bella-companion 0.0.29__py3-none-any.whl → 0.0.32__py3-none-any.whl
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- bella_companion/eucovid/run_beast.py +5 -11
- bella_companion/platyrrhine/run_beast.py +1 -6
- bella_companion-0.0.32.dist-info/METADATA +11 -0
- bella_companion-0.0.32.dist-info/RECORD +41 -0
- {bella_companion-0.0.29.dist-info → bella_companion-0.0.32.dist-info}/WHEEL +2 -1
- bella_companion-0.0.32.dist-info/entry_points.txt +2 -0
- bella_companion-0.0.32.dist-info/top_level.txt +1 -0
- bella_companion/eucovid/beast_configs/GLM.xml +0 -169
- bella_companion/eucovid/beast_configs/MLP.xml +0 -170
- bella_companion/eucovid/beast_configs/Nonparametric.xml +0 -399
- bella_companion/eucovid/data/case_data.tsv +0 -346
- bella_companion/eucovid/data/change_dates.tsv +0 -8
- bella_companion/eucovid/data/msa.fasta +0 -79500
- bella_companion/eucovid/data/osi.tsv +0 -376
- bella_companion/eucovid/data/predictors/all/closedborders_7e_nt.tsv +0 -35
- bella_companion/eucovid/data/predictors/all/dist_7e_ls.tsv +0 -35
- bella_companion/eucovid/data/predictors/all/flight_7e_ls.tsv +0 -35
- bella_companion/eucovid/data/predictors/all/flight_pop_x_7e_ls.tsv +0 -35
- bella_companion/eucovid/data/predictors/all/osi_x_7e_ls.tsv +0 -35
- bella_companion/eucovid/data/predictors/all/osi_y_7e_ls.tsv +0 -35
- bella_companion/eucovid/data/predictors/all/pop_x_7e_ls.tsv +0 -35
- bella_companion/eucovid/data/predictors/all/pop_y_7e_ls.tsv +0 -35
- bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv +0 -35
- bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv +0 -6
- bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv +0 -3
- bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv +0 -20
- bella_companion/platyrrhine/beast_config.xml +0 -117
- bella_companion/platyrrhine/data/change_times.csv +0 -12
- bella_companion/platyrrhine/data/traits.csv +0 -122
- bella_companion/platyrrhine/data/trees.nwk +0 -100
- bella_companion/simulations/beast_configs/epi-multitype/GLM.xml +0 -81
- bella_companion/simulations/beast_configs/epi-multitype/MLP.xml +0 -81
- bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml +0 -65
- bella_companion/simulations/beast_configs/epi-skyline/GLM.xml +0 -71
- bella_companion/simulations/beast_configs/epi-skyline/MLP.xml +0 -73
- bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml +0 -57
- bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml +0 -101
- bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml +0 -98
- bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml +0 -70
- bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml +0 -88
- bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml +0 -86
- bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml +0 -62
- bella_companion-0.0.29.dist-info/METADATA +0 -16
- bella_companion-0.0.29.dist-info/RECORD +0 -75
- bella_companion-0.0.29.dist-info/entry_points.txt +0 -3
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Metadata-Version: 2.4
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Name: bella-companion
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Version: 0.0.32
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Summary: Add your description here
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Requires-Python: >=3.10
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Description-Content-Type: text/markdown
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Requires-Dist: arviz>=0.22.0
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Requires-Dist: bella-lumiere>=0.0.14
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bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
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bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
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bella_companion/eucovid/run_beast.py,sha256=etaD_4SVdy_Pmz5s4jvDLzp2K_QV8leEY8Pe3xySBsk,3443
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bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
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bella_companion/platyrrhine/results.py,sha256=qosxqstTy7uadHARRt1WqmxZzxnQ3hiTjtw6V-YWKGA,2556
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bella_companion/platyrrhine/run_beast.py,sha256=_9Ex2B65zu6I68uY6s3_dohPYPaFP3E7u-uyWuDLAJc,2477
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bella_companion/platyrrhine/summarize_logs.py,sha256=82N7rcmLthCyQqmP4Yub4KUsIjNzQl9vEuFLMvIv03o,951
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bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZqAtPZJCMVE,454
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bella_companion/simulations/features.py,sha256=DZOBpJGlQ0UinqUZYbEtoemZ2eQGVLV_i-DfpW31qJI,104
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bella_companion/simulations/generate_data.py,sha256=edfhXrs76hl30i_xizup4z6qgzXZyaDzX_PVC62Ytpw,849
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bella_companion/simulations/generate_figures.py,sha256=layMgoj3Bfl78Ceb1oE7YirAQ8zhjDyD9IrxDRXf6go,657
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bella_companion/simulations/metrics.py,sha256=duIkPb8cCXmIzjKA2yk9HLf4Y9eFIB_hRWaH05uIDws,1876
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bella_companion/simulations/run_beast.py,sha256=qniy326i-vDCeHzzHpQRrSnY2ULqNNrO0z3GEsWx4Mc,3208
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bella_companion/simulations/summarize_logs.py,sha256=Shf3Dx9k4lTbmO__MSLw-aIA8a8kTCXhbctBcV6Izug,1216
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bella_companion/simulations/figures/__init__.py,sha256=aBYbJntH4egFmkSSWiVMYDEApXPYxJD7eA3TCPNNegM,658
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bella_companion/simulations/figures/epi_multitype_results.py,sha256=j85WgvN5AyAtX-CalMegr2lwlAZBmzyJxkikBPXRjCc,2629
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bella_companion/simulations/figures/epi_skyline_results.py,sha256=gI5Ha-OIEShcZLmqVuy0W8hJzkrsydQE-Coa65_BFCo,1667
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bella_companion/simulations/figures/fbd_2traits_results.py,sha256=JiXrbYkH1HwdJQhTHXj6KhMEXYgQmQ6LmDboAIO1CPA,2728
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bella_companion/simulations/figures/fbd_no_traits_results.py,sha256=fLsgpV3IbLLtxQEFNOL9K4jEEJrG324ziUM0rxIv7_k,1962
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bella_companion/simulations/figures/scenarios.py,sha256=gbMz1TUxxT2RSIq2kQlFioNdgSHk-gQY2OQuf6-7Fww,2817
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bella_companion/simulations/figures/utils.py,sha256=0M5OrxaEuqcj9rR2uAc_O7utQvhEceZGH0sKrGRWaWs,3129
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bella_companion-0.0.32.dist-info/top_level.txt,sha256=q0loZYv4vf3zF_tOATyAJqeyLOEuPyLbObNqIGP7Fmc,16
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<TypeMappedTree id="typeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@tree"/>
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<stateNode id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
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<samplingProportion id="samplingProportionSP" spec="SkylineVectorParameter" skylineValues="@samplingProportion" changeTimes="0.123 0.205" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
