rbouckaert/babel

BEAST analysis backing effective linguistics

babel's Issues

pseudo Dollo modification?

Hi,

I'm curious if it is possible to modify the pseudo-Dollo model, from a global one where regains are possible on any branch to a local one where regains are only possible on branches connected by relatively short divergences? I'm not sure if that makes sense in the context of language evolution, but in the context of biological evolution, such a model could allow for regains of a lost trait through processes like incomplete lineage sorting (ILS) or introgression (hybridization). We are studying gene loss events in mammals, which should be a Dollo character in that once lost a homologous gene can never re-evolve -- unless it is re-acquired through things like horizontal gene transfer, ILS, or introgression (the latter two of which are probably common for closely related species).

Best,
Vinny

For binarycovarion import both partitions and calibrations don't work

When importing from NEXUS. See mail from Michael Dunn 4 september 2017 for an example.

SpeciesTreeDistanceLogger confused by different taxon orderings

When gene trees have different taxon orderings, SpeciesTreeDistanceLogger appears to get confused and produces incorrect output. When only a single gene tree is used, everything is fine.

HeatMapMaker option to change colour range

inspired by CompEvol/beast2#835
Also, update the tutorial with HeatMapMaker the latest inputs.

Unable to use SDollo template

Beauti gives this error:

beast.util.XMLParserException:
Error 1017 parsing the xml input file

nullClass could not be found. Did you mean beast.evolution.substitutionmodel.MutationDeathModel?

Error detected about here:
  <beast>
      <alignment id='orgdata.utoaztecan' spec='beast.evolution.alignment.FilteredAlignment'>
          <userDataType spec='beast.evolution.datatype.MutationDeathType'>

    at beast.util.XMLParser.createObject(Unknown Source)
    at beast.util.XMLParser.parseInputs(Unknown Source)
    at beast.util.XMLParser.createObject(Unknown Source)
    at beast.util.XMLParser.parseTemplate(Unknown Source)
    at beast.app.beauti.BeautiSubTemplate.createSubNet(Unknown Source)
    at beast.app.beauti.BeautiSubTemplate.createSubNet(Unknown Source)
    at beast.app.beauti.BeautiDoc.addAlignmentWithSubnet(Unknown Source)
    at beast.app.beauti.BeautiAlignmentProvider.addAlignments(Unknown Source)
    at beast.app.beauti.BeautiAlignmentProvider.getAlignments(Unknown Source)
    at beast.app.beauti.BeautiAlignmentProvider.getAlignments(Unknown Source)
    at beast.app.beauti.Beauti$1.actionPerformed(Unknown Source)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
    at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
    at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
    at java.awt.Component.processMouseEvent(Component.java:6525)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3322)
    at java.awt.Component.processEvent(Component.java:6290)
    at java.awt.Container.processEvent(Container.java:2234)
    at java.awt.Component.dispatchEventImpl(Component.java:4881)
    at java.awt.Container.dispatchEventImpl(Container.java:2292)
    at java.awt.Component.dispatchEvent(Component.java:4703)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
    at java.awt.Container.dispatchEventImpl(Container.java:2278)
    at java.awt.Window.dispatchEventImpl(Window.java:2739)
    at java.awt.Component.dispatchEvent(Component.java:4703)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:702)
    at java.awt.EventQueue$3.run(EventQueue.java:696)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
    at java.awt.EventQueue$4.run(EventQueue.java:724)
    at java.awt.EventQueue$4.run(EventQueue.java:722)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:721)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
PARTITIONS0:

[[], [], []]
InPosterior=posterior prior likelihood
Could not find beastObject with id treeLikelihood.Species. Typo in template perhaps?

PARTITIONS0:

[[], [], []]
PARTITIONS0:

[[], [], []]
PARTITIONS0:

[[], [], []]
PARTITIONS0:

[[], [], []]
Validation message: At least one input of name 'xx' must be specified.
PARTITIONS0:

[[], [], []]
class beast.core.MCMC != class beast.core.Runnable
PARTITIONS0:

[[], [], []]
Validation message: At least one input of name 'xx' must be specified.
class beast.core.MCMC != class beast.core.Runnable

can the models here (binaryctmc, covarion etc) be exposed as models in BEAUTi?

As far as I can see the only way to set up a binary ctmc or covarion analysis in BEAUTi is to use the included templates. This makes it hard to use a different template (e.g. MultiTypeTree or something) as the only site models listed are then Lewis Mk or mutation death.

New Template?

I like to run analyses using CTMC+Gamma=1 to compare to CTMC+Gamma=4 (especially for small datasets). The current BinaryCTMC template defaults to CTMC+Gamma=4. It's not too much hassle to turn off Gamma in BEAUTi, but it strikes me as easier done with a template.

Is this the type of thing Babel wants to have (e.g. rename BinaryCTMC to BinaryCTMCGamma and create a new template for BinaryCTMC)? If so I can rework the existing template and submit a pull request.