Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z A AbstractClockModel (class in torchtree.evolution.branch_model) AbstractCoalescentDistribution (class in torchtree.evolution.coalescent) AbstractCoalescentModel (class in torchtree.evolution.coalescent) AbstractDataType (class in torchtree.evolution.datatype) AbstractParameter (class in torchtree.core.abstractparameter) AbstractSubstitutionModel (class in torchtree.evolution.substitution_model.abstract) AbstractTreeModel (class in torchtree.evolution.tree_model) accept() (torchtree.inference.mcmc.operator.MCMCOperator method) adapt_base_window (torchtree.inference.hmc.stan_adaptation.StanWindowedAdaptation attribute) adapt_init_buffer (torchtree.inference.hmc.stan_adaptation.StanWindowedAdaptation attribute) adapt_term_buffer (torchtree.inference.hmc.stan_adaptation.StanWindowedAdaptation attribute) adaptable_parameter (torchtree.inference.mcmc.operator.MCMCOperator property) adaptable_parameter() (torchtree.inference.hmc.operator.HMCOperator method) (torchtree.inference.mcmc.gmrf_block_updating.GMRFPiecewiseCoalescentBlockUpdatingOperator method) (torchtree.inference.mcmc.operator.DirichletOperator method) (torchtree.inference.mcmc.operator.ScalerOperator method) (torchtree.inference.mcmc.operator.SlidingWindowOperator method) AdaptiveStepSize (class in torchtree.inference.hmc.adaptation) Adaptor (class in torchtree.inference.hmc.adaptation) add_birth_death() (in module torchtree.cli.evolution) add_coalescent() (in module torchtree.cli.evolution) add_model_listener() (torchtree.core.model.Model method) add_parameter_listener() (torchtree.core.abstractparameter.AbstractParameter method) (torchtree.core.model.Model method) (torchtree.core.parameter.CatParameter method) (torchtree.core.parameter.ModuleParameter method) (torchtree.core.parameter.Parameter method) (torchtree.core.parameter.TransformedParameter method) (torchtree.core.parameter.ViewParameter method) (torchtree.evolution.root_transform.RootParameter method) add_sample() (torchtree.ops.welford.WelfordVariance method) Alignment (class in torchtree.evolution.alignment) alignment (torchtree.evolution.site_pattern.SitePattern attribute) alpha (torchtree.distributions.bayesian_bridge.BayesianBridge attribute) (torchtree.distributions.tree_prior.CompoundGammaDirichletPrior attribute) (torchtree.evolution.coalescent.ConstantCoalescentIntegrated attribute) (torchtree.evolution.coalescent.ConstantCoalescentIntegratedModel attribute) (torchtree.evolution.substitution_model.codon.MG94 attribute) (torchtree.variational.renyi.VR attribute) AlternativeAttributeError ambiguities (torchtree.evolution.datatype.GeneralDataType attribute) AMINO_ACIDS (torchtree.evolution.datatype.AminoAcidDataType attribute) AMINO_ACIDS_AMBIGUITY_STATES (torchtree.evolution.datatype.AminoAcidDataType attribute) AMINO_ACIDS_STATES (torchtree.evolution.datatype.AminoAcidDataType attribute) AminoAcidDataType (class in torchtree.evolution.datatype) apply_affine_transform() (in module torchtree.cli.advi) apply_exp_transform() (in module torchtree.cli.advi) apply_flow() (torchtree.nf.flow.NormalizingFlow method) (torchtree.nf.realnvp.RealNVP method) apply_sigmoid_transformed() (in module torchtree.cli.advi) apply_simplex_transform() (in module torchtree.cli.advi) apply_transforms_for_fullrank() (in module torchtree.cli.advi) arg_constraints (torchtree.distributions.inverse_gamma.InverseGamma attribute) (torchtree.distributions.one_on_x.OneOnX attribute) (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) (torchtree.evolution.birth_death.BirthDeath attribute) (torchtree.evolution.coalescent.AbstractCoalescentDistribution attribute) (torchtree.evolution.coalescent.ConstantCoalescentIntegrated attribute) (torchtree.evolution.coalescent.ExponentialCoalescent attribute) (torchtree.evolution.coalescent.PiecewiseExponentialCoalescentGrid attribute) (torchtree.evolution.coalescent.PiecewiseLinearCoalescentGrid attribute) as_newick() (torchtree.evolution.tree_model.AbstractTreeModel method) as_tensor() (in module torchtree.core.utils) assign() (torchtree.core.parameter.ViewParameter method) attribute (torchtree.evolution.attribute_pattern.AttributePattern attribute) AttributePattern (class in torchtree.evolution.attribute_pattern) B b (torchtree.nf.planar.PlanarTransform attribute) base (torchtree.nf.flow.NormalizingFlow attribute) base_dist (torchtree.nf.realnvp.RealNVP attribute) BaseConvergence (class in torchtree.optim.convergence) batch_shape (torchtree.distributions.deterministic_normal.DeterministicNormal property) (torchtree.distributions.distributions.Distribution property) (torchtree.distributions.multivariate_normal.MultivariateNormal property) (torchtree.nf.realnvp.RealNVP property) BatchNorm (class in torchtree.nf.realnvp) BayesianBridge (class in torchtree.distributions.bayesian_bridge) BDSKModel (class in torchtree.evolution.bdsk) beta (torchtree.distributions.gmrf.GMRFCovariate attribute) (torchtree.evolution.coalescent.ConstantCoalescentIntegrated attribute) (torchtree.evolution.coalescent.ConstantCoalescentIntegratedModel attribute) (torchtree.evolution.substitution_model.codon.MG94 attribute) (torchtree.nf.realnvp.BatchNorm attribute) bias (torchtree.distributions.transforms.LinearTransform attribute) bijective (torchtree.distributions.transforms.CumSumExpTransform attribute) (torchtree.distributions.transforms.CumSumSoftPlusTransform attribute) (torchtree.distributions.transforms.CumSumTransform attribute) (torchtree.distributions.transforms.LogTransform attribute) (torchtree.distributions.transforms.SoftPlusTransform attribute) (torchtree.distributions.transforms.TrilExpDiagonalTransform attribute) (torchtree.evolution.rate_transform.LogDifferenceRateTransform attribute) (torchtree.evolution.rate_transform.RescaledRateTransform attribute) (torchtree.evolution.tree_height_transform.DifferenceNodeHeightTransform attribute) (torchtree.evolution.tree_height_transform.GeneralNodeHeightTransform attribute) BirthDeath (class in