foundation; either version 2
  ~ of the License, or (at your option) any later version.
  ~
  ~  BEAST is distributed in the hope that it will be useful,
  ~  but WITHOUT ANY WARRANTY; without even the implied warranty of
  ~  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  ~  GNU Lesser General Public License for more details.
  ~
  ~ You should have received a copy of the GNU Lesser General Public
  ~ License along with BEAST; if not, write to the
  ~ Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
  ~ Boston, MA  02110-1301  USA
  -->

<beast>
    <matrixParameter id="locations" transpose="true">
        <parameter id="branch.rates.1" value="1.0 2.0 3.0"/>
        <parameter id="branch.rates.2" value="4.0 5.0 6.0"/>
    </matrixParameter>

    <operators id="operators" optimizationSchedule="log">
        <randomWalkOperator windowSize="1.0" weight="273">
            <matrixParameter idref="locations"/>
        </randomWalkOperator>
    </operators>

    <mcmc id="mcmc" chainLength="10000000" autoOptimize="true">
        <posterior id="posterior">
            <prior id="prior">
                <multivariateNormalPrior id="rootPrior">
                    <meanParameter>
                        <parameter value="10.0 0.0"/>
                    </meanParameter>
                    <precisionParameter>
                        <matrixParameter>
                            <parameter value="10.0 -1.0"/>
                            <parameter value="-1.0  5.0"/>
                        </matrixParameter>
                    </precisionParameter>
                    <data>
                        <matrixParameter idref="locations"/>
                    </data>
                </multivariateNormalPrior>
            </prior>
        </posterior>

        <operators idref="operators"/>

        <log id="screenLog" logEvery="100000">
            <column label="Posterior" dp="4" width="12">
                <posterior idref="posterior"/>
            </column>
        </log>

        <log id="fileLog2" logEvery="10000" fileName="testMVN.log">
            <matrixParameter idref="locations"/>
        </log>
    </mcmc>

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