4ment/flc

Local clock model using relaxed and strict clocks

flc's Issues

xml example with fixed clockrate in internal branches and tips

Hi,

Can you give an example of xml with a dozen of sequences and a fixed clockrate of 0.001 in internal branches and 0.01 in tips ?

Thanks a lot.

Adding an external package repository

Hi Mathieu, just in case you weren't aware: you can create your own external package file, host it somewhere (eg github pages) and tell potential users to add its url via the "manage external repositories" button in the beauti package manager. Your package (and any updates you make) will then be automatically available for download using the package manager, meaning that people can avoid having to do the installation by hand.

implementing the FLC

PCG4.BEAST2FLC.pdf

Hi Mathieu,

Would you be able to help me implement your FLC package. I have successfully run it through BEAST but the output tree is suggesting I've done something wrong. I'm trying to set one rate across the whole tree except for one clade which has a much higher rate of evolution (labelled in red). Instead its giving me lots of short terminal branches and very long branches closer to the root. It seems as if it is giving me two rates, one for terminal branches and one closer to the root. Can you let me know if you can think of anything that would help. I've emailed you my XML file.

Cheers,
Toby

NullPointerException during initialization for UCRelaxedCladeClockModel

java.lang.NullPointerException
	at mf.beast.evolution.branchratemodel.UCRelaxedCladeClockModel.setUpMap(Unknown Source)
	at mf.beast.evolution.branchratemodel.UCRelaxedCladeClockModel.initAndValidate(Unknown Source)
	at beast.util.XMLParser.initBEASTObjects(Unknown Source)
	at beast.util.XMLParser.parse(Unknown Source)
	at beast.util.XMLParser.parseFile(Unknown Source)
	at beast.app.BeastMCMC.parseArgs(Unknown Source)
	at beast.app.beastapp.BeastMain.main(Unknown Source)

Error 110 parsing the xml input file

validate and intialize error: null

Error detected about here:
  <beast>
      <run id='mcmc' spec='MCMC'>
          <distribution id='posterior' spec='util.CompoundDistribution'>
              <distribution id='likelihood' spec='util.CompoundDistribution'>
                  <distribution id='treeLikelihood.methylations' spec='TreeLikelihood'>
                      <branchRateModel id='branchRates' spec='mf.beast.evolution.branchratemodel.FlexibleLocalClockModel'>
                          <cladeClockModel id='rate.clade' spec='mf.beast.evolution.branchratemodel.UCRelaxedCladeClockModel'>

The difference (from what I understand) seems to be in setUpMap between UCRelaxedCladeClockModel and UCRelaxedMultiCladeClockModel.

In Clade model, the SetUpMap first goes into the leaf nodes and then increments BranchCladeCount. In MultiClade model, it does this in opposite way, which while it makes a little less sense to me, it works.

Well, kind of. With MultiCladeModel I get:

AbstractUCRelaxedClockModel: rate.clade using 0 rate categories to approximate rate distribution across branches.
Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
TreeLikelihood(treeLikelihood.methylations) uses BeerLikelihoodCore
  FilteredAlignment(bin.methylations): [taxa, patterns, sites] = [22, 643, 18705]
WARNING: the dimension of the parameter is 1 at the start of the run.
         The operator FixMeanMutationRatesOperator has no effect (if this does not change).
java.lang.IllegalArgumentException: howMany it too large: must be less than half the dimension of the parameter
	at beast.evolution.operators.SwapOperator.initAndValidate(Unknown Source)
	at beast.util.XMLParser.initBEASTObjects(Unknown Source)
	at beast.util.XMLParser.parse(Unknown Source)
	at beast.util.XMLParser.parseFile(Unknown Source)
	at beast.app.BeastMCMC.parseArgs(Unknown Source)
	at beast.app.beastapp.BeastMain.main(Unknown Source)

Error 110 parsing the xml input file

validate and intialize error: howMany it too large: must be less than half the dimension of the parameter

Error detected about here:
  <beast>
      <run id='mcmc' spec='MCMC'>
          <operator id='CategoriesSwapOperator.clade' spec='SwapOperator'>

Strangely, code runs when the created monophyletic taxon includes taxa in the same order as they are included in the alignment, starting from first taxa. Which might point to something, however the example file runs fine and doesn't have this pattern.

Did I misspecified something?