torchtree.evolution.birth_death) BirthDeathModel (class in torchtree.evolution.birth_death) branch_count (torchtree.evolution.branch_model.StrictClockModel attribute) branch_lengths() (torchtree.evolution.tree_model.TimeTreeModel method) (torchtree.evolution.tree_model.TreeModel method) (torchtree.evolution.tree_model.UnRootedTreeModel method) branch_lengths_need_update (torchtree.evolution.tree_model.TimeTreeModel attribute) BranchModel (class in torchtree.evolution.branch_model) build_advi() (in module torchtree.cli.advi) build_alignment() (in module torchtree.cli.evolution) build_hmc() (in module torchtree.cli.hmc) build_mcmc() (in module torchtree.cli.mcmc) build_optimizer() (in module torchtree.cli.map) C c (torchtree.distributions.tree_prior.CompoundGammaDirichletPrior attribute) calculate_F3x4() (in module torchtree.evolution.alignment) calculate_F3x4_from_nucleotide() (in module torchtree.evolution.alignment) calculate_frequencies() (in module torchtree.evolution.alignment) calculate_frequencies_per_codon_position() (in module torchtree.evolution.alignment) calculate_kappa() (in module torchtree.evolution.alignment) calculate_substitutions() (in module torchtree.evolution.alignment) calculate_treelikelihood() (in module torchtree.evolution.tree_likelihood) calculate_treelikelihood_discrete() (in module torchtree.evolution.tree_likelihood) calculate_treelikelihood_discrete_rescaled() (in module torchtree.evolution.tree_likelihood) calculate_treelikelihood_discrete_safe() (in module torchtree.evolution.tree_likelihood) calculate_treelikelihood_tip_states_discrete() (in module torchtree.evolution.tree_likelihood) calculate_treelikelihood_tip_states_discrete_rescaled() (in module torchtree.evolution.tree_likelihood) calculate_ts_tv() (in module torchtree.evolution.alignment) calculate_with_tip_partials() (torchtree.evolution.tree_likelihood.TreeLikelihoodModel method) calculate_with_tip_states() (torchtree.evolution.tree_likelihood.TreeLikelihoodModel method) CallableModel (class in torchtree.core.model) callables() (torchtree.core.container.Container method) CatParameter (class in torchtree.core.parameter) check() (torchtree.optim.convergence.BaseConvergence method) (torchtree.optim.convergence.StanVariationalConvergence method) (torchtree.optim.convergence.VariationalConvergence method) check_arguments() (in module torchtree.cli.evolution) checkpoint (torchtree.inference.hmc.hmc.HMC attribute) (torchtree.inference.mcmc.mcmc.MCMC attribute) (torchtree.optim.optimizer.Optimizer attribute) checkpoint_all (torchtree.optim.optimizer.Optimizer attribute) checkpoint_frequency (torchtree.inference.hmc.hmc.HMC attribute) (torchtree.inference.mcmc.mcmc.MCMC attribute) (torchtree.optim.optimizer.Optimizer attribute) children (torchtree.evolution.io.Node attribute) classproperty (class in torchtree.core.classproperty_decorator) clock_model (torchtree.evolution.poisson_tree_likelihood.PoissonTreeLikelihood attribute) (torchtree.evolution.tree_likelihood.TreeLikelihoodModel attribute) clone() (torchtree.core.parameter.Parameter method) (torchtree.core.parameter.ViewParameter method) close() (torchtree.core.logger.ContainerLogger method) (torchtree.core.logger.Logger method) (torchtree.core.logger.LoggerInterface method) (torchtree.core.logger.TreeLogger method) coalescent (torchtree.inference.mcmc.gmrf_block_updating.GMRFPiecewiseCoalescentBlockUpdatingOperator attribute) COALESCENT_PIECEWISE (in module torchtree.cli.evolution) codes (torchtree.evolution.datatype.GeneralDataType attribute) codomain (torchtree.distributions.transforms.ConvexCombinationTransform attribute) (torchtree.distributions.transforms.CumSumExpTransform attribute) (torchtree.distributions.transforms.CumSumSoftPlusTransform attribute) (torchtree.distributions.transforms.CumSumTransform attribute) (torchtree.distributions.transforms.LinearTransform attribute) (torchtree.distributions.transforms.LogTransform attribute) (torchtree.distributions.transforms.SoftPlusTransform attribute) CODON_TRIPLETS (torchtree.evolution.datatype.CodonDataType attribute) CodonDataType (class in torchtree.evolution.datatype) components (torchtree.variational.kl.SELBO attribute) CompoundGammaDirichletPrior (class in torchtree.distributions.tree_prior) compress() (in module torchtree.evolution.site_pattern) compress_alignment() (in module torchtree.evolution.site_pattern) compress_alignment_states() (in module torchtree.evolution.site_pattern) compute_tips_partials() (torchtree.evolution.attribute_pattern.AttributePattern method) (torchtree.evolution.site_pattern.SitePattern method) compute_tips_states() (torchtree.evolution.attribute_pattern.AttributePattern method) (torchtree.evolution.site_pattern.SitePattern method) concentration (torchtree.distributions.inverse_gamma.InverseGamma property) constant_term (torchtree.distributions.gmrf_integrated.GMRFGammaIntegrated attribute) ConstantCoalescent (class in torchtree.evolution.coalescent) ConstantCoalescentIntegrated (class in torchtree.evolution.coalescent) ConstantCoalescentIntegratedModel (class in torchtree.evolution.coalescent) ConstantCoalescentModel (class in torchtree.evolution.coalescent) ConstantSiteModel (class in torchtree.evolution.site_model) CONSTRAINT (class in torchtree.cli.utils) CONSTRAINT_PREFIX (in module torchtree.cli.utils) Container (class in torchtree.core.container) container (torchtree.core.logger.ContainerLogger attribute) ContainerLogger (class in torchtree.core.logger) convergence (torchtree.optim.optimizer.Optimizer attribute) convert_date_to_real() (in module torchtree.cli.utils) convert_samples_to_nexus() (in module torchtree.evolution.io) ConvexCombinationTransform (class in torchtree.distributions.transforms) copy_() (torchtree.core.parameter.Parameter method) covariates (torchtree.distributions.gmrf.GMRFCovariate attribute) cpu() (torchtree.core.abstractparameter.Device method) (torchtree.core.model.Model method) (torchtree.core.parameter.CatParameter method) (torchtree.core.parameter.ModuleParameter