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The purpose of beautier is to create a valid
BEAST2 XML input file from its function argument. In this
way, a scientific pipeline using BEAST2 can be fully
scripted, instead of using BEAUti’s GUI.
beautier is part of the babette package
suite (website at https://github.com/ropensci/babette).
babette allows to use BEAST2 (and its tools) from R.
For all examples, do load beautier:
Each example shows a picture of a BEAUti dialog to achieve the same.
BEAUti is part of the BEAST2 tool suite and it’s a GUI to create BEAST2
input files. beautier is an R package to supplement BEAUti,
by providing to do the same from an R script.
Each example reads the alignment from a FASTA file called
anthus_aco_sub.fas, which is part of the files supplied
with beautier:
In this vignette, the generated BEAST2 XML is shown. Use
create_beast2_input_file to save the resulting XML directly
to file instead.
Using all default settings, only specify a DNA alignment.
create_beast2_input(
input_filename
)
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><beast beautitemplate='Standard' beautistatus='' namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" required=\"\" version=\"2.4\">"
[2] ""
[3] ""
[4] " <data"
[5] "id=\"anthus_aco_sub\""
[6] "name=\"alignment\">"
[7] " <sequence id=\"seq_61430_aco\" taxon=\"61430_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[8] " <sequence id=\"seq_626029_aco\" taxon=\"626029_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacgattgtctgttttt\"/>"
[9] " <sequence id=\"seq_630116_aco\" taxon=\"630116_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[10] " <sequence id=\"seq_630210_aco\" taxon=\"630210_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[11] " <sequence id=\"seq_B25702_aco\" taxon=\"B25702_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[12] " </data>"
[13] ""
[14] ""
[15] " "
[16] ""
[17] ""
[18] " "
[19] ""
[20] ""
[21] " "
[22] "<map name=\"Uniform\" >beast.math.distributions.Uniform</map>"
[23] "<map name=\"Exponential\" >beast.math.distributions.Exponential</map>"
[24] "<map name=\"LogNormal\" >beast.math.distributions.LogNormalDistributionModel</map>"
[25] "<map name=\"Normal\" >beast.math.distributions.Normal</map>"
[26] "<map name=\"Beta\" >beast.math.distributions.Beta</map>"
[27] "<map name=\"Gamma\" >beast.math.distributions.Gamma</map>"
[28] "<map name=\"LaplaceDistribution\" >beast.math.distributions.LaplaceDistribution</map>"
[29] "<map name=\"prior\" >beast.math.distributions.Prior</map>"
[30] "<map name=\"InverseGamma\" >beast.math.distributions.InverseGamma</map>"
[31] "<map name=\"OneOnX\" >beast.math.distributions.OneOnX</map>"
[32] ""
[33] ""
[34] "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"10000000\">"
[35] " <state id=\"state\" storeEvery=\"5000\">"
[36] " <tree id=\"Tree.t:anthus_aco_sub\" name=\"stateNode\">"
[37] " <taxonset id=\"TaxonSet.anthus_aco_sub\" spec=\"TaxonSet\">"
[38] " <alignment idref=\"anthus_aco_sub\"/>"
[39] " </taxonset>"
[40] " </tree>"
[41] " <parameter id=\"birthRate.t:anthus_aco_sub\" name=\"stateNode\">1.0</parameter>"
[42] " </state>"
[43] ""
[44] " <init id=\"RandomTree.t:anthus_aco_sub\" spec=\"beast.evolution.tree.RandomTree\" estimate=\"false\" initial=\"@Tree.t:anthus_aco_sub\" taxa=\"@anthus_aco_sub\">"
[45] " <populationModel id=\"ConstantPopulation0.t:anthus_aco_sub\" spec=\"ConstantPopulation\">"
[46] " <parameter id=\"randomPopSize.t:anthus_aco_sub\" name=\"popSize\">1.0</parameter>"
[47] " </populationModel>"
[48] " </init>"
[49] ""
[50] " <distribution id=\"posterior\" spec=\"util.CompoundDistribution\">"
[51] " <distribution id=\"prior\" spec=\"util.CompoundDistribution\">"
[52] " <distribution id=\"YuleModel.t:anthus_aco_sub\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[53] " <prior id=\"YuleBirthRatePrior.t:anthus_aco_sub\" name=\"distribution\" x=\"@birthRate.t:anthus_aco_sub\">"
[54] " <Uniform id=\"Uniform.100\" name=\"distr\" upper=\"Infinity\"/>"
[55] " </prior>"
[56] " </distribution>"
[57] " <distribution id=\"likelihood\" spec=\"util.CompoundDistribution\" useThreads=\"true\">"
[58] " <distribution id=\"treeLikelihood.anthus_aco_sub\" spec=\"ThreadedTreeLikelihood\" data=\"@anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\">"
[59] " <siteModel id=\"SiteModel.s:anthus_aco_sub\" spec=\"SiteModel\">"
[60] " <parameter id=\"mutationRate.s:anthus_aco_sub\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>"
[61] " <parameter id=\"gammaShape.s:anthus_aco_sub\" estimate=\"false\" name=\"shape\">1.0</parameter>"
[62] " <parameter id=\"proportionInvariant.s:anthus_aco_sub\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.0</parameter>"
[63] " <substModel id=\"JC69.s:anthus_aco_sub\" spec=\"JukesCantor\"/>"
[64] " </siteModel>"
[65] " <branchRateModel id=\"StrictClock.c:anthus_aco_sub\" spec=\"beast.evolution.branchratemodel.StrictClockModel\">"
[66] " <parameter id=\"clockRate.c:anthus_aco_sub\" estimate=\"false\" name=\"clock.rate\">1.0</parameter>"
[67] " </branchRateModel>"
[68] " </distribution>"
[69] " </distribution>"
[70] " </distribution>"
[71] ""
[72] " <operator id=\"YuleBirthRateScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@birthRate.t:anthus_aco_sub\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[73] ""
[74] " <operator id=\"YuleModelTreeScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[75] ""
[76] " <operator id=\"YuleModelTreeRootScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" rootOnly=\"true\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[77] ""
[78] " <operator id=\"YuleModelUniformOperator.t:anthus_aco_sub\" spec=\"Uniform\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"30.0\"/>"
[79] ""
[80] " <operator id=\"YuleModelSubtreeSlide.t:anthus_aco_sub\" spec=\"SubtreeSlide\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[81] ""
[82] " <operator id=\"YuleModelNarrow.t:anthus_aco_sub\" spec=\"Exchange\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[83] ""
[84] " <operator id=\"YuleModelWide.t:anthus_aco_sub\" spec=\"Exchange\" isNarrow=\"false\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[85] ""
[86] " <operator id=\"YuleModelWilsonBalding.t:anthus_aco_sub\" spec=\"WilsonBalding\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[87] ""
[88] " <logger id=\"tracelog\" fileName=\"anthus_aco_sub.log\" logEvery=\"1000\" model=\"@posterior\" sanitiseHeaders=\"true\" sort=\"smart\">"
[89] " <log idref=\"posterior\"/>"
[90] " <log idref=\"likelihood\"/>"
[91] " <log idref=\"prior\"/>"
[92] " <log idref=\"treeLikelihood.anthus_aco_sub\"/>"
[93] " <log id=\"TreeHeight.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeHeightLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[94] " <log idref=\"YuleModel.t:anthus_aco_sub\"/>"
[95] " <log idref=\"birthRate.t:anthus_aco_sub\"/>"
[96] " </logger>"
[97] ""
[98] " <logger id=\"screenlog\" logEvery=\"1000\">"
[99] " <log idref=\"posterior\"/>"
[100] " <log id=\"ESS.0\" spec=\"util.ESS\" arg=\"@posterior\"/>"
[101] " <log idref=\"likelihood\"/>"
[102] " <log idref=\"prior\"/>"
[103] " </logger>"
[104] ""
[105] " <logger id=\"treelog.t:anthus_aco_sub\" fileName=\"$(tree).trees\" logEvery=\"1000\" mode=\"tree\">"
[106] " <log id=\"TreeWithMetaDataLogger.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[107] " </logger>"
[108] ""
[109] "</run>"
[110] ""
[111] "</beast>" All other parameters are set to their defaults, as in BEAUti.
