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| { | ||
| "python.testing.pytestArgs": [ | ||
| "tests" | ||
| ], | ||
| "python.testing.unittestEnabled": false, | ||
| "python.testing.pytestEnabled": true | ||
| } |
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Learn more about bidirectional Unicode characters
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|---|---|---|
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| { | ||
| "mcmc.spec": "MCMC", | ||
| "mcmc.chainLength": "3000000", | ||
| "state.spec": "State", | ||
| "state.storeEvery": "5000", | ||
| "Tree.t:hcv.spec": "beast.evolution.tree.Tree", | ||
| "Tree.t:hcv.name": "stateNode", | ||
| "TaxonSet.hcv.spec": "TaxonSet", | ||
| "gammaShape.s:hcv.spec": "parameter.RealParameter", | ||
| "gammaShape.s:hcv.name": "stateNode", | ||
| "gammaShape.s:hcv": "1.0", | ||
| "freqParameter.s:hcv.spec": "parameter.RealParameter", | ||
| "freqParameter.s:hcv.dimension": "4", | ||
| "freqParameter.s:hcv.lower": "0.0", | ||
| "freqParameter.s:hcv.name": "stateNode", | ||
| "freqParameter.s:hcv.upper": "1.0", | ||
| "freqParameter.s:hcv": "0.25", | ||
| "rateAC.s:hcv.spec": "parameter.RealParameter", | ||
| "rateAC.s:hcv.lower": "0.0", | ||
| "rateAC.s:hcv.name": "stateNode", | ||
| "rateAC.s:hcv": "1.0", | ||
| "rateAG.s:hcv.spec": "parameter.RealParameter", | ||
| "rateAG.s:hcv.lower": "0.0", | ||
| "rateAG.s:hcv.name": "stateNode", | ||
| "rateAG.s:hcv": "1.0", | ||
| "rateAT.s:hcv.spec": "parameter.RealParameter", | ||
| "rateAT.s:hcv.lower": "0.0", | ||
| "rateAT.s:hcv.name": "stateNode", | ||
| "rateAT.s:hcv": "1.0", | ||
| "rateCG.s:hcv.spec": "parameter.RealParameter", | ||
| "rateCG.s:hcv.lower": "0.0", | ||
| "rateCG.s:hcv.name": "stateNode", | ||
| "rateCG.s:hcv": "1.0", | ||
| "rateGT.s:hcv.spec": "parameter.RealParameter", | ||
| "rateGT.s:hcv.lower": "0.0", | ||
| "rateGT.s:hcv.name": "stateNode", | ||
| "rateGT.s:hcv": "1.0", | ||
| "bPopSizes.t:hcv.spec": "parameter.RealParameter", | ||
| "bPopSizes.t:hcv.dimension": "4", | ||
| "bPopSizes.t:hcv.lower": "0.0", | ||
| "bPopSizes.t:hcv.name": "stateNode", | ||
| "bPopSizes.t:hcv": "380.0", | ||
| "bGroupSizes.t:hcv.spec": "parameter.IntegerParameter", | ||
| "bGroupSizes.t:hcv.dimension": "4", | ||
| "RandomTree.t:hcv.spec": "beast.evolution.tree.RandomTree", | ||
| "RandomTree.t:hcv.estimate": "false", | ||
| "RandomTree.t:hcv.initial": "@Tree.t:hcv", | ||
| "RandomTree.t:hcv.taxa": "@hcv", | ||
| "ConstantPopulation0.t:hcv.spec": "ConstantPopulation", | ||
| "randomPopSize.t:hcv.spec": "parameter.RealParameter", | ||
| "randomPopSize.t:hcv.name": "popSize", | ||
| "randomPopSize.t:hcv": "1.0", | ||
| "posterior.spec": "util.CompoundDistribution", | ||
| "prior.spec": "util.CompoundDistribution", | ||
| "BayesianSkyline.t:hcv.spec": "BayesianSkyline", | ||
| "BayesianSkyline.t:hcv.groupSizes": "@bGroupSizes.t:hcv", | ||
| "BayesianSkyline.t:hcv.popSizes": "@bPopSizes.t:hcv", | ||