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<startTypePriorProbs id="startTypePriorProbs" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
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<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
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<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
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<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
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<prior id="KappaPrior" name="distribution" x="@kappa">
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<LogNormal name="distr" M="1.0" S="1.25"/>
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</distribution>
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</distribution>
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<operator spec="BactrianScaleOperator" tree="@tree" rootOnly="true" scaleFactor="0.25" weight="5.0"/>
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<operator spec="BactrianNodeOperator" tree="@tree" weight="30.0"/>
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<operator spec="BactrianSubtreeSlide" tree="@tree" weight="15.0"/>
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<operator spec="Exchange" tree="@tree" weight="15.0"/>
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<operator spec="Exchange" tree="@tree" isNarrow="false" weight="3.0"/>
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<operator spec="WilsonBalding" tree="@tree" weight="3.0"/>
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<operator spec="EpochFlexOperator" tree="@tree" scaleFactor="0.1" weight="2.0"/>
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<operator spec="EpochFlexOperator" tree="@tree" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
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<operator spec="TreeStretchOperator" tree="@tree" scaleFactor="0.01" weight="2.0"/>
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<operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
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<operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
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<operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
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<operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW" weight="5.0" scaleFactor="0.1"/>
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<operator spec="AdaptableVarianceMultivariateNormalOperator" weight="5.0" coefficient="1.0" scaleFactor="0.5" beta="0.05" initial="800" burnin="400" every="1">
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<transformations spec="Transform$NoTransform" f="@migrationRateW"/>
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</operator>
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<operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
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<operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
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<logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
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<log idref="posterior"/>
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<log idref="likelihood"/>
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<log idref="prior"/>
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<log idref="BDMMPrime"/>
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<log idref="gammaShape"/>
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<log idref="kappa"/>
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<log idref="processLength"/>
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<log idref="ReSP"/>
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<log idref="samplingProportionSP"/>
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<log idref="migrationRateSP"/>
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<log idref="migrationRateW"/>
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<log idref="migrationRateScaler"/>
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</logger>
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<logger spec="Logger" fileName="typedTrees.trees" logEvery="10000" mode="tree">
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<log idref="typeMappedTree"/>
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</logger>
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<logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="10000" mode="tree">
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<log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
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</logger>
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<logger spec="Logger" fileName="trajectories.csv" logEvery="10000">
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<log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
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</logger>
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</run>
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</beast>
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@@ -1,170 +0,0 @@
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<?xml version="1.0"?>
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<beast
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namespace="
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:beast.base.evolution
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:beast.base.evolution.alignment
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:beast.base.evolution.branchratemodel
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:beast.base.evolution.likelihood
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:beast.base.evolution.operator
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:beast.base.evolution.operator.kernel
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:beast.base.evolution.sitemodel
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:beast.base.evolution.substitutionmodel
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:beast.base.evolution.tree
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:beast.base.evolution.tree.coalescent
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:beast.base.inference
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:beast.base.inference.parameter
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:beast.base.inference.operator.kernel
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:bdmmprime.distribution
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:bdmmprime.mapping
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:bdmmprime.trajectories
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:bdmmprime.parameterization
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:bdmmprime.util
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:bdmmprime.util.operators
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:bdmmprime.util.priors