method) (torchtree.core.parameter.Parameter method) (torchtree.core.parameter.TransformedParameter method) (torchtree.core.parameter.ViewParameter method) (torchtree.distributions.ctmc_scale.CTMCScale method) (torchtree.evolution.attribute_pattern.AttributePattern method) (torchtree.evolution.site_model.ConstantSiteModel method) (torchtree.evolution.site_model.InvariantSiteModel method) (torchtree.evolution.site_model.UnivariateDiscretizedSiteModel method) (torchtree.evolution.site_pattern.SitePattern method) (torchtree.evolution.substitution_model.general.GeneralJC69 method) (torchtree.evolution.substitution_model.nucleotide.JC69 method) (torchtree.evolution.tree_model.ReparameterizedTimeTreeModel method) (torchtree.evolution.tree_model.TimeTreeModel method) (torchtree.nf.flow.NormalizingFlow method) (torchtree.nn.module.Module method) create_advi() (in module torchtree.cli.advi) create_alignment() (in module torchtree.cli.evolution) create_bd_prior() (in module torchtree.cli.evolution) create_bdsk() (in module torchtree.cli.evolution) create_bdsk_prior() (in module torchtree.cli.evolution) create_birth_death() (in module torchtree.cli.evolution) create_block_updating_operator() (in module torchtree.cli.operators) create_branch_model() (in module torchtree.cli.evolution) create_clock_horseshoe_prior() (in module torchtree.cli.priors) create_clock_prior() (in module torchtree.cli.evolution) create_coalesent() (in module torchtree.cli.evolution) create_constant_bd_prior() (in module torchtree.cli.evolution) create_constant_birth_death() (in module torchtree.cli.evolution) create_data_type() (in module torchtree.cli.evolution) create_evolution_joint() (in module torchtree.cli.evolution) create_evolution_parser() (in module torchtree.cli.evolution) create_evolution_priors() (in module torchtree.cli.evolution) create_flexible_variational() (in module torchtree.cli.advi) create_fullrank() (in module torchtree.cli.advi) create_fullrank_from_meanfield() (in module torchtree.cli.advi) create_gamma_distribution() (in module torchtree.cli.advi) create_general_data_type() (in module torchtree.cli.evolution) create_hmc() (in module torchtree.cli.hmc) create_hmc_operator() (in module torchtree.cli.hmc) create_hmc_parser() (in module torchtree.cli.hmc) create_jacobians() (in module torchtree.cli.jacobians) create_logger() (in module torchtree.cli.advi) (in module torchtree.cli.map) create_loggers() (in module torchtree.cli.loggers) create_map_parser() (in module torchtree.cli.map) create_mcmc() (in module torchtree.cli.mcmc) create_mcmc_parser() (in module torchtree.cli.mcmc) create_meanfield() (in module torchtree.cli.advi) create_normal_distribution() (in module torchtree.cli.advi) create_one_on_x_prior() (in module torchtree.cli.priors) create_optimizer() (in module torchtree.cli.map) create_poisson_evolution_joint() (in module torchtree.cli.evolution) create_poisson_tree_likelihood() (in module torchtree.cli.evolution) create_rate_matrix() (torchtree.evolution.substitution_model.general.EmpiricalSubstitutionModel static method) create_realnp_distribution() (in module torchtree.cli.advi) create_realnvp() (in module torchtree.cli.advi) create_sampler() (in module torchtree.cli.advi) create_scaler_operator() (in module torchtree.cli.operators) create_show_parser() (in module torchtree.cli.cli) create_site_model() (in module torchtree.cli.evolution) create_site_model_srd06_mus() (in module torchtree.cli.evolution) create_site_pattern() (in module torchtree.cli.evolution) create_sliding_window_operator() (in module torchtree.cli.operators) create_stan_windowed_adaptation() (in module torchtree.cli.hmc) create_substitution_model() (in module torchtree.cli.evolution) create_substitution_model_priors() (in module torchtree.cli.evolution) create_taxa() (in module torchtree.cli.evolution) create_time_tree_prior() (in module torchtree.cli.evolution) create_tree_likelihood() (in module torchtree.cli.evolution) create_tree_likelihood_general() (in module torchtree.cli.evolution) create_tree_likelihood_single() (in module torchtree.cli.evolution) create_tree_logger() (in module torchtree.cli.map) create_tree_model() (in module torchtree.cli.evolution) create_tril() (in module torchtree.cli.advi) create_ucln_prior() (in module torchtree.cli.evolution) create_variational_model() (in module torchtree.cli.advi) create_variational_parser() (in module torchtree.cli.advi) create_weibull_distribution() (in module torchtree.cli.advi) CSV (class in torchtree.core.logger) CTMCScale (class in torchtree.distributions.ctmc_scale) CUBO (class in torchtree.variational.chi) cuda() (torchtree.core.abstractparameter.Device method) (torchtree.core.model.Model method) (torchtree.core.parameter.CatParameter method) (torchtree.core.parameter.ModuleParameter method) (torchtree.core.parameter.Parameter method) (torchtree.core.parameter.TransformedParameter method) (torchtree.core.parameter.ViewParameter method) (torchtree.distributions.ctmc_scale.CTMCScale method) (torchtree.evolution.attribute_pattern.AttributePattern method) (torchtree.evolution.site_model.ConstantSiteModel method) (torchtree.evolution.site_model.InvariantSiteModel method) (torchtree.evolution.site_model.UnivariateDiscretizedSiteModel method) (torchtree.evolution.site_pattern.SitePattern method) (torchtree.evolution.substitution_model.general.GeneralJC69 method) (torchtree.evolution.substitution_model.nucleotide.JC69 method) (torchtree.evolution.tree_model.ReparameterizedTimeTreeModel method) (torchtree.evolution.tree_model.TimeTreeModel method) (torchtree.nf.flow.NormalizingFlow method) (torchtree.nn.module.Module method) CumSumExpTransform (class in torchtree.distributions.transforms) CumSumSoftPlusTransform (class in torchtree.distributions.transforms) CumSumTransform (class in torchtree.distributions.transforms) D data_type (torchtree.evolution.alignment.Alignment property) (torchtree.evolution.attribute_pattern.AttributePattern attribute) (torchtree.evolution.substitution_model.codon.MG94 