create_beast2_input(
input_filename,
site_model = create_jc69_site_model()
)
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><beast beautitemplate='Standard' beautistatus='' namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" required=\"\" version=\"2.4\">"
[2] ""
[3] ""
[4] " <data"
[5] "id=\"anthus_aco_sub\""
[6] "name=\"alignment\">"
[7] " <sequence id=\"seq_61430_aco\" taxon=\"61430_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[8] " <sequence id=\"seq_626029_aco\" taxon=\"626029_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacgattgtctgttttt\"/>"
[9] " <sequence id=\"seq_630116_aco\" taxon=\"630116_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[10] " <sequence id=\"seq_630210_aco\" taxon=\"630210_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[11] " <sequence id=\"seq_B25702_aco\" taxon=\"B25702_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[12] " </data>"
[13] ""
[14] ""
[15] " "
[16] ""
[17] ""
[18] " "
[19] ""
[20] ""
[21] " "
[22] "<map name=\"Uniform\" >beast.math.distributions.Uniform</map>"
[23] "<map name=\"Exponential\" >beast.math.distributions.Exponential</map>"
[24] "<map name=\"LogNormal\" >beast.math.distributions.LogNormalDistributionModel</map>"
[25] "<map name=\"Normal\" >beast.math.distributions.Normal</map>"
[26] "<map name=\"Beta\" >beast.math.distributions.Beta</map>"
[27] "<map name=\"Gamma\" >beast.math.distributions.Gamma</map>"
[28] "<map name=\"LaplaceDistribution\" >beast.math.distributions.LaplaceDistribution</map>"
[29] "<map name=\"prior\" >beast.math.distributions.Prior</map>"
[30] "<map name=\"InverseGamma\" >beast.math.distributions.InverseGamma</map>"
[31] "<map name=\"OneOnX\" >beast.math.distributions.OneOnX</map>"
[32] ""
[33] ""
[34] "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"10000000\">"
[35] " <state id=\"state\" storeEvery=\"5000\">"
[36] " <tree id=\"Tree.t:anthus_aco_sub\" name=\"stateNode\">"
[37] " <taxonset id=\"TaxonSet.anthus_aco_sub\" spec=\"TaxonSet\">"
[38] " <alignment idref=\"anthus_aco_sub\"/>"
[39] " </taxonset>"
[40] " </tree>"
[41] " <parameter id=\"birthRate.t:anthus_aco_sub\" name=\"stateNode\">1.0</parameter>"
[42] " </state>"
[43] ""
[44] " <init id=\"RandomTree.t:anthus_aco_sub\" spec=\"beast.evolution.tree.RandomTree\" estimate=\"false\" initial=\"@Tree.t:anthus_aco_sub\" taxa=\"@anthus_aco_sub\">"
[45] " <populationModel id=\"ConstantPopulation0.t:anthus_aco_sub\" spec=\"ConstantPopulation\">"
[46] " <parameter id=\"randomPopSize.t:anthus_aco_sub\" name=\"popSize\">1.0</parameter>"
[47] " </populationModel>"
[48] " </init>"
[49] ""
[50] " <distribution id=\"posterior\" spec=\"util.CompoundDistribution\">"
[51] " <distribution id=\"prior\" spec=\"util.CompoundDistribution\">"
[52] " <distribution id=\"YuleModel.t:anthus_aco_sub\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[53] " <prior id=\"YuleBirthRatePrior.t:anthus_aco_sub\" name=\"distribution\" x=\"@birthRate.t:anthus_aco_sub\">"
[54] " <Uniform id=\"Uniform.100\" name=\"distr\" upper=\"Infinity\"/>"
[55] " </prior>"
[56] " </distribution>"
[57] " <distribution id=\"likelihood\" spec=\"util.CompoundDistribution\" useThreads=\"true\">"
[58] " <distribution id=\"treeLikelihood.anthus_aco_sub\" spec=\"ThreadedTreeLikelihood\" data=\"@anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\">"
[59] " <siteModel id=\"SiteModel.s:anthus_aco_sub\" spec=\"SiteModel\">"
[60] " <parameter id=\"mutationRate.s:anthus_aco_sub\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>"
[61] " <parameter id=\"gammaShape.s:anthus_aco_sub\" estimate=\"false\" name=\"shape\">1.0</parameter>"
[62] " <parameter id=\"proportionInvariant.s:anthus_aco_sub\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.0</parameter>"
[63] " <substModel id=\"JC69.s:anthus_aco_sub\" spec=\"JukesCantor\"/>"
[64] " </siteModel>"
[65] " <branchRateModel id=\"StrictClock.c:anthus_aco_sub\" spec=\"beast.evolution.branchratemodel.StrictClockModel\">"
[66] " <parameter id=\"clockRate.c:anthus_aco_sub\" estimate=\"false\" name=\"clock.rate\">1.0</parameter>"
[67] " </branchRateModel>"
[68] " </distribution>"
[69] " </distribution>"
[70] " </distribution>"
[71] ""
[72] " <operator id=\"YuleBirthRateScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@birthRate.t:anthus_aco_sub\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[73] ""
[74] " <operator id=\"YuleModelTreeScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[75] ""
[76] " <operator id=\"YuleModelTreeRootScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" rootOnly=\"true\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[77] ""
[78] " <operator id=\"YuleModelUniformOperator.t:anthus_aco_sub\" spec=\"Uniform\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"30.0\"/>"
[79] ""
[80] " <operator id=\"YuleModelSubtreeSlide.t:anthus_aco_sub\" spec=\"SubtreeSlide\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[81] ""
[82] " <operator id=\"YuleModelNarrow.t:anthus_aco_sub\" spec=\"Exchange\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[83] ""
[84] " <operator id=\"YuleModelWide.t:anthus_aco_sub\" spec=\"Exchange\" isNarrow=\"false\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[85] ""
[86] " <operator id=\"YuleModelWilsonBalding.t:anthus_aco_sub\" spec=\"WilsonBalding\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[87] ""
[88] " <logger id=\"tracelog\" fileName=\"anthus_aco_sub.log\" logEvery=\"1000\" model=\"@posterior\" sanitiseHeaders=\"true\" sort=\"smart\">"
[89] " <log idref=\"posterior\"/>"
[90] " <log idref=\"likelihood\"/>"
[91] " <log idref=\"prior\"/>"
[92] " <log idref=\"treeLikelihood.anthus_aco_sub\"/>"
[93] " <log id=\"TreeHeight.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeHeightLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[94] " <log idref=\"YuleModel.t:anthus_aco_sub\"/>"
[95] " <log idref=\"birthRate.t:anthus_aco_sub\"/>"
[96] " </logger>"
[97] ""
[98] " <logger id=\"screenlog\" logEvery=\"1000\">"
[99] " <log idref=\"posterior\"/>"
[100] " <log id=\"ESS.0\" spec=\"util.ESS\" arg=\"@posterior\"/>"
[101] " <log idref=\"likelihood\"/>"
[102] " <log idref=\"prior\"/>"
[103] " </logger>"
[104] ""
[105] " <logger id=\"treelog.t:anthus_aco_sub\" fileName=\"$(tree).trees\" logEvery=\"1000\" mode=\"tree\">"
[106] " <log id=\"TreeWithMetaDataLogger.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[107] " </logger>"
[108] ""
[109] "</run>"
[110] ""
[111] "</beast>" 
create_beast2_input(
input_filename,
clock_model = create_rln_clock_model()
)
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><beast beautitemplate='Standard' beautistatus='' namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" required=\"\" version=\"2.4\">"
[2] ""
[3] ""
[4] " <data"
[5] "id=\"anthus_aco_sub\""
[6] "name=\"alignment\">"
[7] " <sequence id=\"seq_61430_aco\" taxon=\"61430_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[8] " <sequence id=\"seq_626029_aco\" taxon=\"626029_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacgattgtctgttttt\"/>"
[9] " <sequence id=\"seq_630116_aco\" taxon=\"630116_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[10] " <sequence id=\"seq_630210_aco\" taxon=\"630210_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[11] " <sequence id=\"seq_B25702_aco\" taxon=\"B25702_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[12] " </data>"
[13] ""
[14] ""
[15] " "
[16] ""
[17] ""
[18] " "
[19] ""
[20] ""
[21] " "
[22] "<map name=\"Uniform\" >beast.math.distributions.Uniform</map>"
[23] "<map name=\"Exponential\" >beast.math.distributions.Exponential</map>"
[24] "<map name=\"LogNormal\" >beast.math.distributions.LogNormalDistributionModel</map>"
[25] "<map name=\"Normal\" >beast.math.distributions.Normal</map>"
[26] "<map name=\"Beta\" >beast.math.distributions.Beta</map>"
[27] "<map name=\"Gamma\" >beast.math.distributions.Gamma</map>"
[28] "<map name=\"LaplaceDistribution\" >beast.math.distributions.LaplaceDistribution</map>"
[29] "<map name=\"prior\" >beast.math.distributions.Prior</map>"
[30] "<map name=\"InverseGamma\" >beast.math.distributions.InverseGamma</map>"
[31] "<map name=\"OneOnX\" >beast.math.distributions.OneOnX</map>"
[32] ""
[33] ""
[34] "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"10000000\">"
[35] " <state id=\"state\" storeEvery=\"5000\">"
[36] " <tree id=\"Tree.t:anthus_aco_sub\" name=\"stateNode\">"
[37] " <taxonset id=\"TaxonSet.anthus_aco_sub\" spec=\"TaxonSet\">"
[38] " <alignment idref=\"anthus_aco_sub\"/>"
[39] " </taxonset>"
[40] " </tree>"
[41] " <parameter id=\"ucldStdev.c:anthus_aco_sub\" lower=\"0.0\" name=\"stateNode\">0.1</parameter>"