| "BSPTreeIntervals.t:hcv.spec": "TreeIntervals", | ||
| "BSPTreeIntervals.t:hcv.tree": "@Tree.t:hcv", | ||
| "MarkovChainedPopSizes.t:hcv.spec": "beast.math.distributions.MarkovChainDistribution", | ||
| "MarkovChainedPopSizes.t:hcv.jeffreys": "true", | ||
| "MarkovChainedPopSizes.t:hcv.parameter": "@bPopSizes.t:hcv", | ||
| "FrequenciesPrior.s:hcv.name": "distribution", | ||
| "FrequenciesPrior.s:hcv.x": "@freqParameter.s:hcv", | ||
| "Uniform.3.name": "distr", | ||
| "GammaShapePrior.s:hcv.name": "distribution", | ||
| "GammaShapePrior.s:hcv.x": "@gammaShape.s:hcv", | ||
| "Exponential.0.name": "distr", | ||
| "RealParameter.0.spec": "parameter.RealParameter", | ||
| "RealParameter.0.estimate": "false", | ||
| "RealParameter.0.name": "mean", | ||
| "RealParameter.0": "1.0", | ||
| "RateACPrior.s:hcv.name": "distribution", | ||
| "RateACPrior.s:hcv.x": "@rateAC.s:hcv", | ||
| "Gamma.0.name": "distr", | ||
| "RealParameter.1.spec": "parameter.RealParameter", | ||
| "RealParameter.1.estimate": "false", | ||
| "RealParameter.1.name": "alpha", | ||
| "RealParameter.1": "0.05", | ||
| "RealParameter.2.spec": "parameter.RealParameter", | ||
| "RealParameter.2.estimate": "false", | ||
| "RealParameter.2.name": "beta", | ||
| "RealParameter.2": "10.0", | ||
| "RateAGPrior.s:hcv.name": "distribution", | ||
| "RateAGPrior.s:hcv.x": "@rateAG.s:hcv", | ||
| "Gamma.1.name": "distr", | ||
| "RealParameter.3.spec": "parameter.RealParameter", | ||
| "RealParameter.3.estimate": "false", | ||
| "RealParameter.3.name": "alpha", | ||
| "RealParameter.3": "0.05", | ||
| "RealParameter.4.spec": "parameter.RealParameter", | ||
| "RealParameter.4.estimate": "false", | ||
| "RealParameter.4.name": "beta", | ||
| "RealParameter.4": "20.0", | ||
| "RateATPrior.s:hcv.name": "distribution", | ||
| "RateATPrior.s:hcv.x": "@rateAT.s:hcv", | ||
| "Gamma.2.name": "distr", | ||
| "RealParameter.5.spec": "parameter.RealParameter", | ||
| "RealParameter.5.estimate": "false", | ||
| "RealParameter.5.name": "alpha", | ||
| "RealParameter.5": "0.05", | ||
| "RealParameter.6.spec": "parameter.RealParameter", | ||
| "RealParameter.6.estimate": "false", | ||
| "RealParameter.6.name": "beta", | ||
| "RealParameter.6": "10.0", | ||
| "RateCGPrior.s:hcv.name": "distribution", | ||
| "RateCGPrior.s:hcv.x": "@rateCG.s:hcv", | ||
| "Gamma.3.name": "distr", | ||
| "RealParameter.7.spec": "parameter.RealParameter", | ||
| "RealParameter.7.estimate": "false", | ||
| "RealParameter.7.name": "alpha", | ||
| "RealParameter.7": "0.05", | ||
| "RealParameter.8.spec": "parameter.RealParameter", | ||
| "RealParameter.8.estimate": "false", | ||
| "RealParameter.8.name": "beta", | ||
| "RealParameter.8": "10.0", | ||
| "RateGTPrior.s:hcv.name": "distribution", | ||
| "RateGTPrior.s:hcv.x": "@rateGT.s:hcv", | ||
| "Gamma.5.name": "distr", | ||
| "RealParameter.11.spec": "parameter.RealParameter", | ||
| "RealParameter.11.estimate": "false", | ||
| "RealParameter.11.name": "alpha", | ||