attribute) (torchtree.evolution.substitution_model.general.GeneralNonSymmetricSubstitutionModel attribute) (torchtree.evolution.substitution_model.general.GeneralSymmetricSubstitutionModel attribute) DataType (class in torchtree.evolution.datatype) default() (torchtree.core.parameter_encoder.ParameterEncoder method) (torchtree.core.utils.TensorEncoder method) delta (torchtree.evolution.bdsk.BDSKModel attribute) delta_elbo (torchtree.optim.convergence.StanVariationalConvergence attribute) delta_elbo_ave (torchtree.optim.convergence.StanVariationalConvergence attribute) delta_elbo_med (torchtree.optim.convergence.StanVariationalConvergence attribute) desc (torchtree.nf.energy_functions.EnergyFunctionModel attribute) detach() (torchtree.core.parameter.Parameter method) DeterministicNormal (class in torchtree.distributions.deterministic_normal) Device (class in torchtree.core.abstractparameter) device (torchtree.core.abstractparameter.AbstractParameter property) (torchtree.core.abstractparameter.Device property) (torchtree.core.parameter.CatParameter property) dict_parameters (torchtree.distributions.distributions.Distribution attribute) DifferenceNodeHeightTransform (class in torchtree.evolution.tree_height_transform) dim() (torchtree.core.abstractparameter.AbstractParameter method) dimension (torchtree.inference.hmc.hmc.HMC attribute) DirichletOperator (class in torchtree.inference.mcmc.operator) disable_plugins() (torchtree.cli.plugin_manager.PluginManager method) dist (torchtree.distributions.distributions.Distribution attribute) distance (torchtree.evolution.root_transform.RootParameter attribute) Distribution (class in torchtree.distributions.distributions) distribution (torchtree.distributions.distributions.Distribution property) distribution() (torchtree.evolution.coalescent.AbstractCoalescentModel method) (torchtree.evolution.coalescent.ConstantCoalescentIntegratedModel method) (torchtree.evolution.coalescent.ConstantCoalescentModel method) (torchtree.evolution.coalescent.ExponentialCoalescentModel method) (torchtree.evolution.coalescent.PiecewiseConstantCoalescentGridModel method) (torchtree.evolution.coalescent.PiecewiseConstantCoalescentModel method) (torchtree.evolution.coalescent.PiecewiseExponentialCoalescentGridModel method) (torchtree.evolution.coalescent.PiecewiseLinearCoalescentGridModel method) distribution_parameters (torchtree.distributions.distributions.Distribution attribute) distribution_type() (in module torchtree.cli.evolution) DistributionModel (class in torchtree.distributions.distributions) distributions (torchtree.optim.optimizer.Optimizer attribute) domain (torchtree.distributions.transforms.ConvexCombinationTransform attribute) (torchtree.distributions.transforms.CumSumExpTransform attribute) (torchtree.distributions.transforms.CumSumSoftPlusTransform attribute) (torchtree.distributions.transforms.CumSumTransform attribute) (torchtree.distributions.transforms.LinearTransform attribute) (torchtree.distributions.transforms.LogTransform attribute) (torchtree.distributions.transforms.SoftPlusTransform attribute) dtype (torchtree.core.abstractparameter.AbstractParameter property) (torchtree.core.parameter.ViewParameter property) DualAveraging (class in torchtree.ops.dual_averaging) DualAveragingStepSize (class in torchtree.inference.hmc.adaptation) Dumper (class in torchtree.core.logger) E edge_lengths (torchtree.evolution.poisson_tree_likelihood.PoissonTreeLikelihood attribute) eigen() (torchtree.evolution.substitution_model.abstract.NonSymmetricSubstitutionModel method) (torchtree.evolution.substitution_model.abstract.SymmetricSubstitutionModel method) (torchtree.evolution.substitution_model.general.EmpiricalSubstitutionModel method) ELBO (class in torchtree.variational.kl) elbo (torchtree.optim.convergence.StanVariationalConvergence attribute) elbo_best (torchtree.optim.convergence.StanVariationalConvergence attribute) elbo_diff (torchtree.optim.convergence.StanVariationalConvergence attribute) elbo_prev (torchtree.optim.convergence.StanVariationalConvergence attribute) EmpiricalSubstitutionModel (class in torchtree.evolution.substitution_model.general) encoding() (torchtree.evolution.datatype.AminoAcidDataType method) (torchtree.evolution.datatype.CodonDataType method) (torchtree.evolution.datatype.DataType method) (torchtree.evolution.datatype.GeneralDataType method) (torchtree.evolution.datatype.NucleotideDataType method) EnergyFunctionModel (class in torchtree.nf.energy_functions) entropy (torchtree.variational.kl.ELBO attribute) (torchtree.variational.kl.SELBO attribute) entropy() (torchtree.distributions.deterministic_normal.DeterministicNormal method) (torchtree.distributions.distributions.Distribution method) (torchtree.distributions.distributions.DistributionModel method) (torchtree.distributions.joint_distribution.JointDistributionModel method) (torchtree.distributions.multivariate_normal.MultivariateNormal method) (torchtree.nf.flow.NormalizingFlow method) (torchtree.nf.realnvp.RealNVP method) epidemiology_to_birth_death() (in module torchtree.evolution.bdsk) eps (torchtree.distributions.deterministic_normal.DeterministicNormal attribute) (torchtree.nf.realnvp.BatchNorm attribute) event_shape (torchtree.distributions.deterministic_normal.DeterministicNormal property) (torchtree.distributions.distributions.Distribution property) (torchtree.distributions.multivariate_normal.MultivariateNormal property) every (torchtree.core.logger.ContainerLogger attribute) (torchtree.core.logger.Logger attribute) (torchtree.core.logger.TreeLogger attribute) (torchtree.inference.hmc.hmc.HMC attribute) (torchtree.inference.mcmc.mcmc.MCMC attribute) (torchtree.optim.convergence.VariationalConvergence attribute) exit() (torchtree.core.utils.SignalHandler method) expand() (torchtree.distributions.inverse_gamma.InverseGamma method) expand_plates() (in module torchtree.core.utils) ExponentialCoalescent (class in torchtree.evolution.coalescent) ExponentialCoalescentModel (class in