[42] " <stateNode id=\"rateCategories.c:anthus_aco_sub\" spec=\"parameter.IntegerParameter\" dimension=\"8\">1</stateNode>"
[43] " <parameter id=\"birthRate.t:anthus_aco_sub\" name=\"stateNode\">1.0</parameter>"
[44] " </state>"
[45] ""
[46] " <init id=\"RandomTree.t:anthus_aco_sub\" spec=\"beast.evolution.tree.RandomTree\" estimate=\"false\" initial=\"@Tree.t:anthus_aco_sub\" taxa=\"@anthus_aco_sub\">"
[47] " <populationModel id=\"ConstantPopulation0.t:anthus_aco_sub\" spec=\"ConstantPopulation\">"
[48] " <parameter id=\"randomPopSize.t:anthus_aco_sub\" name=\"popSize\">1.0</parameter>"
[49] " </populationModel>"
[50] " </init>"
[51] ""
[52] " <distribution id=\"posterior\" spec=\"util.CompoundDistribution\">"
[53] " <distribution id=\"prior\" spec=\"util.CompoundDistribution\">"
[54] " <distribution id=\"YuleModel.t:anthus_aco_sub\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[55] " <prior id=\"YuleBirthRatePrior.t:anthus_aco_sub\" name=\"distribution\" x=\"@birthRate.t:anthus_aco_sub\">"
[56] " <Uniform id=\"Uniform.100\" name=\"distr\" upper=\"Infinity\"/>"
[57] " </prior>"
[58] " <prior id=\"ucldStdevPrior.c:anthus_aco_sub\" name=\"distribution\" x=\"@ucldStdev.c:anthus_aco_sub\">"
[59] " <Gamma id=\"Gamma.0\" name=\"distr\">"
[60] " <parameter id=\"RealParameter.0\" estimate=\"false\" name=\"alpha\">0.5396</parameter>"
[61] " <parameter id=\"RealParameter.1\" estimate=\"false\" name=\"beta\">0.3819</parameter>"
[62] " </Gamma>"
[63] " </prior>"
[64] " </distribution>"
[65] " <distribution id=\"likelihood\" spec=\"util.CompoundDistribution\" useThreads=\"true\">"
[66] " <distribution id=\"treeLikelihood.anthus_aco_sub\" spec=\"ThreadedTreeLikelihood\" data=\"@anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\">"
[67] " <siteModel id=\"SiteModel.s:anthus_aco_sub\" spec=\"SiteModel\">"
[68] " <parameter id=\"mutationRate.s:anthus_aco_sub\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>"
[69] " <parameter id=\"gammaShape.s:anthus_aco_sub\" estimate=\"false\" name=\"shape\">1.0</parameter>"
[70] " <parameter id=\"proportionInvariant.s:anthus_aco_sub\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.0</parameter>"
[71] " <substModel id=\"JC69.s:anthus_aco_sub\" spec=\"JukesCantor\"/>"
[72] " </siteModel>"
[73] " <branchRateModel id=\"RelaxedClock.c:anthus_aco_sub\" spec=\"beast.evolution.branchratemodel.UCRelaxedClockModel\" rateCategories=\"@rateCategories.c:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\">"
[74] " <LogNormal id=\"LogNormalDistributionModel.c:anthus_aco_sub\" S=\"@ucldStdev.c:anthus_aco_sub\" meanInRealSpace=\"true\" name=\"distr\">"
[75] " <parameter id=\"RealParameter.2\" estimate=\"false\" lower=\"0.0\" name=\"M\" upper=\"1.0\">1.0</parameter>"
[76] " </LogNormal>"
[77] " <parameter id=\"ucldMean.c:anthus_aco_sub\" estimate=\"false\" name=\"clock.rate\">1.0</parameter>"
[78] " </branchRateModel>"
[79] " </distribution>"
[80] " </distribution>"
[81] " </distribution>"
[82] ""
[83] " <operator id=\"YuleBirthRateScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@birthRate.t:anthus_aco_sub\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[84] ""
[85] " <operator id=\"YuleModelTreeScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[86] ""
[87] " <operator id=\"YuleModelTreeRootScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" rootOnly=\"true\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[88] ""
[89] " <operator id=\"YuleModelUniformOperator.t:anthus_aco_sub\" spec=\"Uniform\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"30.0\"/>"
[90] ""
[91] " <operator id=\"YuleModelSubtreeSlide.t:anthus_aco_sub\" spec=\"SubtreeSlide\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[92] ""
[93] " <operator id=\"YuleModelNarrow.t:anthus_aco_sub\" spec=\"Exchange\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[94] ""
[95] " <operator id=\"YuleModelWide.t:anthus_aco_sub\" spec=\"Exchange\" isNarrow=\"false\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[96] ""
[97] " <operator id=\"YuleModelWilsonBalding.t:anthus_aco_sub\" spec=\"WilsonBalding\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[98] ""
[99] " <operator id=\"ucldStdevScaler.c:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@ucldStdev.c:anthus_aco_sub\" scaleFactor=\"0.5\" weight=\"3.0\"/>"
[100] ""
[101] " <operator id=\"CategoriesRandomWalk.c:anthus_aco_sub\" spec=\"IntRandomWalkOperator\" parameter=\"@rateCategories.c:anthus_aco_sub\" weight=\"10.0\" windowSize=\"1\"/>"
[102] ""
[103] " <operator id=\"CategoriesSwapOperator.c:anthus_aco_sub\" spec=\"SwapOperator\" intparameter=\"@rateCategories.c:anthus_aco_sub\" weight=\"10.0\"/>"
[104] ""
[105] " <operator id=\"CategoriesUniform.c:anthus_aco_sub\" spec=\"UniformOperator\" parameter=\"@rateCategories.c:anthus_aco_sub\" weight=\"10.0\"/>"
[106] ""
[107] " <logger id=\"tracelog\" fileName=\"anthus_aco_sub.log\" logEvery=\"1000\" model=\"@posterior\" sanitiseHeaders=\"true\" sort=\"smart\">"
[108] " <log idref=\"posterior\"/>"
[109] " <log idref=\"likelihood\"/>"
[110] " <log idref=\"prior\"/>"
[111] " <log idref=\"treeLikelihood.anthus_aco_sub\"/>"
[112] " <log id=\"TreeHeight.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeHeightLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[113] " <log idref=\"ucldStdev.c:anthus_aco_sub\"/>"
[114] " <log id=\"rate.c:anthus_aco_sub\" spec=\"beast.evolution.branchratemodel.RateStatistic\" branchratemodel=\"@RelaxedClock.c:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[115] " <log idref=\"YuleModel.t:anthus_aco_sub\"/>"
[116] " <log idref=\"birthRate.t:anthus_aco_sub\"/>"
[117] " </logger>"
[118] ""
[119] " <logger id=\"screenlog\" logEvery=\"1000\">"
[120] " <log idref=\"posterior\"/>"
[121] " <log id=\"ESS.0\" spec=\"util.ESS\" arg=\"@posterior\"/>"
[122] " <log idref=\"likelihood\"/>"
[123] " <log idref=\"prior\"/>"
[124] " </logger>"
[125] ""
[126] " <logger id=\"treelog.t:anthus_aco_sub\" fileName=\"$(tree).trees\" logEvery=\"1000\" mode=\"tree\">"
[127] " <log id=\"TreeWithMetaDataLogger.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" branchratemodel=\"@RelaxedClock.c:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[128] " </logger>"
[129] ""
[130] "</run>"
[131] ""
[132] "</beast>" 
create_beast2_input(
input_filename,
tree_prior = create_bd_tree_prior()
)
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><beast beautitemplate='Standard' beautistatus='' namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" required=\"\" version=\"2.4\">"
[2] ""
[3] ""
[4] " <data"
[5] "id=\"anthus_aco_sub\""
[6] "name=\"alignment\">"
[7] " <sequence id=\"seq_61430_aco\" taxon=\"61430_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[8] " <sequence id=\"seq_626029_aco\" taxon=\"626029_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacgattgtctgttttt\"/>"
[9] " <sequence id=\"seq_630116_aco\" taxon=\"630116_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[10] " <sequence id=\"seq_630210_aco\" taxon=\"630210_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[11] " <sequence id=\"seq_B25702_aco\" taxon=\"B25702_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[12] " </data>"
[13] ""
[14] ""
[15] " "
[16] ""
[17] ""
[18] " "
[19] ""
[20] ""
[21] " "
[22] "<map name=\"Uniform\" >beast.math.distributions.Uniform</map>"
[23] "<map name=\"Exponential\" >beast.math.distributions.Exponential</map>"
[24] "<map name=\"LogNormal\" >beast.math.distributions.LogNormalDistributionModel</map>"
[25] "<map name=\"Normal\" >beast.math.distributions.Normal</map>"
[26] "<map name=\"Beta\" >beast.math.distributions.Beta</map>"
[27] "<map name=\"Gamma\" >beast.math.distributions.Gamma</map>"
[28] "<map name=\"LaplaceDistribution\" >beast.math.distributions.LaplaceDistribution</map>"
[29] "<map name=\"prior\" >beast.math.distributions.Prior</map>"
[30] "<map name=\"InverseGamma\" >beast.math.distributions.InverseGamma</map>"
[31] "<map name=\"OneOnX\" >beast.math.distributions.OneOnX</map>"
[32] ""
[33] ""
[34] "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"10000000\">"
[35] " <state id=\"state\" storeEvery=\"5000\">"
[36] " <tree id=\"Tree.t:anthus_aco_sub\" name=\"stateNode\">"
[37] " <taxonset id=\"TaxonSet.anthus_aco_sub\" spec=\"TaxonSet\">"
[38] " <alignment idref=\"anthus_aco_sub\"/>"
[39] " </taxonset>"
[40] " </tree>"
[41] " <parameter id=\"BDBirthRate.t:anthus_aco_sub\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>"
[42] " <parameter id=\"BDDeathRate.t:anthus_aco_sub\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>"
[43] " </state>"
[44] ""