| "RealParameter.11": "0.05", | ||
| "RealParameter.12.spec": "parameter.RealParameter", | ||
| "RealParameter.12.estimate": "false", | ||
| "RealParameter.12.name": "beta", | ||
| "RealParameter.12": "10.0", | ||
| "likelihood.spec": "util.CompoundDistribution", | ||
| "likelihood.useThreads": "true", | ||
| "treeLikelihood.hcv.spec": "ThreadedTreeLikelihood", | ||
| "treeLikelihood.hcv.data": "@hcv", | ||
| "treeLikelihood.hcv.tree": "@Tree.t:hcv", | ||
| "SiteModel.s:hcv.spec": "SiteModel", | ||
| "SiteModel.s:hcv.gammaCategoryCount": "4", | ||
| "SiteModel.s:hcv.shape": "@gammaShape.s:hcv", | ||
| "mutationRate.s:hcv.spec": "parameter.RealParameter", | ||
| "mutationRate.s:hcv.estimate": "false", | ||
| "mutationRate.s:hcv.name": "mutationRate", | ||
| "mutationRate.s:hcv": "1.0", | ||
| "proportionInvariant.s:hcv.spec": "parameter.RealParameter", | ||
| "proportionInvariant.s:hcv.estimate": "false", | ||
| "proportionInvariant.s:hcv.lower": "0.0", | ||
| "proportionInvariant.s:hcv.name": "proportionInvariant", | ||
| "proportionInvariant.s:hcv.upper": "1.0", | ||
| "proportionInvariant.s:hcv": "0.0", | ||
| "gtr.s:hcv.spec": "GTR", | ||
| "gtr.s:hcv.rateAC": "@rateAC.s:hcv", | ||
| "gtr.s:hcv.rateAG": "@rateAG.s:hcv", | ||
| "gtr.s:hcv.rateAT": "@rateAT.s:hcv", | ||
| "gtr.s:hcv.rateCG": "@rateCG.s:hcv", | ||
| "gtr.s:hcv.rateGT": "@rateGT.s:hcv", | ||
| "rateCT.s:hcv.spec": "parameter.RealParameter", | ||
| "rateCT.s:hcv.estimate": "false", | ||
| "rateCT.s:hcv.lower": "0.0", | ||
| "rateCT.s:hcv.name": "rateCT", | ||
| "rateCT.s:hcv": "1.0", | ||
| "estimatedFreqs.s:hcv.spec": "Frequencies", | ||
| "estimatedFreqs.s:hcv.frequencies": "@freqParameter.s:hcv", | ||
| "StrictClock.c:hcv.spec": "beast.evolution.branchratemodel.StrictClockModel", | ||
| "clockRate.c:hcv.spec": "parameter.RealParameter", | ||
| "clockRate.c:hcv.estimate": "false", | ||
| "clockRate.c:hcv.name": "clock.rate", | ||
| "clockRate.c:hcv": "7.9E-4", | ||
| "gammaShapeScaler.s:hcv.spec": "ScaleOperator", | ||
| "gammaShapeScaler.s:hcv.parameter": "@gammaShape.s:hcv", | ||
| "gammaShapeScaler.s:hcv.scaleFactor": "0.5", | ||
| "gammaShapeScaler.s:hcv.weight": "0.1", | ||
| "FrequenciesExchanger.s:hcv.spec": "DeltaExchangeOperator", | ||
| "FrequenciesExchanger.s:hcv.delta": "0.01", | ||
| "FrequenciesExchanger.s:hcv.weight": "0.1", | ||
| "RateACScaler.s:hcv.spec": "ScaleOperator", | ||
| "RateACScaler.s:hcv.parameter": "@rateAC.s:hcv", | ||
| "RateACScaler.s:hcv.scaleFactor": "0.5", | ||
| "RateACScaler.s:hcv.weight": "0.1", | ||
| "RateAGScaler.s:hcv.spec": "ScaleOperator", | ||
| "RateAGScaler.s:hcv.parameter": "@rateAG.s:hcv", | ||
| "RateAGScaler.s:hcv.scaleFactor": "0.5", | ||
| "RateAGScaler.s:hcv.weight": "0.1", | ||
| "RateATScaler.s:hcv.spec": "ScaleOperator", | ||
| "RateATScaler.s:hcv.parameter": "@rateAT.s:hcv", | ||
| "RateATScaler.s:hcv.scaleFactor": "0.5", | ||
| "RateATScaler.s:hcv.weight": "0.1", | ||