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:feast.fileio"
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|
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version="2.7"
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|
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>
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<map name="Uniform">beast.base.inference.distribution.Uniform</map>
|
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|
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<map name="Exponential">beast.base.inference.distribution.Exponential</map>
|
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|
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<map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
|
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<map name="Normal">beast.base.inference.distribution.Normal</map>
|
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<map name="prior">beast.base.inference.distribution.Prior</map>
|
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|
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<map name="AlignmentFromFasta">feast.fileio.AlignmentFromFasta</map>
|
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<map name="TaxonSet">beast.base.evolution.alignment.TaxonSet</map>
|
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<map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
|
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<map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
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<map name="TypeMappedTree">bdmmprime.mapping.TypeMappedTree</map>
|
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<AlignmentFromFasta id="alignment" fileName="$(msa_file)"/>
|
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|
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<TaxonSet id="taxonSet" alignment="@alignment"/>
|
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|
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<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
|
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|
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<TypeSet id="typeSet" typeTraitSet="@typeTraitSet"/>
|
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|
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<TraitSetFromTaxonSet id="dateTrait" traitname="date" dateFormat="yyyy-M-dd" delimiter="|" everythingAfterLast="true" taxa="@taxonSet"/>
|
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|
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<TypeMappedTree id="typeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@tree"/>
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|
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<run spec="MCMC" chainLength="10000000">
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<state id="state" spec="State">
|
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47
|
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<stateNode id="tree" spec="RandomTree" taxa="@alignment" trait="@dateTrait">
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|
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<populationModel spec="ConstantPopulation" popSize="0.1"/>
|
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|
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</stateNode>
|
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50
|
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<stateNode id="Re" spec="RealParameter" value="1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4"/>
|
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|
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<stateNode id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
|
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52
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<plate var="n" range="$(layersRange)">
|
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53
|
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<stateNode spec="RealParameter" id="migrationRateW$(n)" value="0"/>
|
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54
|
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</plate>
|
|
55
|
-
<stateNode id="processLength" spec="RealParameter" value="10.0"/>
|
|
56
|
-
<stateNode id="gammaShape" spec="RealParameter" value="1.0"/>
|
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57
|
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<stateNode id="kappa" spec="RealParameter" value="2.0"/>
|
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</state>
|
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59
|
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|
|
60
|
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<distribution id="posterior" spec="CompoundDistribution">
|
|
61
|
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<distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
|
|
62
|
-
<distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@alignment" tree="@tree">
|
|
63
|
-
<siteModel spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape" mutationRate="1.0">
|
|
64
|
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<substModel spec="HKY" kappa="@kappa">
|
|
65
|
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<frequencies spec="Frequencies" data="@alignment"/>
|
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|
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</substModel>
|
|
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|
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</siteModel>
|
|
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|
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<branchRateModel spec="StrictClockModel" clock.rate="8.0E-4"/>
|
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|
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</distribution>
|
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|
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</distribution>
|
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|
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|
|
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|
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<distribution id="prior" spec="CompoundDistribution">
|
|
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|
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<distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution" tree="@tree" conditionOnSurvival="true" typeTraitSet="@typeTraitSet">
|
|
74
|
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<parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization" processLength="@processLength" typeSet="@typeSet">
|
|
75
|
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<Re id="ReSP" spec="SkylineVectorParameter" skylineValues="@Re" changeTimes="0.123" timesAreAges="true" processLength="@processLength" typeSet="@typeSet" />
|
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<samplingProportion id="samplingProportionSP" spec="SkylineVectorParameter" skylineValues="@samplingProportion" changeTimes="0.123 0.205" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
|