[45] " <init id=\"RandomTree.t:anthus_aco_sub\" spec=\"beast.evolution.tree.RandomTree\" estimate=\"false\" initial=\"@Tree.t:anthus_aco_sub\" taxa=\"@anthus_aco_sub\">"
[46] " <populationModel id=\"ConstantPopulation0.t:anthus_aco_sub\" spec=\"ConstantPopulation\">"
[47] " <parameter id=\"randomPopSize.t:anthus_aco_sub\" name=\"popSize\">1.0</parameter>"
[48] " </populationModel>"
[49] " </init>"
[50] ""
[51] " <distribution id=\"posterior\" spec=\"util.CompoundDistribution\">"
[52] " <distribution id=\"prior\" spec=\"util.CompoundDistribution\">"
[53] " <distribution id=\"BirthDeath.t:anthus_aco_sub\" spec=\"beast.evolution.speciation.BirthDeathGernhard08Model\" birthDiffRate=\"@BDBirthRate.t:anthus_aco_sub\" relativeDeathRate=\"@BDDeathRate.t:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[54] " <prior id=\"BirthRatePrior.t:anthus_aco_sub\" name=\"distribution\" x=\"@BDBirthRate.t:anthus_aco_sub\">"
[55] " <Uniform id=\"Uniform.100\" name=\"distr\" upper=\"Infinity\"/>"
[56] " </prior>"
[57] " <prior id=\"DeathRatePrior.t:anthus_aco_sub\" name=\"distribution\" x=\"@BDDeathRate.t:anthus_aco_sub\">"
[58] " <Uniform id=\"Uniform.101\" name=\"distr\" upper=\"Infinity\"/>"
[59] " </prior>"
[60] " </distribution>"
[61] " <distribution id=\"likelihood\" spec=\"util.CompoundDistribution\" useThreads=\"true\">"
[62] " <distribution id=\"treeLikelihood.anthus_aco_sub\" spec=\"ThreadedTreeLikelihood\" data=\"@anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\">"
[63] " <siteModel id=\"SiteModel.s:anthus_aco_sub\" spec=\"SiteModel\">"
[64] " <parameter id=\"mutationRate.s:anthus_aco_sub\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>"
[65] " <parameter id=\"gammaShape.s:anthus_aco_sub\" estimate=\"false\" name=\"shape\">1.0</parameter>"
[66] " <parameter id=\"proportionInvariant.s:anthus_aco_sub\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.0</parameter>"
[67] " <substModel id=\"JC69.s:anthus_aco_sub\" spec=\"JukesCantor\"/>"
[68] " </siteModel>"
[69] " <branchRateModel id=\"StrictClock.c:anthus_aco_sub\" spec=\"beast.evolution.branchratemodel.StrictClockModel\">"
[70] " <parameter id=\"clockRate.c:anthus_aco_sub\" estimate=\"false\" name=\"clock.rate\">1.0</parameter>"
[71] " </branchRateModel>"
[72] " </distribution>"
[73] " </distribution>"
[74] " </distribution>"
[75] ""
[76] " <operator id=\"BirthRateScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@BDBirthRate.t:anthus_aco_sub\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[77] ""
[78] " <operator id=\"DeathRateScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@BDDeathRate.t:anthus_aco_sub\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[79] ""
[80] " <operator id=\"BirthDeathTreeScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[81] ""
[82] " <operator id=\"BirthDeathTreeRootScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" rootOnly=\"true\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[83] ""
[84] " <operator id=\"BirthDeathUniformOperator.t:anthus_aco_sub\" spec=\"Uniform\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"30.0\"/>"
[85] ""
[86] " <operator id=\"BirthDeathSubtreeSlide.t:anthus_aco_sub\" spec=\"SubtreeSlide\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[87] ""
[88] " <operator id=\"BirthDeathNarrow.t:anthus_aco_sub\" spec=\"Exchange\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[89] ""
[90] " <operator id=\"BirthDeathWide.t:anthus_aco_sub\" spec=\"Exchange\" isNarrow=\"false\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[91] ""
[92] " <operator id=\"BirthDeathWilsonBalding.t:anthus_aco_sub\" spec=\"WilsonBalding\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[93] ""
[94] " <logger id=\"tracelog\" fileName=\"anthus_aco_sub.log\" logEvery=\"1000\" model=\"@posterior\" sanitiseHeaders=\"true\" sort=\"smart\">"
[95] " <log idref=\"posterior\"/>"
[96] " <log idref=\"likelihood\"/>"
[97] " <log idref=\"prior\"/>"
[98] " <log idref=\"treeLikelihood.anthus_aco_sub\"/>"
[99] " <log id=\"TreeHeight.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeHeightLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[100] " <log idref=\"BirthDeath.t:anthus_aco_sub\"/>"
[101] " <log idref=\"BDBirthRate.t:anthus_aco_sub\"/>"
[102] " <log idref=\"BDDeathRate.t:anthus_aco_sub\"/>"
[103] " </logger>"
[104] ""
[105] " <logger id=\"screenlog\" logEvery=\"1000\">"
[106] " <log idref=\"posterior\"/>"
[107] " <log id=\"ESS.0\" spec=\"util.ESS\" arg=\"@posterior\"/>"
[108] " <log idref=\"likelihood\"/>"
[109] " <log idref=\"prior\"/>"
[110] " </logger>"
[111] ""
[112] " <logger id=\"treelog.t:anthus_aco_sub\" fileName=\"$(tree).trees\" logEvery=\"1000\" mode=\"tree\">"
[113] " <log id=\"TreeWithMetaDataLogger.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[114] " </logger>"
[115] ""
[116] "</run>"
[117] ""
[118] "</beast>" 
create_beast2_input(
input_filename,
tree_prior = create_yule_tree_prior(
birth_rate_distr = create_normal_distr()
)
)
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><beast beautitemplate='Standard' beautistatus='' namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" required=\"\" version=\"2.4\">"
[2] ""
[3] ""
[4] " <data"
[5] "id=\"anthus_aco_sub\""
[6] "name=\"alignment\">"
[7] " <sequence id=\"seq_61430_aco\" taxon=\"61430_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[8] " <sequence id=\"seq_626029_aco\" taxon=\"626029_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacgattgtctgttttt\"/>"
[9] " <sequence id=\"seq_630116_aco\" taxon=\"630116_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[10] " <sequence id=\"seq_630210_aco\" taxon=\"630210_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[11] " <sequence id=\"seq_B25702_aco\" taxon=\"B25702_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[12] " </data>"
[13] ""
[14] ""
[15] " "
[16] ""
[17] ""
[18] " "
[19] ""
[20] ""
[21] " "
[22] "<map name=\"Uniform\" >beast.math.distributions.Uniform</map>"
[23] "<map name=\"Exponential\" >beast.math.distributions.Exponential</map>"
[24] "<map name=\"LogNormal\" >beast.math.distributions.LogNormalDistributionModel</map>"
[25] "<map name=\"Normal\" >beast.math.distributions.Normal</map>"
[26] "<map name=\"Beta\" >beast.math.distributions.Beta</map>"
[27] "<map name=\"Gamma\" >beast.math.distributions.Gamma</map>"
[28] "<map name=\"LaplaceDistribution\" >beast.math.distributions.LaplaceDistribution</map>"
[29] "<map name=\"prior\" >beast.math.distributions.Prior</map>"
[30] "<map name=\"InverseGamma\" >beast.math.distributions.InverseGamma</map>"
[31] "<map name=\"OneOnX\" >beast.math.distributions.OneOnX</map>"
[32] ""
[33] ""
[34] "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"10000000\">"
[35] " <state id=\"state\" storeEvery=\"5000\">"
[36] " <tree id=\"Tree.t:anthus_aco_sub\" name=\"stateNode\">"
[37] " <taxonset id=\"TaxonSet.anthus_aco_sub\" spec=\"TaxonSet\">"
[38] " <alignment idref=\"anthus_aco_sub\"/>"
[39] " </taxonset>"
[40] " </tree>"
[41] " <parameter id=\"birthRate.t:anthus_aco_sub\" name=\"stateNode\">1.0</parameter>"
[42] " </state>"
[43] ""
[44] " <init id=\"RandomTree.t:anthus_aco_sub\" spec=\"beast.evolution.tree.RandomTree\" estimate=\"false\" initial=\"@Tree.t:anthus_aco_sub\" taxa=\"@anthus_aco_sub\">"
[45] " <populationModel id=\"ConstantPopulation0.t:anthus_aco_sub\" spec=\"ConstantPopulation\">"
[46] " <parameter id=\"randomPopSize.t:anthus_aco_sub\" name=\"popSize\">1.0</parameter>"
[47] " </populationModel>"
[48] " </init>"
[49] ""
[50] " <distribution id=\"posterior\" spec=\"util.CompoundDistribution\">"
[51] " <distribution id=\"prior\" spec=\"util.CompoundDistribution\">"
[52] " <distribution id=\"YuleModel.t:anthus_aco_sub\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[53] " <prior id=\"YuleBirthRatePrior.t:anthus_aco_sub\" name=\"distribution\" x=\"@birthRate.t:anthus_aco_sub\">"
[54] " <Normal id=\"Normal.100\" name=\"distr\">"
[55] " <parameter id=\"RealParameter.200\" estimate=\"false\" name=\"mean\">0</parameter>"
[56] " <parameter id=\"RealParameter.201\" estimate=\"false\" name=\"sigma\">1</parameter>"
[57] " </Normal>"
[58] " </prior>"
[59] " </distribution>"
[60] " <distribution id=\"likelihood\" spec=\"util.CompoundDistribution\" useThreads=\"true\">"
[61] " <distribution id=\"treeLikelihood.anthus_aco_sub\" spec=\"ThreadedTreeLikelihood\" data=\"@anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\">"
[62] " <siteModel id=\"SiteModel.s:anthus_aco_sub\" spec=\"SiteModel\">"
[63] " <parameter id=\"mutationRate.s:anthus_aco_sub\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>"
[64] " <parameter id=\"gammaShape.s:anthus_aco_sub\" estimate=\"false\" name=\"shape\">1.0</parameter>"
