Hi Dr. Baele
Thank you for your response. I am extremely sorry to say that the problem was actually in the xml file. This is the error message--------
Attempting theta (98/101) = 8.389527766075414E-6 for 1000000 iterations + 100000 burnin.
Attempting theta (99/101) = 2.171534093275924E-6 for 1000000 iterations + 100000 burnin.
Attempting theta (100/101) = 2.1544346900318824E-7 for 1000000 iterations + 100000 burnin.
Attempting theta (101/101) = 0.0 for 1000000 iterations + 100000 burnin.
3 file(s) found with marginal likelihood samples
dr.xml.XMLParseException: Error parsing '<pathSamplingAnalysis>' element with id, 'null':
File 'C:\Users\Sikandar\Documents\second bayesian analysis\denv-1' can not be opened for pathSamplingAnalysis element.
at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.parse(Unknown Source)
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)
May 21, 2015 8:47:27 AM dr.app.beast.BeastMain <init>
SEVERE: Parsing error - poorly formed BEAST file, denv-1 strict bayesian.xml:
Error parsing '<pathSamplingAnalysis>' element with id, 'null':
File 'C:\Users\Sikandar\Documents\second bayesian analysis\denv-1' can not be opened for pathSamplingAnalysis element.
java.lang.RuntimeException: Terminate
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)
BEAST has terminated with an error. Please select QUIT from the menu.
These are the xml blocks of the concerned file
<!-- START Marginal Likelihood Estimator
-->
- <!-- Define marginal likelihood estimator settings
-->
- <marginalLikelihoodEstimator chainLength="1000000" pathSteps="100" pathScheme="betaquantile" alpha="0.3">
- <pathLikelihood id="pathLikelihood">
<posterior idref="posterior" />
</source>
</pathLikelihood>
- <log id="MLELog" logEvery="1000" fileName="denv-1 strict bayesian.mle.log">
<pathLikelihood idref="pathLikelihood" />
</log>
</marginalLikelihoodEstimator>
- <!-- Path sampling estimator from collected samples
-->
- <pathSamplingAnalysis fileName="denv-1 strict bayesian.mle.log">
<likelihoodColumn name="pathLikelihood.delta" />
<thetaColumn name="pathLikelihood.theta" />
</pathSamplingAnalysis>
- <!-- Stepping-stone sampling estimator from collected samples
-->
- <steppingStoneSamplingAnalysis fileName="denv-1 strict bayesian.mle.log">
<likelihoodColumn name="pathLikelihood.delta" />
<thetaColumn name="pathLikelihood.theta" />
</steppingStoneSamplingAnalysis>
- <!-- END Marginal Likelihood Estimator
-->
- <property name="timer">
</report>
</beast>
First few lines of the mle file
# BEAST v1.8.1, r6542
# Generated Wed May 20 23:45:11 IST 2015 [seed=1432138736004]
state pathLikelihood.delta pathLikelihood.source pathLikelihood.destination pathLikelihood.theta pathLikelihood.pathLikelihood
100000 -2459.4502030120375 -7568.197477308087 -5108.74727429605 1.0 -7568.197477308087
101000 -2449.3076364727212 -7557.721830809901 -5108.41419433718 1.0 -7557.721830809901
102000 -2447.913228985204 -7560.33326055104 -5112.420031565836 1.0 -7560.33326055104
103000 -2443.5134459617884 -7547.766004477944 -5104.252558516156 1.0 -7547.766004477944
104000 -2458.9397058205295 -7570.346895138111 -5111.4071893175815 1.0 -7570.346895138111
105000 -2449.961104361034 -7562.945440774977 -5112.984336413943 1.0 -7562.945440774977
106000 -2444.7838659186173 -7556.575840562156 -5111.791974643539 1.0 -7556.575840562156
107000 -2451.8810488224326 -7560.5195169028675 -5108.638468080435 1.0 -7560.5195169028675
I hope this information will help in identifying the problem. Kindly help me in carrying out the path sampling analysis.
Thanks in advance.
Best Regards
Sarah Afreen