torchtree.evolution.coalescent) extract_taxa() (in module torchtree.evolution.io) extract_tensors_and_parameters() (in module torchtree.inference.utils) F f (torchtree.core.logger.Logger attribute) (torchtree.core.logger.TreeLogger attribute) FakeTreeModel (class in torchtree.evolution.coalescent) field (torchtree.distributions.gmrf.GMRF attribute) (torchtree.distributions.gmrf_integrated.GMRFGammaIntegrated attribute) file_name (torchtree.core.logger.CSV attribute) (torchtree.core.logger.TreeLogger attribute) (torchtree.optim.convergence.VariationalConvergence attribute) find_reasonable_step_size() (in module torchtree.inference.hmc.adaptation) (torchtree.inference.hmc.hmc.HMC method) find_step_size (torchtree.inference.hmc.hmc.HMC attribute) fire_model_changed() (torchtree.core.model.Model method) fire_parameter_changed() (torchtree.core.abstractparameter.AbstractParameter method) (torchtree.core.parameter.CatParameter method) (torchtree.core.parameter.ModuleParameter method) (torchtree.core.parameter.Parameter method) (torchtree.core.parameter.TransformedParameter method) (torchtree.core.parameter.ViewParameter method) (torchtree.evolution.root_transform.RootParameter method) FlexibleTimeTreeModel (class in torchtree.evolution.tree_model_flexible) FlowSequential (class in torchtree.nf.realnvp) forward() (torchtree.nf.flow.NormalizingFlow method) (torchtree.nf.planar.PlanarTransform method) (torchtree.nf.realnvp.BatchNorm method) (torchtree.nf.realnvp.FlowSequential method) (torchtree.nf.realnvp.LinearMaskedCoupling method) (torchtree.nf.realnvp.RealNVP method) frequencies (torchtree.evolution.substitution_model.abstract.AbstractSubstitutionModel property) (torchtree.evolution.substitution_model.abstract.SubstitutionModel property) (torchtree.evolution.substitution_model.general.EmpiricalSubstitutionModel property) (torchtree.evolution.substitution_model.general.GeneralJC69 property) (torchtree.evolution.substitution_model.nucleotide.JC69 property) from_json() (torchtree.core.container.Container class method) (torchtree.core.logger.ContainerLogger class method) (torchtree.core.logger.CSV class method) (torchtree.core.logger.Dumper class method) (torchtree.core.logger.Logger class method) (torchtree.core.logger.TreeLogger class method) (torchtree.core.parameter.CatParameter class method) (torchtree.core.parameter.ModuleParameter class method) (torchtree.core.parameter.Parameter class method) (torchtree.core.parameter.TransformedParameter class method) (torchtree.core.parameter.ViewParameter class method) (torchtree.core.serializable.JSONSerializable class method) (torchtree.distributions.bayesian_bridge.BayesianBridge class method) (torchtree.distributions.ctmc_scale.CTMCScale class method) (torchtree.distributions.deterministic_normal.DeterministicNormal class method) (torchtree.distributions.distributions.Distribution class method) (torchtree.distributions.gmrf.GMRF class method) (torchtree.distributions.gmrf.GMRFCovariate class method) (torchtree.distributions.gmrf_integrated.GMRFGammaIntegrated class method) (torchtree.distributions.joint_distribution.JointDistributionModel class method) (torchtree.distributions.multivariate_normal.MultivariateNormal class method) (torchtree.distributions.scale_mixture.ScaleMixtureNormal class method) (torchtree.distributions.tree_prior.CompoundGammaDirichletPrior class method) (torchtree.evolution.alignment.Alignment class method) (torchtree.evolution.attribute_pattern.AttributePattern class method) (torchtree.evolution.bdsk.BDSKModel class method) (torchtree.evolution.birth_death.BirthDeathModel class method) (torchtree.evolution.branch_model.SimpleClockModel class method) (torchtree.evolution.branch_model.StrictClockModel class method) (torchtree.evolution.coalescent.ConstantCoalescentIntegratedModel class method) (torchtree.evolution.coalescent.ConstantCoalescentModel class method) (torchtree.evolution.coalescent.ExponentialCoalescentModel class method) (torchtree.evolution.coalescent.PiecewiseConstantCoalescentGridModel class method) (torchtree.evolution.coalescent.PiecewiseConstantCoalescentModel class method) (torchtree.evolution.coalescent.PiecewiseExponentialCoalescentGridModel class method) (torchtree.evolution.coalescent.PiecewiseLinearCoalescentGridModel class method) (torchtree.evolution.datatype.AminoAcidDataType class method) (torchtree.evolution.datatype.CodonDataType class method) (torchtree.evolution.datatype.GeneralDataType class method) (torchtree.evolution.datatype.NucleotideDataType class method) (torchtree.evolution.poisson_tree_likelihood.PoissonTreeLikelihood class method) (torchtree.evolution.root_transform.RootParameter class method) (torchtree.evolution.site_model.ConstantSiteModel class method) (torchtree.evolution.site_model.InvariantSiteModel class method) (torchtree.evolution.site_model.WeibullSiteModel class method) (torchtree.evolution.site_pattern.SitePattern class method) (torchtree.evolution.substitution_model.amino_acid.LG class method) (torchtree.evolution.substitution_model.amino_acid.WAG class method) (torchtree.evolution.substitution_model.codon.MG94 class method) (torchtree.evolution.substitution_model.general.EmpiricalSubstitutionModel class method) (torchtree.evolution.substitution_model.general.GeneralJC69 class method) (torchtree.evolution.substitution_model.general.GeneralNonSymmetricSubstitutionModel class method) (torchtree.evolution.substitution_model.general.GeneralSymmetricSubstitutionModel class method) (torchtree.evolution.substitution_model.nucleotide.GTR class method) (torchtree.evolution.substitution_model.nucleotide.HKY class method) (torchtree.evolution.substitution_model.nucleotide.JC69 class method) (torchtree.evolution.taxa.Taxa class method) (torchtree.evolution.taxa.Taxon class method) (torchtree.evolution.tree_likelihood.TreeLikelihoodModel class method) (torchtree.evolution.tree_model.ReparameterizedTimeTreeModel class method) (torchtree.evolution.tree_model.TimeTreeModel class method) (torchtree.evolution.tree_model.UnRootedTreeModel