[65] " <parameter id=\"proportionInvariant.s:anthus_aco_sub\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.0</parameter>"
[66] " <substModel id=\"JC69.s:anthus_aco_sub\" spec=\"JukesCantor\"/>"
[67] " </siteModel>"
[68] " <branchRateModel id=\"StrictClock.c:anthus_aco_sub\" spec=\"beast.evolution.branchratemodel.StrictClockModel\">"
[69] " <parameter id=\"clockRate.c:anthus_aco_sub\" estimate=\"false\" name=\"clock.rate\">1.0</parameter>"
[70] " </branchRateModel>"
[71] " </distribution>"
[72] " </distribution>"
[73] " </distribution>"
[74] ""
[75] " <operator id=\"YuleBirthRateScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@birthRate.t:anthus_aco_sub\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[76] ""
[77] " <operator id=\"YuleModelTreeScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[78] ""
[79] " <operator id=\"YuleModelTreeRootScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" rootOnly=\"true\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[80] ""
[81] " <operator id=\"YuleModelUniformOperator.t:anthus_aco_sub\" spec=\"Uniform\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"30.0\"/>"
[82] ""
[83] " <operator id=\"YuleModelSubtreeSlide.t:anthus_aco_sub\" spec=\"SubtreeSlide\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[84] ""
[85] " <operator id=\"YuleModelNarrow.t:anthus_aco_sub\" spec=\"Exchange\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[86] ""
[87] " <operator id=\"YuleModelWide.t:anthus_aco_sub\" spec=\"Exchange\" isNarrow=\"false\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[88] ""
[89] " <operator id=\"YuleModelWilsonBalding.t:anthus_aco_sub\" spec=\"WilsonBalding\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[90] ""
[91] " <logger id=\"tracelog\" fileName=\"anthus_aco_sub.log\" logEvery=\"1000\" model=\"@posterior\" sanitiseHeaders=\"true\" sort=\"smart\">"
[92] " <log idref=\"posterior\"/>"
[93] " <log idref=\"likelihood\"/>"
[94] " <log idref=\"prior\"/>"
[95] " <log idref=\"treeLikelihood.anthus_aco_sub\"/>"
[96] " <log id=\"TreeHeight.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeHeightLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[97] " <log idref=\"YuleModel.t:anthus_aco_sub\"/>"
[98] " <log idref=\"birthRate.t:anthus_aco_sub\"/>"
[99] " </logger>"
[100] ""
[101] " <logger id=\"screenlog\" logEvery=\"1000\">"
[102] " <log idref=\"posterior\"/>"
[103] " <log id=\"ESS.0\" spec=\"util.ESS\" arg=\"@posterior\"/>"
[104] " <log idref=\"likelihood\"/>"
[105] " <log idref=\"prior\"/>"
[106] " </logger>"
[107] ""
[108] " <logger id=\"treelog.t:anthus_aco_sub\" fileName=\"$(tree).trees\" logEvery=\"1000\" mode=\"tree\">"
[109] " <log id=\"TreeWithMetaDataLogger.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[110] " </logger>"
[111] ""
[112] "</run>"
[113] ""
[114] "</beast>" Thanks to Yacine Ben Chehida for this use case
create_beast2_input(
input_filename,
site_model = create_hky_site_model(
gamma_site_model = create_gamma_site_model(prop_invariant = 0.5)
)
)
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><beast beautitemplate='Standard' beautistatus='' namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" required=\"\" version=\"2.4\">"
[2] ""
[3] ""
[4] " <data"
[5] "id=\"anthus_aco_sub\""
[6] "name=\"alignment\">"
[7] " <sequence id=\"seq_61430_aco\" taxon=\"61430_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[8] " <sequence id=\"seq_626029_aco\" taxon=\"626029_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacgattgtctgttttt\"/>"
[9] " <sequence id=\"seq_630116_aco\" taxon=\"630116_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[10] " <sequence id=\"seq_630210_aco\" taxon=\"630210_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[11] " <sequence id=\"seq_B25702_aco\" taxon=\"B25702_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[12] " </data>"
[13] ""
[14] ""
[15] " "
[16] ""
[17] ""
[18] " "
[19] ""
[20] ""
[21] " "
[22] "<map name=\"Uniform\" >beast.math.distributions.Uniform</map>"
[23] "<map name=\"Exponential\" >beast.math.distributions.Exponential</map>"
[24] "<map name=\"LogNormal\" >beast.math.distributions.LogNormalDistributionModel</map>"
[25] "<map name=\"Normal\" >beast.math.distributions.Normal</map>"
[26] "<map name=\"Beta\" >beast.math.distributions.Beta</map>"
[27] "<map name=\"Gamma\" >beast.math.distributions.Gamma</map>"
[28] "<map name=\"LaplaceDistribution\" >beast.math.distributions.LaplaceDistribution</map>"
[29] "<map name=\"prior\" >beast.math.distributions.Prior</map>"
[30] "<map name=\"InverseGamma\" >beast.math.distributions.InverseGamma</map>"
[31] "<map name=\"OneOnX\" >beast.math.distributions.OneOnX</map>"
[32] ""
[33] ""
[34] "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"10000000\">"
[35] " <state id=\"state\" storeEvery=\"5000\">"
[36] " <tree id=\"Tree.t:anthus_aco_sub\" name=\"stateNode\">"
[37] " <taxonset id=\"TaxonSet.anthus_aco_sub\" spec=\"TaxonSet\">"
[38] " <alignment idref=\"anthus_aco_sub\"/>"
[39] " </taxonset>"
[40] " </tree>"
[41] " <parameter id=\"kappa.s:anthus_aco_sub\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>"
[42] " <parameter id=\"freqParameter.s:anthus_aco_sub\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>"
[43] " <parameter id=\"birthRate.t:anthus_aco_sub\" name=\"stateNode\">1.0</parameter>"
[44] " </state>"
[45] ""
[46] " <init id=\"RandomTree.t:anthus_aco_sub\" spec=\"beast.evolution.tree.RandomTree\" estimate=\"false\" initial=\"@Tree.t:anthus_aco_sub\" taxa=\"@anthus_aco_sub\">"
[47] " <populationModel id=\"ConstantPopulation0.t:anthus_aco_sub\" spec=\"ConstantPopulation\">"
[48] " <parameter id=\"randomPopSize.t:anthus_aco_sub\" name=\"popSize\">1.0</parameter>"
[49] " </populationModel>"
[50] " </init>"
[51] ""
[52] " <distribution id=\"posterior\" spec=\"util.CompoundDistribution\">"
[53] " <distribution id=\"prior\" spec=\"util.CompoundDistribution\">"
[54] " <distribution id=\"YuleModel.t:anthus_aco_sub\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[55] " <prior id=\"YuleBirthRatePrior.t:anthus_aco_sub\" name=\"distribution\" x=\"@birthRate.t:anthus_aco_sub\">"
[56] " <Uniform id=\"Uniform.100\" name=\"distr\" upper=\"Infinity\"/>"
[57] " </prior>"
[58] " <prior id=\"KappaPrior.s:anthus_aco_sub\" name=\"distribution\" x=\"@kappa.s:anthus_aco_sub\">"
[59] " <LogNormal id=\"LogNormalDistributionModel.0\" name=\"distr\">"
[60] " <parameter id=\"RealParameter.0\" estimate=\"false\" name=\"M\">1.0</parameter>"
[61] " <parameter id=\"RealParameter.1\" estimate=\"false\" name=\"S\">1.25</parameter>"
[62] " </LogNormal>"
[63] " </prior>"
[64] " </distribution>"
[65] " <distribution id=\"likelihood\" spec=\"util.CompoundDistribution\" useThreads=\"true\">"
[66] " <distribution id=\"treeLikelihood.anthus_aco_sub\" spec=\"ThreadedTreeLikelihood\" data=\"@anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\">"
[67] " <siteModel id=\"SiteModel.s:anthus_aco_sub\" spec=\"SiteModel\">"
[68] " <parameter id=\"mutationRate.s:anthus_aco_sub\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>"
[69] " <parameter id=\"gammaShape.s:anthus_aco_sub\" estimate=\"false\" name=\"shape\">1.0</parameter>"
[70] " <parameter id=\"proportionInvariant.s:anthus_aco_sub\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.5</parameter>"
[71] " <substModel id=\"hky.s:anthus_aco_sub\" spec=\"HKY\" kappa=\"@kappa.s:anthus_aco_sub\">"
[72] " <frequencies id=\"estimatedFreqs.s:anthus_aco_sub\" spec=\"Frequencies\" frequencies=\"@freqParameter.s:anthus_aco_sub\"/>"
[73] " </substModel>"
[74] " </siteModel>"
[75] " <branchRateModel id=\"StrictClock.c:anthus_aco_sub\" spec=\"beast.evolution.branchratemodel.StrictClockModel\">"
[76] " <parameter id=\"clockRate.c:anthus_aco_sub\" estimate=\"false\" name=\"clock.rate\">1.0</parameter>"
[77] " </branchRateModel>"
[78] " </distribution>"
[79] " </distribution>"
[80] " </distribution>"
[81] ""
[82] " <operator id=\"YuleBirthRateScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@birthRate.t:anthus_aco_sub\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[83] ""
[84] " <operator id=\"YuleModelTreeScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[85] ""
[86] " <operator id=\"YuleModelTreeRootScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" rootOnly=\"true\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[87] ""
[88] " <operator id=\"YuleModelUniformOperator.t:anthus_aco_sub\" spec=\"Uniform\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"30.0\"/>"
[89] ""
[90] " <operator id=\"YuleModelSubtreeSlide.t:anthus_aco_sub\" spec=\"SubtreeSlide\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[91] ""
