niconeureiter / contactrees Goto Github PK

Hi Nico :)

Well done on this package and the publication! I just noticed however that you haven't explicitly noted the license under which this package is released. Given that it directly uses GPL 3 code from Bacter, I believe contacTrees should be similarly licensed.

Thank you!

Tim

In some parts of the walkthrough given in starting-with-beastling, there is a contactrees.operators missing that is present in the final xml-file bantu-contactrees.xml.

<operator id="GibbsSampleMovesPerConversion.t" spec="contactrees.operators.GibbsSampleMovesPerConversion"

As well as in all operators at the end of the xml file:
<distribution id="ConvMovePrior" spec="ConversionMovePrior" network="@Tree.t:beastlingTree" pMove="@pMove">

should be

<distribution id="ConvMovePrior" spec="contactrees.model.ConversionMovePrior" network="@Tree.t:beastlingTree" pMove="@pMove">

Also the operators need another specification of their likelihood.

Currently: treeLikelihood.$(concept)

should be

featureLikelihood:bantu-vocabulary:$(concept)

I am currently trying to reproduce the example and to apply the procedure to my own data. In both cases however, both when running bantu-contactrees.xml and with the xml of my own data, I receive the following error message:

         Sample ESS(posterior)          prior     likelihood      posterior
              0              N       -25.9378   -198254.1509   -198280.0887 --
java.lang.RuntimeException: Negative branch length: -1.389820202614457
	at beast.evolution.likelihood.BeagleTreeLikelihood.traverse(Unknown Source)
	at beast.evolution.likelihood.BeagleTreeLikelihood.calculateLogP(Unknown Source)
	at beast.evolution.likelihood.TreeLikelihood.calculateLogP(Unknown Source)
	at beast.core.util.CompoundDistribution.calculateLogP(Unknown Source)
	at beast.core.util.CompoundDistribution.calculateLogP(Unknown Source)
	at beast.core.MCMC.propagateState(Unknown Source)
	at beast.core.MCMC.doLoop(Unknown Source)
	at beast.core.MCMC.run(Unknown Source)
	at beast.app.BeastMCMC.run(Unknown Source)
	at beast.app.beastapp.BeastMain.<init>(Unknown Source)
	at beast.app.beastapp.BeastMain.main(Unknown Source)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)Fatal exception: Negative branch length: -1.389820202614457

	at beast.app.beastapp.BeastLauncher.run(Unknown Source)
	at beast.app.beastapp.BeastLauncher.main(Unknown Source)
Fatal exception: Negative branch length: -1.389820202614457

BEAST has terminated with an error. Please select QUIT from the menu.

This is with Beast version v.2.6.7

Building an example, I just noticed that

It seems that ConversionRate has no state (or ignores its state), so why is it not a Function instead? Are there BEAST2 objects that we want to feed a ConversionRate into which expect a RealParameter even though a Function should suffice? It wouldn't be the first time.