| "RateCGScaler.s:hcv.spec": "ScaleOperator", | ||
| "RateCGScaler.s:hcv.parameter": "@rateCG.s:hcv", | ||
| "RateCGScaler.s:hcv.scaleFactor": "0.5", | ||
| "RateCGScaler.s:hcv.weight": "0.1", | ||
| "RateGTScaler.s:hcv.spec": "ScaleOperator", | ||
| "RateGTScaler.s:hcv.parameter": "@rateGT.s:hcv", | ||
| "RateGTScaler.s:hcv.scaleFactor": "0.5", | ||
| "RateGTScaler.s:hcv.weight": "0.1", | ||
| "BayesianSkylineTreeScaler.t:hcv.spec": "ScaleOperator", | ||
| "BayesianSkylineTreeScaler.t:hcv.scaleFactor": "0.5", | ||
| "BayesianSkylineTreeScaler.t:hcv.tree": "@Tree.t:hcv", | ||
| "BayesianSkylineTreeScaler.t:hcv.weight": "3.0", | ||
| "BayesianSkylineTreeRootScaler.t:hcv.spec": "ScaleOperator", | ||
| "BayesianSkylineTreeRootScaler.t:hcv.rootOnly": "true", | ||
| "BayesianSkylineTreeRootScaler.t:hcv.scaleFactor": "0.5", | ||
| "BayesianSkylineTreeRootScaler.t:hcv.tree": "@Tree.t:hcv", | ||
| "BayesianSkylineTreeRootScaler.t:hcv.weight": "3.0", | ||
| "BayesianSkylineUniformOperator.t:hcv.spec": "Uniform", | ||
| "BayesianSkylineUniformOperator.t:hcv.tree": "@Tree.t:hcv", | ||
| "BayesianSkylineUniformOperator.t:hcv.weight": "30.0", | ||
| "BayesianSkylineSubtreeSlide.t:hcv.spec": "SubtreeSlide", | ||
| "BayesianSkylineSubtreeSlide.t:hcv.tree": "@Tree.t:hcv", | ||
| "BayesianSkylineSubtreeSlide.t:hcv.weight": "15.0", | ||
| "BayesianSkylineNarrow.t:hcv.spec": "Exchange", | ||
| "BayesianSkylineNarrow.t:hcv.tree": "@Tree.t:hcv", | ||
| "BayesianSkylineNarrow.t:hcv.weight": "15.0", | ||
| "BayesianSkylineWide.t:hcv.spec": "Exchange", | ||
| "BayesianSkylineWide.t:hcv.isNarrow": "false", | ||
| "BayesianSkylineWide.t:hcv.tree": "@Tree.t:hcv", | ||
| "BayesianSkylineWide.t:hcv.weight": "3.0", | ||
| "BayesianSkylineWilsonBalding.t:hcv.spec": "WilsonBalding", | ||
| "BayesianSkylineWilsonBalding.t:hcv.tree": "@Tree.t:hcv", | ||
| "BayesianSkylineWilsonBalding.t:hcv.weight": "3.0", | ||
| "popSizesScaler.t:hcv.spec": "ScaleOperator", | ||
| "popSizesScaler.t:hcv.parameter": "@bPopSizes.t:hcv", | ||
| "popSizesScaler.t:hcv.scaleFactor": "0.75", | ||
| "popSizesScaler.t:hcv.weight": "15.0", | ||
| "groupSizesDelta.t:hcv.spec": "DeltaExchangeOperator", | ||
| "groupSizesDelta.t:hcv.integer": "true", | ||
| "groupSizesDelta.t:hcv.weight": "6.0", | ||
| "tracelog.spec": "Logger", | ||
| "tracelog.logEvery": "3000", | ||
| "tracelog.model": "@posterior", | ||
| "tracelog.sanitiseHeaders": "true", | ||
| "tracelog.sort": "smart", | ||
| "TreeHeight.t:hcv.spec": "beast.evolution.tree.TreeHeightLogger", | ||
| "TreeHeight.t:hcv.tree": "@Tree.t:hcv", | ||
| "screenlog.spec": "Logger", | ||
| "screenlog.logEvery": "1000", | ||
| "treelog.t:hcv.spec": "Logger", | ||
| "treelog.t:hcv.logEvery": "3000", | ||
| "treelog.t:hcv.mode": "tree", | ||
| "TreeWithMetaDataLogger.t:hcv.spec": "beast.evolution.tree.TreeWithMetaDataLogger", | ||
| "TreeWithMetaDataLogger.t:hcv.tree": "@Tree.t:hcv" | ||
| } |
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