[92] " <operator id=\"YuleModelNarrow.t:anthus_aco_sub\" spec=\"Exchange\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[93] ""
[94] " <operator id=\"YuleModelWide.t:anthus_aco_sub\" spec=\"Exchange\" isNarrow=\"false\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[95] ""
[96] " <operator id=\"YuleModelWilsonBalding.t:anthus_aco_sub\" spec=\"WilsonBalding\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[97] ""
[98] " <operator id=\"KappaScaler.s:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@kappa.s:anthus_aco_sub\" scaleFactor=\"0.5\" weight=\"0.1\"/>"
[99] ""
[100] " <operator id=\"FrequenciesExchanger.s:anthus_aco_sub\" spec=\"DeltaExchangeOperator\" delta=\"0.01\" weight=\"0.1\">"
[101] " <parameter idref=\"freqParameter.s:anthus_aco_sub\"/>"
[102] " </operator>"
[103] ""
[104] " <logger id=\"tracelog\" fileName=\"anthus_aco_sub.log\" logEvery=\"1000\" model=\"@posterior\" sanitiseHeaders=\"true\" sort=\"smart\">"
[105] " <log idref=\"posterior\"/>"
[106] " <log idref=\"likelihood\"/>"
[107] " <log idref=\"prior\"/>"
[108] " <log idref=\"treeLikelihood.anthus_aco_sub\"/>"
[109] " <log id=\"TreeHeight.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeHeightLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[110] " <log idref=\"kappa.s:anthus_aco_sub\"/>"
[111] " <log idref=\"freqParameter.s:anthus_aco_sub\"/>"
[112] " <log idref=\"YuleModel.t:anthus_aco_sub\"/>"
[113] " <log idref=\"birthRate.t:anthus_aco_sub\"/>"
[114] " </logger>"
[115] ""
[116] " <logger id=\"screenlog\" logEvery=\"1000\">"
[117] " <log idref=\"posterior\"/>"
[118] " <log id=\"ESS.0\" spec=\"util.ESS\" arg=\"@posterior\"/>"
[119] " <log idref=\"likelihood\"/>"
[120] " <log idref=\"prior\"/>"
[121] " </logger>"
[122] ""
[123] " <logger id=\"treelog.t:anthus_aco_sub\" fileName=\"$(tree).trees\" logEvery=\"1000\" mode=\"tree\">"
[124] " <log id=\"TreeWithMetaDataLogger.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[125] " </logger>"
[126] ""
[127] "</run>"
[128] ""
[129] "</beast>" Thanks to Yacine Ben Chehida for this use case
create_beast2_input(
input_filename,
clock_model = create_strict_clock_model(
clock_rate_param = 0.5
)
)
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><beast beautitemplate='Standard' beautistatus='' namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" required=\"\" version=\"2.4\">"
[2] ""
[3] ""
[4] " <data"
[5] "id=\"anthus_aco_sub\""
[6] "name=\"alignment\">"
[7] " <sequence id=\"seq_61430_aco\" taxon=\"61430_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[8] " <sequence id=\"seq_626029_aco\" taxon=\"626029_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacgattgtctgttttt\"/>"
[9] " <sequence id=\"seq_630116_aco\" taxon=\"630116_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[10] " <sequence id=\"seq_630210_aco\" taxon=\"630210_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[11] " <sequence id=\"seq_B25702_aco\" taxon=\"B25702_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[12] " </data>"
[13] ""
[14] ""
[15] " "
[16] ""
[17] ""
[18] " "
[19] ""
[20] ""
[21] " "
[22] "<map name=\"Uniform\" >beast.math.distributions.Uniform</map>"
[23] "<map name=\"Exponential\" >beast.math.distributions.Exponential</map>"
[24] "<map name=\"LogNormal\" >beast.math.distributions.LogNormalDistributionModel</map>"
[25] "<map name=\"Normal\" >beast.math.distributions.Normal</map>"
[26] "<map name=\"Beta\" >beast.math.distributions.Beta</map>"
[27] "<map name=\"Gamma\" >beast.math.distributions.Gamma</map>"
[28] "<map name=\"LaplaceDistribution\" >beast.math.distributions.LaplaceDistribution</map>"
[29] "<map name=\"prior\" >beast.math.distributions.Prior</map>"
[30] "<map name=\"InverseGamma\" >beast.math.distributions.InverseGamma</map>"
[31] "<map name=\"OneOnX\" >beast.math.distributions.OneOnX</map>"
[32] ""
[33] ""
[34] "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"10000000\">"
[35] " <state id=\"state\" storeEvery=\"5000\">"
[36] " <tree id=\"Tree.t:anthus_aco_sub\" name=\"stateNode\">"
[37] " <taxonset id=\"TaxonSet.anthus_aco_sub\" spec=\"TaxonSet\">"
[38] " <alignment idref=\"anthus_aco_sub\"/>"
[39] " </taxonset>"
[40] " </tree>"
[41] " <parameter id=\"birthRate.t:anthus_aco_sub\" name=\"stateNode\">1.0</parameter>"
[42] " </state>"
[43] ""
[44] " <init id=\"RandomTree.t:anthus_aco_sub\" spec=\"beast.evolution.tree.RandomTree\" estimate=\"false\" initial=\"@Tree.t:anthus_aco_sub\" taxa=\"@anthus_aco_sub\">"
[45] " <populationModel id=\"ConstantPopulation0.t:anthus_aco_sub\" spec=\"ConstantPopulation\">"
[46] " <parameter id=\"randomPopSize.t:anthus_aco_sub\" name=\"popSize\">1.0</parameter>"
[47] " </populationModel>"
[48] " </init>"
[49] ""
[50] " <distribution id=\"posterior\" spec=\"util.CompoundDistribution\">"
[51] " <distribution id=\"prior\" spec=\"util.CompoundDistribution\">"
[52] " <distribution id=\"YuleModel.t:anthus_aco_sub\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[53] " <prior id=\"YuleBirthRatePrior.t:anthus_aco_sub\" name=\"distribution\" x=\"@birthRate.t:anthus_aco_sub\">"
[54] " <Uniform id=\"Uniform.100\" name=\"distr\" upper=\"Infinity\"/>"
[55] " </prior>"
[56] " </distribution>"
[57] " <distribution id=\"likelihood\" spec=\"util.CompoundDistribution\" useThreads=\"true\">"
[58] " <distribution id=\"treeLikelihood.anthus_aco_sub\" spec=\"ThreadedTreeLikelihood\" data=\"@anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\">"
[59] " <siteModel id=\"SiteModel.s:anthus_aco_sub\" spec=\"SiteModel\">"
[60] " <parameter id=\"mutationRate.s:anthus_aco_sub\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>"
[61] " <parameter id=\"gammaShape.s:anthus_aco_sub\" estimate=\"false\" name=\"shape\">1.0</parameter>"
[62] " <parameter id=\"proportionInvariant.s:anthus_aco_sub\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.0</parameter>"
[63] " <substModel id=\"JC69.s:anthus_aco_sub\" spec=\"JukesCantor\"/>"
[64] " </siteModel>"
[65] " <branchRateModel id=\"StrictClock.c:anthus_aco_sub\" spec=\"beast.evolution.branchratemodel.StrictClockModel\">"
[66] " <parameter id=\"clockRate.c:anthus_aco_sub\" estimate=\"false\" name=\"clock.rate\">0.5</parameter>"
[67] " </branchRateModel>"
[68] " </distribution>"
[69] " </distribution>"
[70] " </distribution>"
[71] ""
[72] " <operator id=\"YuleBirthRateScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@birthRate.t:anthus_aco_sub\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[73] ""
[74] " <operator id=\"YuleModelTreeScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[75] ""
[76] " <operator id=\"YuleModelTreeRootScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" rootOnly=\"true\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[77] ""
[78] " <operator id=\"YuleModelUniformOperator.t:anthus_aco_sub\" spec=\"Uniform\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"30.0\"/>"
[79] ""
[80] " <operator id=\"YuleModelSubtreeSlide.t:anthus_aco_sub\" spec=\"SubtreeSlide\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[81] ""
[82] " <operator id=\"YuleModelNarrow.t:anthus_aco_sub\" spec=\"Exchange\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[83] ""
[84] " <operator id=\"YuleModelWide.t:anthus_aco_sub\" spec=\"Exchange\" isNarrow=\"false\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[85] ""
[86] " <operator id=\"YuleModelWilsonBalding.t:anthus_aco_sub\" spec=\"WilsonBalding\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[87] ""
[88] " <logger id=\"tracelog\" fileName=\"anthus_aco_sub.log\" logEvery=\"1000\" model=\"@posterior\" sanitiseHeaders=\"true\" sort=\"smart\">"
[89] " <log idref=\"posterior\"/>"
[90] " <log idref=\"likelihood\"/>"
[91] " <log idref=\"prior\"/>"
[92] " <log idref=\"treeLikelihood.anthus_aco_sub\"/>"
[93] " <log id=\"TreeHeight.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeHeightLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[94] " <log idref=\"YuleModel.t:anthus_aco_sub\"/>"
[95] " <log idref=\"birthRate.t:anthus_aco_sub\"/>"
[96] " </logger>"
[97] ""
[98] " <logger id=\"screenlog\" logEvery=\"1000\">"
[99] " <log idref=\"posterior\"/>"
[100] " <log id=\"ESS.0\" spec=\"util.ESS\" arg=\"@posterior\"/>"
[101] " <log idref=\"likelihood\"/>"
[102] " <log idref=\"prior\"/>"
[103] " </logger>"
[104] ""
[105] " <logger id=\"treelog.t:anthus_aco_sub\" fileName=\"$(tree).trees\" logEvery=\"1000\" mode=\"tree\">"
[106] " <log id=\"TreeWithMetaDataLogger.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[107] " </logger>"
[108] ""
[109] "</run>"
[110] ""
[111] "</beast>" Thanks to Paul van Els and Yacine Ben Chehida for this use case.
