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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.
First, beautier is loaded:
A BEAST2 XML input file needs an alignment (as BEAST2 infers
phylogenies and parameters on DNA sequences). This demonstration uses a
testing FASTA file used by beautier:
We can display the alignment in the file:
Specify the filename for our XML file, here I use a temporary filename, so there is no need to clean up afterwards:
output_filename <- get_beautier_tempfilename()
output_filename
[1] "~/.cache/beautier/file48fb11ae48a1"Now we can create our XML file. We do not specify any inference model, and just use the BEAUti default settings:
The file indeed is a BEAST2 input file:
readLines(output_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=\"test_output_0\""
[6] "name=\"alignment\">"
[7] " <sequence id=\"seq_t1\" taxon=\"t1\" totalcount=\"4\" value=\"acttgttgcgactgcgcctg\"/>"
[8] " <sequence id=\"seq_t2\" taxon=\"t2\" totalcount=\"4\" value=\"acttattgcgactgaggccg\"/>"
[9] " <sequence id=\"seq_t3\" taxon=\"t3\" totalcount=\"4\" value=\"acttaatgcgaatgagcccg\"/>"
[10] " <sequence id=\"seq_t4\" taxon=\"t4\" totalcount=\"4\" value=\"aacgacccgcgatcggggat\"/>"
[11] " <sequence id=\"seq_t5\" taxon=\"t5\" totalcount=\"4\" value=\"acttgttgcgactgagcctg\"/>"
[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:test_output_0\" name=\"stateNode\">"
[37] " <taxonset id=\"TaxonSet.test_output_0\" spec=\"TaxonSet\">"
[38] " <alignment idref=\"test_output_0\"/>"
[39] " </taxonset>"
[40] " </tree>"
[41] " <parameter id=\"birthRate.t:test_output_0\" name=\"stateNode\">1.0</parameter>"
[42] " </state>"
[43] ""
[44] " <init id=\"RandomTree.t:test_output_0\" spec=\"beast.evolution.tree.RandomTree\" estimate=\"false\" initial=\"@Tree.t:test_output_0\" taxa=\"@test_output_0\">"
[45] " <populationModel id=\"ConstantPopulation0.t:test_output_0\" spec=\"ConstantPopulation\">"
[46] " <parameter id=\"randomPopSize.t:test_output_0\" 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:test_output_0\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:test_output_0\" tree=\"@Tree.t:test_output_0\"/>"
[53] " <prior id=\"YuleBirthRatePrior.t:test_output_0\" name=\"distribution\" x=\"@birthRate.t:test_output_0\">"
[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.test_output_0\" spec=\"ThreadedTreeLikelihood\" data=\"@test_output_0\" tree=\"@Tree.t:test_output_0\">"
[59] " <siteModel id=\"SiteModel.s:test_output_0\" spec=\"SiteModel\">"
[60] " <parameter id=\"mutationRate.s:test_output_0\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>"
[61] " <parameter id=\"gammaShape.s:test_output_0\" estimate=\"false\" name=\"shape\">1.0</parameter>"
[62] " <parameter id=\"proportionInvariant.s:test_output_0\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.0</parameter>"
[63] " <substModel id=\"JC69.s:test_output_0\" spec=\"JukesCantor\"/>"
[64] " </siteModel>"
[65] " <branchRateModel id=\"StrictClock.c:test_output_0\" spec=\"beast.evolution.branchratemodel.StrictClockModel\">"
[66] " <parameter id=\"clockRate.c:test_output_0\" estimate=\"false\" name=\"clock.rate\">1.0</parameter>"
[67] " </branchRateModel>"
[68] " </distribution>"
[69] " </distribution>"
[70] " </distribution>"
[71] ""
[72] " <operator id=\"YuleBirthRateScaler.t:test_output_0\" spec=\"ScaleOperator\" parameter=\"@birthRate.t:test_output_0\" scaleFactor=\"0.75\" weight=\"3.0\"/>"
[73] ""
[74] " <operator id=\"YuleModelTreeScaler.t:test_output_0\" spec=\"ScaleOperator\" scaleFactor=\"0.5\" tree=\"@Tree.t:test_output_0\" weight=\"3.0\"/>"
[75] ""
[76] " <operator id=\"YuleModelTreeRootScaler.t:test_output_0\" spec=\"ScaleOperator\" rootOnly=\"true\" scaleFactor=\"0.5\" tree=\"@Tree.t:test_output_0\" weight=\"3.0\"/>"
[77] ""
[78] " <operator id=\"YuleModelUniformOperator.t:test_output_0\" spec=\"Uniform\" tree=\"@Tree.t:test_output_0\" weight=\"30.0\"/>"
[79] ""
[80] " <operator id=\"YuleModelSubtreeSlide.t:test_output_0\" spec=\"SubtreeSlide\" tree=\"@Tree.t:test_output_0\" weight=\"15.0\"/>"
[81] ""
[82] " <operator id=\"YuleModelNarrow.t:test_output_0\" spec=\"Exchange\" tree=\"@Tree.t:test_output_0\" weight=\"15.0\"/>"
[83] ""
[84] " <operator id=\"YuleModelWide.t:test_output_0\" spec=\"Exchange\" isNarrow=\"false\" tree=\"@Tree.t:test_output_0\" weight=\"3.0\"/>"
[85] ""
[86] " <operator id=\"YuleModelWilsonBalding.t:test_output_0\" spec=\"WilsonBalding\" tree=\"@Tree.t:test_output_0\" weight=\"3.0\"/>"
[87] ""
[88] " <logger id=\"tracelog\" fileName=\"test_output_0.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.test_output_0\"/>"
[93] " <log id=\"TreeHeight.t:test_output_0\" spec=\"beast.evolution.tree.TreeHeightLogger\" tree=\"@Tree.t:test_output_0\"/>"
[94] " <log idref=\"YuleModel.t:test_output_0\"/>"
[95] " <log idref=\"birthRate.t:test_output_0\"/>"
[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:test_output_0\" fileName=\"$(tree).trees\" logEvery=\"1000\" mode=\"tree\">"
[106] " <log id=\"TreeWithMetaDataLogger.t:test_output_0\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:test_output_0\"/>"
[107] " </logger>"
[108] ""
[109] "</run>"
[110] ""
[111] "</beast>" This XML input file can be read by BEAST2.
You can use beastier to run BEAST2 from R, see https://github.com/ropensci/beastier.
You can use babette to do a BEAST2 inference directly, see
https://github.com/ropensci/babette.
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.