class method) (torchtree.evolution.tree_model_flexible.FlexibleTimeTreeModel class method) (torchtree.inference.hmc.adaptation.AdaptiveStepSize class method) (torchtree.inference.hmc.adaptation.DualAveragingStepSize class method) (torchtree.inference.hmc.adaptation.MassMatrixAdaptor class method) (torchtree.inference.hmc.hamiltonian.Hamiltonian class method) (torchtree.inference.hmc.hmc.HMC class method) (torchtree.inference.hmc.integrator.LeapfrogIntegrator class method) (torchtree.inference.hmc.operator.HMCOperator class method) (torchtree.inference.hmc.stan_adaptation.StanWindowedAdaptation class method) (torchtree.inference.mcmc.gmrf_block_updating.GMRFPiecewiseCoalescentBlockUpdatingOperator class method) (torchtree.inference.mcmc.mcmc.MCMC class method) (torchtree.inference.mcmc.operator.DirichletOperator class method) (torchtree.inference.mcmc.operator.ScalerOperator class method) (torchtree.inference.mcmc.operator.SlidingWindowOperator class method) (torchtree.inference.sampler.Sampler class method) (torchtree.nf.energy_functions.EnergyFunctionModel class method) (torchtree.nf.flow.NormalizingFlow class method) (torchtree.nf.realnvp.RealNVP class method) (torchtree.nn.module.Module class method) (torchtree.optim.convergence.StanVariationalConvergence class method) (torchtree.optim.convergence.VariationalConvergence class method) (torchtree.optim.lr_scheduler.Scheduler class method) (torchtree.optim.optimizer.Optimizer class method) (torchtree.variational.chi.CUBO class method) (torchtree.variational.kl.ELBO class method) (torchtree.variational.kl.KLpq class method) (torchtree.variational.kl.KLpqImportance class method) (torchtree.variational.kl.SELBO class method) (torchtree.variational.renyi.VR class method) from_json_safe() (torchtree.core.serializable.JSONSerializable class method) G gather_parameters() (in module torchtree.cli.advi) GeneralDataType (class in torchtree.evolution.datatype) GeneralJC69 (class in torchtree.evolution.substitution_model.general) GeneralNodeHeightTransform (class in torchtree.evolution.tree_height_transform) GeneralNonSymmetricSubstitutionModel (class in torchtree.evolution.substitution_model.general) GeneralSymmetricSubstitutionModel (class in torchtree.evolution.substitution_model.general) GENETIC_CODE_NAMES (torchtree.evolution.datatype.CodonDataType attribute) GENETIC_CODE_TABLES (torchtree.evolution.datatype.CodonDataType attribute) get() (torchtree.evolution.alignment.Alignment class method) get_class() (in module torchtree.core.utils) get_engine() (in module torchtree.cli.evolution) GMRF (class in torchtree.distributions.gmrf) gmrf (torchtree.inference.mcmc.gmrf_block_updating.GMRFPiecewiseCoalescentBlockUpdatingOperator attribute) GMRFCovariate (class in torchtree.distributions.gmrf) GMRFGammaIntegrated (class in torchtree.distributions.gmrf_integrated) GMRFPiecewiseCoalescentBlockUpdatingOperator (class in torchtree.inference.mcmc.gmrf_block_updating) gobal_scale (torchtree.distributions.scale_mixture.ScaleMixtureNormal attribute) grad (torchtree.core.parameter.Parameter property) grad_fn (torchtree.core.parameter.Parameter property) gradient() (torchtree.inference.mcmc.gmrf_block_updating.GMRFPiecewiseCoalescentBlockUpdatingOperator method) grid (torchtree.evolution.coalescent.PiecewiseConstantCoalescentGrid attribute) (torchtree.evolution.coalescent.PiecewiseConstantCoalescentGridModel attribute) (torchtree.evolution.coalescent.PiecewiseExponentialCoalescentGrid attribute) (torchtree.evolution.coalescent.PiecewiseExponentialCoalescentGridModel attribute) (torchtree.evolution.coalescent.PiecewiseLinearCoalescentGrid attribute) (torchtree.evolution.coalescent.PiecewiseLinearCoalescentGridModel attribute) (torchtree.evolution.coalescent.SoftPiecewiseConstantCoalescentGrid attribute) growth (torchtree.evolution.coalescent.ExponentialCoalescent attribute) (torchtree.evolution.coalescent.ExponentialCoalescentModel attribute) (torchtree.evolution.coalescent.PiecewiseExponentialCoalescentGrid attribute) (torchtree.evolution.coalescent.PiecewiseExponentialCoalescentGridModel attribute) GTR (class in torchtree.evolution.substitution_model.nucleotide) H Hamiltonian (class in torchtree.inference.hmc.hamiltonian) hamiltonian() (torchtree.inference.hmc.hmc.HMC method) handle_model_changed() (torchtree.core.container.Container method) (torchtree.core.model.CallableModel method) (torchtree.core.parameter.CatParameter method) (torchtree.core.parameter.ModuleParameter method) (torchtree.core.parameter.TransformedParameter method) (torchtree.core.parametric.ModelListener method) (torchtree.distributions.bayesian_bridge.BayesianBridge method) (torchtree.distributions.deterministic_normal.DeterministicNormal method) (torchtree.distributions.scale_mixture.ScaleMixtureNormal method) (torchtree.evolution.attribute_pattern.AttributePattern method) (torchtree.evolution.birth_death.BirthDeathModel method) (torchtree.evolution.branch_model.AbstractClockModel method) (torchtree.evolution.root_transform.RootParameter method) (torchtree.evolution.site_model.SiteModel method) (torchtree.evolution.site_pattern.SitePattern method) (torchtree.evolution.substitution_model.codon.MG94 method) (torchtree.evolution.substitution_model.general.EmpiricalSubstitutionModel method) (torchtree.evolution.substitution_model.general.GeneralJC69 method) (torchtree.evolution.substitution_model.general.GeneralNonSymmetricSubstitutionModel method) (torchtree.evolution.substitution_model.general.GeneralSymmetricSubstitutionModel method) (torchtree.evolution.substitution_model.nucleotide.GTR method) (torchtree.evolution.substitution_model.nucleotide.HKY method) (torchtree.evolution.substitution_model.nucleotide.JC69 method) (torchtree.evolution.tree_model.AbstractTreeModel method) (torchtree.evolution.tree_model.ReparameterizedTimeTreeModel method) (torchtree.nf.energy_functions.EnergyFunctionModel method) handle_parameter_changed() (torchtree.core.container.Container method) (torchtree.core.model.CallableModel