create_beast2_input(
input_filename,
mrca_prior = create_mrca_prior()
)
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><beast beautitemplate='Standard' beautistatus='' namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" required=\"\" version=\"2.4\">"
[2] ""
[3] ""
[4] " <data"
[5] "id=\"anthus_aco_sub\""
[6] "name=\"alignment\">"
[7] " <sequence id=\"seq_61430_aco\" taxon=\"61430_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[8] " <sequence id=\"seq_626029_aco\" taxon=\"626029_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacgattgtctgttttt\"/>"
[9] " <sequence id=\"seq_630116_aco\" taxon=\"630116_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[10] " <sequence id=\"seq_630210_aco\" taxon=\"630210_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[11] " <sequence id=\"seq_B25702_aco\" taxon=\"B25702_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[12] " </data>"
[13] ""
[14] ""
[15] " "
[16] ""
[17] ""
[18] " "
[19] ""
[20] ""
[21] " "
[22] "<map name=\"Uniform\" >beast.math.distributions.Uniform</map>"
[23] "<map name=\"Exponential\" >beast.math.distributions.Exponential</map>"
[24] "<map name=\"LogNormal\" >beast.math.distributions.LogNormalDistributionModel</map>"
[25] "<map name=\"Normal\" >beast.math.distributions.Normal</map>"
[26] "<map name=\"Beta\" >beast.math.distributions.Beta</map>"
[27] "<map name=\"Gamma\" >beast.math.distributions.Gamma</map>"
[28] "<map name=\"LaplaceDistribution\" >beast.math.distributions.LaplaceDistribution</map>"
[29] "<map name=\"prior\" >beast.math.distributions.Prior</map>"
[30] "<map name=\"InverseGamma\" >beast.math.distributions.InverseGamma</map>"
[31] "<map name=\"OneOnX\" >beast.math.distributions.OneOnX</map>"
[32] ""
[33] ""
[34] "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"10000000\">"
[35] " <state id=\"state\" storeEvery=\"5000\">"
[36] " <tree id=\"Tree.t:anthus_aco_sub\" name=\"stateNode\">"
[37] " <taxonset id=\"TaxonSet.anthus_aco_sub\" spec=\"TaxonSet\">"
[38] " <alignment idref=\"anthus_aco_sub\"/>"
[39] " </taxonset>"
[40] " </tree>"
[41] " <parameter id=\"birthRate.t:anthus_aco_sub\" name=\"stateNode\">1.0</parameter>"
[42] " </state>"
[43] ""
[44] " <init id=\"RandomTree.t:anthus_aco_sub\" spec=\"beast.evolution.tree.RandomTree\" estimate=\"false\" initial=\"@Tree.t:anthus_aco_sub\" taxa=\"@anthus_aco_sub\">"
[45] " <populationModel id=\"ConstantPopulation0.t:anthus_aco_sub\" spec=\"ConstantPopulation\">"
[46] " <parameter id=\"randomPopSize.t:anthus_aco_sub\" name=\"popSize\">1.0</parameter>"
[47] " </populationModel>"
[48] " </init>"
[49] ""
[50] " <distribution id=\"posterior\" spec=\"util.CompoundDistribution\">"
[51] " <distribution id=\"prior\" spec=\"util.CompoundDistribution\">"
[52] " <distribution id=\"YuleModel.t:anthus_aco_sub\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[53] " <prior id=\"YuleBirthRatePrior.t:anthus_aco_sub\" name=\"distribution\" x=\"@birthRate.t:anthus_aco_sub\">"
[54] " <Uniform id=\"Uniform.100\" name=\"distr\" upper=\"Infinity\"/>"
[55] " </prior>"
[56] " <distribution id=\"auto_name_1.prior\" spec=\"beast.math.distributions.MRCAPrior\" tree=\"@Tree.t:anthus_aco_sub\">"
[57] " <taxonset id=\"auto_name_1\" spec=\"TaxonSet\">"
[58] " <taxon id=\"61430_aco\" spec=\"Taxon\"/>"
[59] " <taxon id=\"626029_aco\" spec=\"Taxon\"/>"
[60] " <taxon id=\"630116_aco\" spec=\"Taxon\"/>"
[61] " <taxon id=\"630210_aco\" spec=\"Taxon\"/>"
[62] " <taxon id=\"B25702_aco\" spec=\"Taxon\"/>"
[63] " </taxonset>"
[64] " </distribution>"
[65] " </distribution>"
[66] " <distribution id=\"likelihood\" spec=\"util.CompoundDistribution\" useThreads=\"true\">"
[67] " <distribution id=\"treeLikelihood.anthus_aco_sub\" spec=\"ThreadedTreeLikelihood\" data=\"@anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\">"
[68] " <siteModel id=\"SiteModel.s:anthus_aco_sub\" spec=\"SiteModel\">"
[69] " <parameter id=\"mutationRate.s:anthus_aco_sub\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>"
[70] " <parameter id=\"gammaShape.s:anthus_aco_sub\" estimate=\"false\" name=\"shape\">1.0</parameter>"
[71] " <parameter id=\"proportionInvariant.s:anthus_aco_sub\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.0</parameter>"
[72] " <substModel id=\"JC69.s:anthus_aco_sub\" spec=\"JukesCantor\"/>"
[73] " </siteModel>"
[74] " <branchRateModel id=\"StrictClock.c:anthus_aco_sub\" spec=\"beast.evolution.branchratemodel.StrictClockModel\">"
[75] " <parameter id=\"clockRate.c:anthus_aco_sub\" estimate=\"false\" name=\"clock.rate\">1.0</parameter>"
[76] " </branchRateModel>"
[77] " </distribution>"
[78] " </distribution>"
[79] " </distribution>"
[80] ""
[81] " <operator id=\"YuleBirthRateScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@birthRate.t:anthus_aco_sub\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[82] ""
[83] " <operator id=\"YuleModelTreeScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[84] ""
[85] " <operator id=\"YuleModelTreeRootScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" rootOnly=\"true\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[86] ""
[87] " <operator id=\"YuleModelUniformOperator.t:anthus_aco_sub\" spec=\"Uniform\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"30.0\"/>"
[88] ""
[89] " <operator id=\"YuleModelSubtreeSlide.t:anthus_aco_sub\" spec=\"SubtreeSlide\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[90] ""
[91] " <operator id=\"YuleModelNarrow.t:anthus_aco_sub\" spec=\"Exchange\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[92] ""
[93] " <operator id=\"YuleModelWide.t:anthus_aco_sub\" spec=\"Exchange\" isNarrow=\"false\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[94] ""
[95] " <operator id=\"YuleModelWilsonBalding.t:anthus_aco_sub\" spec=\"WilsonBalding\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[96] ""
[97] " <logger id=\"tracelog\" fileName=\"anthus_aco_sub.log\" logEvery=\"1000\" model=\"@posterior\" sanitiseHeaders=\"true\" sort=\"smart\">"
[98] " <log idref=\"posterior\"/>"
[99] " <log idref=\"likelihood\"/>"
[100] " <log idref=\"prior\"/>"
[101] " <log idref=\"treeLikelihood.anthus_aco_sub\"/>"
[102] " <log id=\"TreeHeight.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeHeightLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[103] " <log idref=\"YuleModel.t:anthus_aco_sub\"/>"
[104] " <log idref=\"birthRate.t:anthus_aco_sub\"/>"
[105] " <log idref=\"auto_name_1.prior\"/>"
[106] " </logger>"
[107] ""
[108] " <logger id=\"screenlog\" logEvery=\"1000\">"
[109] " <log idref=\"posterior\"/>"
[110] " <log id=\"ESS.0\" spec=\"util.ESS\" arg=\"@posterior\"/>"
[111] " <log idref=\"likelihood\"/>"
[112] " <log idref=\"prior\"/>"
[113] " </logger>"
[114] ""
[115] " <logger id=\"treelog.t:anthus_aco_sub\" fileName=\"$(tree).trees\" logEvery=\"1000\" mode=\"tree\">"
[116] " <log id=\"TreeWithMetaDataLogger.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[117] " </logger>"
[118] ""
[119] "</run>"
[120] ""
[121] "</beast>" 
With an MRCA prior, it is possible to specify a close-to-fixed crown age:
crown_age <- 15
create_beast2_input(
input_filename,
mrca_prior = create_mrca_prior(
is_monophyletic = TRUE,
mrca_distr = create_normal_distr(
mean = crown_age,
sigma = 0.001
)
)
)
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><beast beautitemplate='Standard' beautistatus='' namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" required=\"\" version=\"2.4\">"
[2] ""
[3] ""
[4] " <data"
[5] "id=\"anthus_aco_sub\""
[6] "name=\"alignment\">"
[7] " <sequence id=\"seq_61430_aco\" taxon=\"61430_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[8] " <sequence id=\"seq_626029_aco\" taxon=\"626029_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctgcttgtttaatgccctctcctattttattgtgacgattgtctgttttt\"/>"
