search

kbphoton / beast-mcmc

Automatically exported from code.google.com/p/beast-mcmc
0 stars 0 forks source link

add Random local clock model into BEAUti #326

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
state   Likelihood      Root Height     base Rate       rate changes    mean rate   cv        
    L(tree)         L(coalecent)
0   -90460.7772     231.724         1.00000         0.0         1.00000     0E0       
    -89993.8137     -382.8063       -
1000    -9211.4234      187.498         4.40364E-4      2.0         1.00000   
    8.31009E-2  -8603.5528      -510.4974       -
2000    -8616.0698      239.894         2.42038E-4      8.0         1.00000     0.39500   
    -7945.2905      -552.5338       -
3000    -8465.2284      287.067         1.77443E-4      7.0         1.00000     0.46290   
    -7774.8837      -570.3660       -
4000    -8345.6756      350.455         1.59998E-4      8.0         1.00000     0.44974   
    -7632.2349      -586.1363       -
5000    -7878.3265      137.843         3.79753E-4      7.0         1.00000     0.47083   
    -7251.5759      -503.7994       -
Exception in thread "Thread-3" java.lang.AssertionError: INTERNAL ERROR! node 
with number 136 should be the root node.
    at dr.evomodel.tree.TreeParameterModel.getNodeValue(TreeParameterModel.java:122)
    at dr.evomodel.branchratemodel.RandomLocalClockModel.isVariableSelected(RandomLocalClockModel.java:113)
    at dr.evomodel.branchratemodel.RandomLocalClockModel.cubr(RandomLocalClockModel.java:158)
    at dr.evomodel.branchratemodel.RandomLocalClockModel.cubr(RandomLocalClockModel.java:170)
    at dr.evomodel.branchratemodel.RandomLocalClockModel.calculateUnscaledBranchRates(RandomLocalClockModel.java:141)
    at dr.evomodel.branchratemodel.RandomLocalClockModel.recalculateScaleFactor(RandomLocalClockModel.java:176)
    at dr.evomodel.branchratemodel.RandomLocalClockModel.handleModelChangedEvent(RandomLocalClockModel.java:117)
    at dr.inference.model.AbstractModel.modelChangedEvent(AbstractModel.java:206)
    at dr.inference.model.Model$ListenerHelper.fireModelChanged(Model.java:128)
    at dr.inference.model.AbstractModel.fireModelChanged(AbstractModel.java:135)
    at dr.evomodel.tree.TreeParameterModel.handleVariableChangedEvent(TreeParameterModel.java:103)
    at dr.inference.model.AbstractModel.variableChangedEvent(AbstractModel.java:220)
    at dr.inference.model.Parameter$Abstract.fireParameterChangedEvent(Parameter.java:215)
    at dr.inference.model.CompoundParameter.variableChangedEvent(CompoundParameter.java:289)
    at dr.inference.model.Parameter$Abstract.fireParameterChangedEvent(Parameter.java:215)
    at dr.inference.model.Parameter$Default.setParameterValue(Parameter.java:606)
    at dr.evomodel.tree.TreeModel.swapAllTraits(TreeModel.java:1001)
    at dr.evomodel.tree.TreeModel.swapAllTraits(TreeModel.java:361)
    at dr.evomodel.operators.SubtreeSlideOperator.doOperation(SubtreeSlideOperator.java:227)
    at dr.inference.operators.SimpleMCMCOperator.operate(SimpleMCMCOperator.java:167)
    at dr.inference.markovchain.MarkovChain.runChain(MarkovChain.java:194)
    at dr.inference.mcmc.MCMC.chain(MCMC.java:177)
    at dr.inference.mcmc.MCMC.run(MCMC.java:146)
    at java.lang.Thread.run(Thread.java:595)

Original issue reported on code.google.com by dong.w.xie@gmail.com on 23 Jul 2010 at 12:39

GoogleCodeExporter commented 9 years ago

Original comment by dong.w.xie@gmail.com on 23 Jul 2010 at 2:28

GoogleCodeExporter commented 9 years ago

Original comment by dong.w.xie@gmail.com on 2 Aug 2010 at 11:31