method) (torchtree.core.parameter.CatParameter method) (torchtree.core.parameter.ModuleParameter method) (torchtree.core.parameter.TransformedParameter method) (torchtree.core.parameter.ViewParameter method) (torchtree.core.parametric.ParameterListener method) (torchtree.distributions.joint_distribution.JointDistributionModel method) (torchtree.distributions.tree_prior.CompoundGammaDirichletPrior method) (torchtree.evolution.attribute_pattern.AttributePattern method) (torchtree.evolution.branch_model.AbstractClockModel method) (torchtree.evolution.poisson_tree_likelihood.PoissonTreeLikelihood method) (torchtree.evolution.root_transform.RootParameter method) (torchtree.evolution.site_model.SiteModel method) (torchtree.evolution.site_pattern.SitePattern method) (torchtree.evolution.substitution_model.codon.MG94 method) (torchtree.evolution.substitution_model.general.EmpiricalSubstitutionModel method) (torchtree.evolution.substitution_model.general.GeneralJC69 method) (torchtree.evolution.substitution_model.general.GeneralNonSymmetricSubstitutionModel method) (torchtree.evolution.substitution_model.general.GeneralSymmetricSubstitutionModel method) (torchtree.evolution.substitution_model.nucleotide.GTR method) (torchtree.evolution.substitution_model.nucleotide.HKY method) (torchtree.evolution.substitution_model.nucleotide.JC69 method) (torchtree.evolution.tree_likelihood.TreeLikelihoodModel method) (torchtree.evolution.tree_model.ReparameterizedTimeTreeModel method) (torchtree.evolution.tree_model.TimeTreeModel method) (torchtree.evolution.tree_model.UnRootedTreeModel method) (torchtree.inference.hmc.hamiltonian.Hamiltonian method) (torchtree.inference.hmc.operator.HMCOperator method) (torchtree.variational.chi.CUBO method) (torchtree.variational.kl.ELBO method) (torchtree.variational.kl.KLpq method) (torchtree.variational.kl.KLpqImportance method) (torchtree.variational.kl.SELBO method) (torchtree.variational.renyi.VR method) has_rsample (torchtree.distributions.inverse_gamma.InverseGamma attribute) (torchtree.evolution.coalescent.AbstractCoalescentDistribution attribute) (torchtree.evolution.coalescent.ConstantCoalescent attribute) (torchtree.evolution.coalescent.ConstantCoalescentIntegrated attribute) (torchtree.evolution.coalescent.ExponentialCoalescent attribute) (torchtree.evolution.coalescent.PiecewiseExponentialCoalescentGrid attribute) (torchtree.evolution.coalescent.PiecewiseLinearCoalescentGrid attribute) height (torchtree.evolution.io.Node attribute) heights_from_branch_lengths() (in module torchtree.evolution.tree_model) heights_need_update (torchtree.evolution.tree_model.TimeTreeModel attribute) heights_to_branch_lengths() (in module torchtree.evolution.tree_model) HKY (class in torchtree.evolution.substitution_model.nucleotide) HMC (class in torchtree.inference.hmc.hmc) HMCOperator (class in torchtree.inference.hmc.operator) I ID (in module torchtree.typing) id (torchtree.core.identifiable.Identifiable property) Identifiable (class in torchtree.core.identifiable) indices (torchtree.core.parameter.ViewParameter attribute) (torchtree.evolution.site_pattern.SitePattern attribute) initialize() (torchtree.core.logger.ContainerLogger method) (torchtree.core.logger.Logger method) (torchtree.core.logger.LoggerInterface method) (torchtree.core.logger.TreeLogger method) initialize_dates_from_taxa() (in module torchtree.evolution.tree_model) input_size (torchtree.nf.realnvp.RealNVP attribute) inputs (torchtree.core.logger.ContainerLogger attribute) Integrator (class in torchtree.inference.hmc.integrator) integrator (torchtree.inference.hmc.adaptation.DualAveragingStepSize attribute) (torchtree.inference.hmc.hmc.HMC attribute) invariant (torchtree.evolution.site_model.InvariantSiteModel property) (torchtree.evolution.site_model.UnivariateDiscretizedSiteModel property) InvariantSiteModel (class in torchtree.evolution.site_model) inverse() (torchtree.nf.realnvp.BatchNorm method) (torchtree.nf.realnvp.FlowSequential method) (torchtree.nf.realnvp.LinearMaskedCoupling method) (torchtree.nf.realnvp.RealNVP method) inverse_cdf() (torchtree.evolution.site_model.UnivariateDiscretizedSiteModel method) (torchtree.evolution.site_model.WeibullSiteModel method) inverse_mass_matrix (torchtree.inference.hmc.adaptation.WarmupAdaptation property) InverseGamma (class in torchtree.distributions.inverse_gamma) is_float() (in module torchtree.cli.evolution) iterations (torchtree.inference.hmc.hmc.HMC attribute) (torchtree.inference.mcmc.mcmc.MCMC attribute) (torchtree.optim.optimizer.Optimizer attribute) J jacobian() (torchtree.inference.mcmc.gmrf_block_updating.GMRFPiecewiseCoalescentBlockUpdatingOperator method) JC69 (class in torchtree.evolution.substitution_model.nucleotide) joint (torchtree.inference.hmc.hamiltonian.Hamiltonian attribute) (torchtree.inference.hmc.hmc.HMC attribute) (torchtree.inference.mcmc.mcmc.MCMC attribute) JointDistributionModel (class in torchtree.distributions.joint_distribution) json_factory() (torchtree.core.parameter.Parameter static method) (torchtree.core.parameter.ViewParameter static method) (torchtree.distributions.bayesian_bridge.BayesianBridge static method) (torchtree.distributions.ctmc_scale.CTMCScale static method) (torchtree.distributions.deterministic_normal.DeterministicNormal static method) (torchtree.distributions.distributions.Distribution static method) (torchtree.distributions.scale_mixture.ScaleMixtureNormal static method) (torchtree.evolution.branch_model.SimpleClockModel static method) (torchtree.evolution.tree_model.ReparameterizedTimeTreeModel static method) (torchtree.evolution.tree_model.TimeTreeModel static method) (torchtree.evolution.tree_model.UnRootedTreeModel static method) (torchtree.evolution.tree_model_flexible.FlexibleTimeTreeModel static method) JSONParseError JSONSerializable (class in torchtree.core.serializable) K k (torchtree.evolution.tree_height_transform.DifferenceNodeHeightTransform attribute) kappa (torchtree.evolution.substitution_model.codon.MG94 