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|
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<becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="36.5" typeSet="@typeSet"/>
|
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|
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<migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
|
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|
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<skylineValues id="migrationRate" spec="bella.BayesMLP" nodes="$(nodes)">
|
|
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|
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<plate var="predictorFile" range="$(predictorFiles)">
|
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|
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<predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
|
|
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|
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</plate>
|
|
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|
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<plate var="n" range="$(layersRange)">
|
|
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|
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<weights idref="migrationRateW$(n)"/>
|
|
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|
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</plate>
|
|
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|
-
</skylineValues>
|
|
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|
-
<changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
|
|
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|
-
</migrationRate>
|
|
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|
-
<removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
|
|
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|
-
</parameterization>
|
|
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|
-
<startTypePriorProbs id="startTypePriorProbs" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
|
|
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|
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</distribution>
|
|
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|
-
|
|
94
|
-
<prior name="distribution" x="@processLength">
|
|
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|
-
<LogNormal name="distr" M="-1.0" S="0.2"/>
|
|
96
|
-
</prior>
|
|
97
|
-
<distribution spec="SmartZeroExcludingPrior" x="@Re">
|
|
98
|
-
<LogNormal name="distr" M="0.8" S="0.5"/>
|
|
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|
-
</distribution>
|
|
100
|
-
<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
|
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|
-
<Uniform name="distr" lower="0" upper="0.15"/>
|
|
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|
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</distribution>
|
|
103
|
-
<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
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|
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|
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<Uniform name="distr" lower="0" upper="0.093"/>
|
|
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|
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</distribution>
|
|
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|
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<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
|
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|
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<Uniform name="distr" lower="0" upper="0.10"/>
|
|
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|
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</distribution>
|
|
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|
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<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
|
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|
-
<Uniform name="distr" lower="0" upper="0.005"/>
|
|
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|
-
</distribution>
|
|
112
|
-
<distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
|
|
113
|
-
<Uniform name="distr" lower="0" upper="0.057"/>
|
|
114
|
-
</distribution>
|
|
115
|
-
<plate var="n" range="$(layersRange)">
|
|
116
|
-
<prior name="distribution" x="@migrationRateW$(n)">
|
|
117
|
-
<Normal name="distr" mean="0.0" sigma="1.0"/>
|
|
118
|
-
</prior>
|
|
119
|
-
</plate>
|
|
120
|
-
<prior name="distribution" x="@gammaShape">
|
|
121
|
-
<Exponential name="distr" mean="0.5"/>
|
|
122
|
-
</prior>
|
|
123
|
-
<prior id="KappaPrior" name="distribution" x="@kappa">
|
|
124
|
-
<LogNormal name="distr" M="1.0" S="1.25"/>
|
|
125
|
-
</prior>
|
|
126
|
-
</distribution>
|
|
127
|
-
</distribution>
|
|
128
|
-
|
|
129
|
-
<operator spec="BactrianScaleOperator" tree="@tree" rootOnly="true" scaleFactor="0.25" weight="5.0"/>
|
|
130
|
-
<operator spec="BactrianNodeOperator" tree="@tree" weight="30.0"/>
|
|
131
|
-
<operator spec="BactrianSubtreeSlide" tree="@tree" weight="15.0"/>
|
|
132
|
-
<operator spec="Exchange" tree="@tree" weight="15.0"/>
|
|
133
|
-
<operator spec="Exchange" tree="@tree" isNarrow="false" weight="3.0"/>
|
|
134
|
-
<operator spec="WilsonBalding" tree="@tree" weight="3.0"/>
|
|
135
|
-
<operator spec="EpochFlexOperator" tree="@tree" scaleFactor="0.1" weight="2.0"/>
|
|
136
|
-
<operator spec="EpochFlexOperator" tree="@tree" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
|
|
137
|
-
<operator spec="TreeStretchOperator" tree="@tree" scaleFactor="0.01" weight="2.0"/>
|
|
138
|
-
<operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
|
|
139
|
-
<operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
|
|
140
|
-
<operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
|
|
141
|
-
<plate var="n" range="$(layersRange)">
|
|
142
|
-
<operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW$(n)" weight="5.0"/>
|
|
143
|
-
</plate>
|
|
144
|
-
<operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
|
|
145
|
-
<operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
|
|
146
|
-
|
|
147
|
-
<logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
|
|
148
|
-
<log idref="posterior"/>
|
|
149
|
-
<log idref="likelihood"/>
|
|
150
|
-
<log idref="prior"/>
|
|
151
|
-
<log idref="BDMMPrime"/>
|
|
152
|
-
<log idref="gammaShape"/>
|
|
153
|
-
<log idref="kappa"/>
|
|
154
|
-
<log idref="processLength"/>
|
|
155
|
-
<log idref="ReSP"/>
|
|
156
|
-
<log idref="samplingProportionSP"/>
|
|
157
|
-
<log idref="migrationRateSP"/>
|
|
158
|
-
<log idref="migrationRate"/>
|
|
159
|
-
</logger>
|
|
160
|
-
<logger spec="Logger" fileName="typedTrees.trees" logEvery="100000" mode="tree">
|
|
161
|
-
<log idref="typeMappedTree"/>
|
|
162
|
-
</logger>
|
|
163
|
-
<logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="100000" mode="tree">
|
|
164
|
-
<log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
|
|
165
|
-
</logger>
|
|
166
|
-
<logger spec="Logger" fileName="trajectories.csv" logEvery="100000">
|
|
167
|
-
<log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
|
|
168
|
-
</logger>
|
|
169
|
-
</run>
|
|
170
|
-
</beast>
|