[9] " <sequence id=\"seq_630116_aco\" taxon=\"630116_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgcgaaaattgtctgttttt\"/>"
[10] " <sequence id=\"seq_630210_aco\" taxon=\"630210_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[11] " <sequence id=\"seq_B25702_aco\" taxon=\"B25702_aco\" totalcount=\"4\" value=\"acaggttagaaactactctgttttctggctccttgtttaatgccctgtcctattttattgtgacaattgtctgttttt\"/>"
[12] " </data>"
[13] ""
[14] ""
[15] " "
[16] ""
[17] ""
[18] " "
[19] ""
[20] ""
[21] " "
[22] "<map name=\"Uniform\" >beast.math.distributions.Uniform</map>"
[23] "<map name=\"Exponential\" >beast.math.distributions.Exponential</map>"
[24] "<map name=\"LogNormal\" >beast.math.distributions.LogNormalDistributionModel</map>"
[25] "<map name=\"Normal\" >beast.math.distributions.Normal</map>"
[26] "<map name=\"Beta\" >beast.math.distributions.Beta</map>"
[27] "<map name=\"Gamma\" >beast.math.distributions.Gamma</map>"
[28] "<map name=\"LaplaceDistribution\" >beast.math.distributions.LaplaceDistribution</map>"
[29] "<map name=\"prior\" >beast.math.distributions.Prior</map>"
[30] "<map name=\"InverseGamma\" >beast.math.distributions.InverseGamma</map>"
[31] "<map name=\"OneOnX\" >beast.math.distributions.OneOnX</map>"
[32] ""
[33] ""
[34] "<run id=\"mcmc\" spec=\"MCMC\" chainLength=\"10000000\">"
[35] " <state id=\"state\" storeEvery=\"5000\">"
[36] " <tree id=\"Tree.t:anthus_aco_sub\" name=\"stateNode\">"
[37] " <taxonset id=\"TaxonSet.anthus_aco_sub\" spec=\"TaxonSet\">"
[38] " <alignment idref=\"anthus_aco_sub\"/>"
[39] " </taxonset>"
[40] " </tree>"
[41] " <parameter id=\"birthRate.t:anthus_aco_sub\" name=\"stateNode\">1.0</parameter>"
[42] " <parameter id=\"clockRate.c:anthus_aco_sub\" name=\"stateNode\">1.0</parameter>"
[43] " </state>"
[44] ""
[45] " <init id=\"RandomTree.t:anthus_aco_sub\" spec=\"beast.evolution.tree.RandomTree\" estimate=\"false\" initial=\"@Tree.t:anthus_aco_sub\" taxa=\"@anthus_aco_sub\">"
[46] " <populationModel id=\"ConstantPopulation0.t:anthus_aco_sub\" spec=\"ConstantPopulation\">"
[47] " <parameter id=\"randomPopSize.t:anthus_aco_sub\" name=\"popSize\">1.0</parameter>"
[48] " </populationModel>"
[49] " </init>"
[50] ""
[51] " <distribution id=\"posterior\" spec=\"util.CompoundDistribution\">"
[52] " <distribution id=\"prior\" spec=\"util.CompoundDistribution\">"
[53] " <distribution id=\"YuleModel.t:anthus_aco_sub\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[54] " <prior id=\"YuleBirthRatePrior.t:anthus_aco_sub\" name=\"distribution\" x=\"@birthRate.t:anthus_aco_sub\">"
[55] " <Uniform id=\"Uniform.100\" name=\"distr\" upper=\"Infinity\"/>"
[56] " </prior>"
[57] " <prior id=\"ClockPrior.c:anthus_aco_sub\" name=\"distribution\" x=\"@clockRate.c:anthus_aco_sub\">"
[58] " <Uniform id=\"Uniform.150\" name=\"distr\" upper=\"Infinity\"/>"
[59] " </prior>"
[60] " <distribution id=\"auto_name_1.prior\" spec=\"beast.math.distributions.MRCAPrior\" monophyletic=\"true\" tree=\"@Tree.t:anthus_aco_sub\">"
[61] " <taxonset id=\"auto_name_1\" spec=\"TaxonSet\">"
[62] " <taxon id=\"61430_aco\" spec=\"Taxon\"/>"
[63] " <taxon id=\"626029_aco\" spec=\"Taxon\"/>"
[64] " <taxon id=\"630116_aco\" spec=\"Taxon\"/>"
[65] " <taxon id=\"630210_aco\" spec=\"Taxon\"/>"
[66] " <taxon id=\"B25702_aco\" spec=\"Taxon\"/>"
[67] " </taxonset>"
[68] " <Normal id=\"Normal.151\" name=\"distr\">"
[69] " <parameter id=\"RealParameter.300\" estimate=\"false\" name=\"mean\">15</parameter>"
[70] " <parameter id=\"RealParameter.301\" estimate=\"false\" name=\"sigma\">0.001</parameter>"
[71] " </Normal>"
[72] " </distribution>"
[73] " </distribution>"
[74] " <distribution id=\"likelihood\" spec=\"util.CompoundDistribution\" useThreads=\"true\">"
[75] " <distribution id=\"treeLikelihood.anthus_aco_sub\" spec=\"ThreadedTreeLikelihood\" data=\"@anthus_aco_sub\" tree=\"@Tree.t:anthus_aco_sub\">"
[76] " <siteModel id=\"SiteModel.s:anthus_aco_sub\" spec=\"SiteModel\">"
[77] " <parameter id=\"mutationRate.s:anthus_aco_sub\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>"
[78] " <parameter id=\"gammaShape.s:anthus_aco_sub\" estimate=\"false\" name=\"shape\">1.0</parameter>"
[79] " <parameter id=\"proportionInvariant.s:anthus_aco_sub\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.0</parameter>"
[80] " <substModel id=\"JC69.s:anthus_aco_sub\" spec=\"JukesCantor\"/>"
[81] " </siteModel>"
[82] " <branchRateModel id=\"StrictClock.c:anthus_aco_sub\" spec=\"beast.evolution.branchratemodel.StrictClockModel\" clock.rate=\"@clockRate.c:anthus_aco_sub\"/>"
[83] " </distribution>"
[84] " </distribution>"
[85] " </distribution>"
[86] ""
[87] " <operator id=\"YuleBirthRateScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@birthRate.t:anthus_aco_sub\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[88] ""
[89] " <operator id=\"YuleModelTreeScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[90] ""
[91] " <operator id=\"YuleModelTreeRootScaler.t:anthus_aco_sub\" spec=\"ScaleOperator\" rootOnly=\"true\" scaleFactor=\"0.5\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[92] ""
[93] " <operator id=\"YuleModelUniformOperator.t:anthus_aco_sub\" spec=\"Uniform\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"30.0\"/>"
[94] ""
[95] " <operator id=\"YuleModelSubtreeSlide.t:anthus_aco_sub\" spec=\"SubtreeSlide\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[96] ""
[97] " <operator id=\"YuleModelNarrow.t:anthus_aco_sub\" spec=\"Exchange\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"15.0\"/>"
[98] ""
[99] " <operator id=\"YuleModelWide.t:anthus_aco_sub\" spec=\"Exchange\" isNarrow=\"false\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[100] ""
[101] " <operator id=\"YuleModelWilsonBalding.t:anthus_aco_sub\" spec=\"WilsonBalding\" tree=\"@Tree.t:anthus_aco_sub\" weight=\"3.0\"/>"
[102] ""
[103] " <operator id=\"StrictClockRateScaler.c:anthus_aco_sub\" spec=\"ScaleOperator\" parameter=\"@clockRate.c:anthus_aco_sub\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[104] ""
[105] " <operator id=\"strictClockUpDownOperator.c:anthus_aco_sub\" spec=\"UpDownOperator\" scaleFactor=\"0.75\" weight=\"3.0\">"
[106] " <up idref=\"clockRate.c:anthus_aco_sub\"/>"
[107] " <down idref=\"Tree.t:anthus_aco_sub\"/>"
[108] " </operator>"
[109] ""
[110] " <logger id=\"tracelog\" fileName=\"anthus_aco_sub.log\" logEvery=\"1000\" model=\"@posterior\" sanitiseHeaders=\"true\" sort=\"smart\">"
[111] " <log idref=\"posterior\"/>"
[112] " <log idref=\"likelihood\"/>"
[113] " <log idref=\"prior\"/>"
[114] " <log idref=\"treeLikelihood.anthus_aco_sub\"/>"
[115] " <log id=\"TreeHeight.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeHeightLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[116] " <log idref=\"YuleModel.t:anthus_aco_sub\"/>"
[117] " <log idref=\"birthRate.t:anthus_aco_sub\"/>"
[118] " <log idref=\"auto_name_1.prior\"/>"
[119] " <log idref=\"clockRate.c:anthus_aco_sub\"/>"
[120] " </logger>"
[121] ""
[122] " <logger id=\"screenlog\" logEvery=\"1000\">"
[123] " <log idref=\"posterior\"/>"
[124] " <log id=\"ESS.0\" spec=\"util.ESS\" arg=\"@posterior\"/>"
[125] " <log idref=\"likelihood\"/>"
[126] " <log idref=\"prior\"/>"
[127] " </logger>"
[128] ""
[129] " <logger id=\"treelog.t:anthus_aco_sub\" fileName=\"$(tree).trees\" logEvery=\"1000\" mode=\"tree\">"
[130] " <log id=\"TreeWithMetaDataLogger.t:anthus_aco_sub\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:anthus_aco_sub\"/>"
[131] " </logger>"
[132] ""
[133] "</run>"
[134] ""
[135] "</beast>" These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.