beast2-dev/phylodynamics

Bayesian phylodynamic methods in BEAST2

phylodynamics's Issues

alignment not accepted by the templates

I tried to load my sequences after opening the template (contemp) in the BEAUti, but the window became blank and responded nothing.
My beauti version is 2.4.8, and the phylodynamics version is 1.2.1. Some the last messages with the error were:

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path
TreeLikelihood(treeLikelihood.outbreak_sim0) uses BeerLikelihoodCore4
  Alignment(outbreak_sim): [taxa, patterns, sites] = [20, 10000, 10000]
Adding beast.evolution.sitemodel.SiteModel SiteModel.s:outbreak_sim
Adding beast.evolution.likelihood.ThreadedTreeLikelihood treeLikelihood.outbreak_sim
Adding beast.math.distributions.Prior ClockPrior.c:outbreak_sim
Adding beast.math.distributions.Prior MutationRatePrior.s:outbreak_sim
Adding beast.evolution.alignment.TaxonSet 	TaxonSet.outbreak_sim

Adding beast.evolution.tree.Tree ((((((2:0.00913823207720426,14:0.00913823207720426)20:0.0502941026760681,(6:0.005787716280129395,10:0.005787716280129395)21:0.05364461847314296)22:0.1325052376552091,((7:0.018279534483591313,4:0.018279534483591313)23:0.05469023766567841,16:0.07296977214926972)24:0.11896780025921175)25:0.36631946794955167,8:0.5582570403580331)26:0.1378885021142684,(((11:0.08635200548358422,13:0.08635200548358422)27:0.17975802652227457,(17:0.09797382937468066,12:0.09797382937468066)28:0.16813620263117815)29:0.009694136089329675,(18:0.06720657249130126,(0:0.05603286026672478,19:0.05603286026672478)30:0.011173712224576478)31:0.20859759560388724)32:0.42034137437711305)33:0.09905786193595312,((3:0.36677799503545255,(9:0.05324702569219307,1:0.05324702569219307)34:0.31353096934325947)35:0.26865218527627216,(5:0.18969101821690887,15:0.18969101821690887)36:0.44573916209481584)37:0.15977322409652994)38:0.0
Adding beast.evolution.tree.RandomTree ((((((2:0.00913823207720426,14:0.00913823207720426)20:0.0502941026760681,(6:0.005787716280129395,10:0.005787716280129395)21:0.05364461847314296)22:0.1325052376552091,((7:0.018279534483591313,4:0.018279534483591313)23:0.05469023766567841,16:0.07296977214926972)24:0.11896780025921175)25:0.36631946794955167,8:0.5582570403580331)26:0.1378885021142684,(((11:0.08635200548358422,13:0.08635200548358422)27:0.17975802652227457,(17:0.09797382937468066,12:0.09797382937468066)28:0.16813620263117815)29:0.009694136089329675,(18:0.06720657249130126,(0:0.05603286026672478,19:0.05603286026672478)30:0.011173712224576478)31:0.20859759560388724)32:0.42034137437711305)33:0.09905786193595312,((3:0.36677799503545255,(9:0.05324702569219307,1:0.05324702569219307)34:0.31353096934325947)35:0.26865218527627216,(5:0.18969101821690887,15:0.18969101821690887)36:0.44573916209481584)37:0.15977322409652994)38:0.0
Adding beast.evolution.speciation.YuleModel YuleModel.t:outbreak_sim
Adding beast.evolution.tree.TreeHeightLogger TreeHeight.t:outbreak_sim
Adding beast.core.Logger treelog.t:outbreak_sim
Adding beast.evolution.operators.ScaleOperator ScaleOperator(proportionInvariantScaler.s:outbreak_sim)                    0.5000          0          0        NaN 
Adding beast.evolution.operators.ScaleOperator ScaleOperator(mutationRateScaler.s:outbreak_sim)                           0.5000          0          0        NaN 
Adding beast.evolution.operators.ScaleOperator ScaleOperator(gammaShapeScaler.s:outbreak_sim)                             0.5000          0          0        NaN 
Adding beast.evolution.operators.TipDatesRandomWalker TipDatesRandomWalker(allTipDatesRandomWalker.t:outbreak_sim)               1.0000          0          0        NaN 
Adding beast.evolution.operators.ScaleOperator ScaleOperator(YuleModelTreeScaler.t:outbreak_sim)                          0.5000          0          0        NaN 
Adding beast.evolution.operators.ScaleOperator ScaleOperator(YuleModelTreeRootScaler.t:outbreak_sim)                      0.5000          0          0        NaN 
Adding beast.evolution.operators.Uniform Uniform(YuleModelUniformOperator.t:outbreak_sim)                                -          0          0        NaN 
Adding beast.evolution.operators.SubtreeSlide SubtreeSlide(YuleModelSubtreeSlide.t:outbreak_sim)                         1.0000          0          0        NaN 
Adding beast.evolution.operators.Exchange Exchange(YuleModelNarrow.t:outbreak_sim)                                        -          0          0        NaN 
Adding beast.evolution.operators.Exchange Exchange(YuleModelWide.t:outbreak_sim)                                          -          0          0        NaN 
Adding beast.evolution.operators.WilsonBalding WilsonBalding(YuleModelWilsonBalding.t:outbreak_sim)                            -          0          0        NaN 
Adding beast.math.distributions.Prior YuleBirthRatePrior.t:outbreak_sim
Adding beast.math.distributions.Prior GammaShapePrior.s:outbreak_sim
Adding beast.math.distributions.Prior PropInvariantPrior.s:outbreak_sim
Adding beast.evolution.operators.ScaleOperator ScaleOperator(YuleBirthRateScaler.t:outbreak_sim)                          0.7500          0          0        NaN 
Adding beast.evolution.operators.ScaleOperator ScaleOperator(StrictClockRateScaler.c:outbreak_sim)                        0.7500          0          0        NaN 
Adding beast.evolution.operators.UpDownOperator UpDownOperator(strictClockUpDownOperator.c:outbreak_sim)                   0.7500          0          0        NaN 
BeautiDoc: Could not find object likelihood
BeautiDoc: Could not find object prior
>>> No description for connector YuleModel.t:$(n) == prior
>>> No description for connector ClockPrior.c:$(n) == prior
>>> No description for connector MutationRatePrior.s:$(n) == prior
>>> No description for connector GammaShapePrior.s:$(n) == prior
>>> No description for connector PropInvariantPrior.s:$(n) == prior
>>> No description for connector YuleBirthRatePrior.t:$(n) == prior
InPosterior=posterior prior likelihood 
PARTITIONS:

[[], [], []]
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
class beast.core.util.CompoundDistribution != class beast.core.Distribution

Could you suggest me some possible solutions?

VolzSIRTest error for BEAST 2.5

beast.util.TreeParser$TreeParsingException: mismatched input ';' expecting {COMMA, ')'}
at beast.util.TreeParser$1.syntaxError(TreeParser.java:362)
at org.antlr.v4.runtime.ProxyErrorListener.syntaxError(ProxyErrorListener.java:41)
at org.antlr.v4.runtime.Parser.notifyErrorListeners(Parser.java:544)
at org.antlr.v4.runtime.DefaultErrorStrategy.reportInputMismatch(DefaultErrorStrategy.java:299)
at org.antlr.v4.runtime.DefaultErrorStrategy.reportError(DefaultErrorStrategy.java:124)
at beast.util.treeparser.NewickParser.node(NewickParser.java:225)
at beast.util.treeparser.NewickParser.tree(NewickParser.java:123)
at beast.util.TreeParser.parseNewick(TreeParser.java:380)
at beast.util.TreeParser.initAndValidate(TreeParser.java:157)
at beast.core.BEASTInterface.initByName(BEASTInterface.java:103)
at test.beast.BEASTTestCase.getTree(BEASTTestCase.java:30)
at test.phylodynamics.epidemiology.VolzSIRTest.testVolzSIR(VolzSIRTest.java:30)
...

Template not working with BDSK v1.3.3

The BDSKY package has its "R0" input renamed to "reproductiveNumber", and consequently the BDSIR templates need to be updated. Judging from the code, a simple rename should suffice, but I'll leave that to someone more familiar with the model to change in case there are any side effects I am not aware of.

The phylodynamics package works with BDSKY v1.3.2, so I added an 'atmost=1.3.2' entry to packages.xml in CBAN.

BDSIR.xml not working for BEAST 2.5

The first problem is "&" missing in the meta data section.

StochasticCoalescentTest cannot be found running build.xml

Run "build_all_phylodynamics" in build.xml:

java.lang.ClassNotFoundException: test.phylodynamics.epidemiology.StochasticCoalescentTest
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:338)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)

BDSIR.xml failed in ExampleXmlParsingTest

BDSIR.xml failed in ExampleXmlParsingTest.

It was using seed 127 in ExampleXmlParsingTest to start, and increasing 10 for each example.

Run BDSIR.xml using seed 127:

Start likelihood: -Infinity after 10 initialisation attempts
P(posterior) = -Infinity (was -Infinity)
	P(birthDeath) = -Infinity (was -Infinity)
	P(S0_prior) = -7.830948356464641 (was -7.830948356464641)
	P(reproductiveNumber_prior) = -1.83873288586391 (was -1.83873288586391)
	P(becomeUninf_prior) = -0.4935501999211849 (was -0.4935501999211849)
	P(samplingProportion_prior) = 1.2365574164172264 (was 1.2365574164172264)
Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.

<BDSIR spec="beast.phylodynamics.BDSIR" id="birthDeath" tree="@tree" dS="@dS" dR="@dR" checkTreeConsistent="false">
	<parameter name="origin" id="origin" value ="12.7808530307"/>
	<parameter name="reproductiveNumber" id="reproductiveNumber" value="2.5" lower="0." upper="10."/>
	<parameter name="becomeUninfectiousRate" id="becomeUninfectiousRate" value="0.25" lower="0."/>
	<parameter name="samplingProportion" id="samplingProportion" value="0.10" lower="0." upper="1."/>
	<parameter name="S0" id="S0" value="1000" lower="1"/>
</BDSIR>

DocumentationTest failed

DocumentationTest is used to check if the package is documented properly, for example, the input tip text must be at least 4 words and 15 characters.