attribute) (torchtree.evolution.substitution_model.nucleotide.HKY property) kinetic_energy() (torchtree.inference.hmc.hamiltonian.Hamiltonian method) KLpq (class in torchtree.variational.kl) KLpqImportance (class in torchtree.variational.kl) kwargs (torchtree.core.logger.CSV attribute) (torchtree.core.logger.Dumper attribute) (torchtree.core.logger.Logger attribute) (torchtree.core.logger.TreeLogger attribute) (torchtree.distributions.distributions.Distribution attribute) L lambda_ (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) (torchtree.evolution.birth_death.BirthDeath attribute) (torchtree.evolution.birth_death.BirthDeathModel attribute) layers (torchtree.nf.flow.NormalizingFlow attribute) LeapfrogIntegrator (class in torchtree.inference.hmc.integrator) learn() (torchtree.inference.hmc.adaptation.AdaptiveStepSize method) (torchtree.inference.hmc.adaptation.Adaptor method) (torchtree.inference.hmc.adaptation.DualAveragingStepSize method) (torchtree.inference.hmc.adaptation.MassMatrixAdaptor method) (torchtree.inference.hmc.stan_adaptation.StanWindowedAdaptation method) length_of_tensor_in_dict_parameter() (in module torchtree.cli.utils) LG (class in torchtree.evolution.substitution_model.amino_acid) linear_regression() (in module torchtree.evolution.tree_regression) LinearMaskedCoupling (class in torchtree.nf.realnvp) LinearTransform (class in torchtree.distributions.transforms) list_of_float() (in module torchtree.cli.argparse_utils) list_or_int() (in module torchtree.cli.argparse_utils) listeners (torchtree.core.model.Model attribute) (torchtree.core.parameter.ModuleParameter attribute) (torchtree.core.parameter.Parameter attribute) (torchtree.core.parameter.TransformedParameter attribute) (torchtree.core.parameter.ViewParameter attribute) (torchtree.evolution.root_transform.RootParameter attribute) ListParameter (in module torchtree.typing) ListTensor (in module torchtree.typing) load_arguments() (torchtree.cli.plugin.Plugin method) (torchtree.cli.plugin_manager.PluginManager method) load_plugins() (torchtree.cli.plugin_manager.PluginManager method) load_state_dict() (torchtree.inference.hmc.adaptation.AdaptiveStepSize method) (torchtree.inference.hmc.adaptation.Adaptor method) (torchtree.inference.hmc.adaptation.DualAveragingStepSize method) (torchtree.inference.hmc.adaptation.MassMatrixAdaptor method) (torchtree.inference.hmc.integrator.Integrator method) (torchtree.inference.hmc.integrator.LeapfrogIntegrator method) (torchtree.inference.mcmc.mcmc.MCMC method) (torchtree.inference.mcmc.operator.MCMCOperator method) (torchtree.optim.lr_scheduler.Scheduler method) (torchtree.optim.optimizer.Optimizer method) loc (torchtree.distributions.deterministic_normal.DeterministicNormal attribute) (torchtree.distributions.multivariate_normal.MultivariateNormal attribute) (torchtree.distributions.scale_mixture.ScaleMixtureNormal attribute) local_scale (torchtree.distributions.bayesian_bridge.BayesianBridge attribute) (torchtree.distributions.scale_mixture.ScaleMixtureNormal attribute) log() (torchtree.core.logger.ContainerLogger method) (torchtree.core.logger.Logger method) (torchtree.core.logger.LoggerInterface method) (torchtree.core.logger.TreeLogger method) log_abs_det_jacobian() (torchtree.distributions.transforms.ConvexCombinationTransform method) (torchtree.distributions.transforms.CumSumExpTransform method) (torchtree.distributions.transforms.CumSumSoftPlusTransform method) (torchtree.distributions.transforms.CumSumTransform method) (torchtree.distributions.transforms.LogTransform method) (torchtree.distributions.transforms.SoftPlusTransform method) (torchtree.distributions.transforms.TrilExpDiagonalTransform method) (torchtree.evolution.rate_transform.LogDifferenceRateTransform method) (torchtree.evolution.rate_transform.RescaledRateTransform method) (torchtree.evolution.tree_height_transform.DifferenceNodeHeightTransform method) (torchtree.evolution.tree_height_transform.GeneralNodeHeightTransform method) (torchtree.nf.planar.PlanarTransform method) log_gamma (torchtree.nf.realnvp.BatchNorm attribute) log_gamma_one_half (torchtree.distributions.ctmc_scale.CTMCScale attribute) log_p() (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath method) (torchtree.evolution.birth_death.BirthDeath method) log_prob() (torchtree.distributions.deterministic_normal.DeterministicNormal method) (torchtree.distributions.distributions.Distribution method) (torchtree.distributions.distributions.DistributionModel method) (torchtree.distributions.joint_distribution.JointDistributionModel method) (torchtree.distributions.multivariate_normal.MultivariateNormal method) (torchtree.distributions.one_on_x.OneOnX method) (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath method) (torchtree.evolution.birth_death.BirthDeath method) (torchtree.evolution.coalescent.ConstantCoalescent method) (torchtree.evolution.coalescent.ConstantCoalescentIntegrated method) (torchtree.evolution.coalescent.ExponentialCoalescent method) (torchtree.evolution.coalescent.PiecewiseConstantCoalescent method) (torchtree.evolution.coalescent.PiecewiseConstantCoalescentGrid method) (torchtree.evolution.coalescent.PiecewiseExponentialCoalescentGrid method) (torchtree.evolution.coalescent.PiecewiseLinearCoalescentGrid method) (torchtree.evolution.coalescent.SoftPiecewiseConstantCoalescentGrid method) (torchtree.nf.flow.NormalizingFlow method) (torchtree.nf.realnvp.RealNVP method) log_q() (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath method) (torchtree.evolution.birth_death.BirthDeath method) LogDifferenceRateTransform (class in torchtree.evolution.rate_transform) Logger (class in torchtree.core.logger) logger (in module torchtree.cli.advi) (in module torchtree.cli.evolution) LoggerInterface (class in torchtree.core.logger) loggers (torchtree.inference.hmc.hmc.HMC attribute) (torchtree.inference.mcmc.mcmc.MCMC attribute) (torchtree.inference.sampler.Sampler attribute) (torchtree.optim.optimizer.Optimizer attribute) LogNormal (class in torchtree.distributions.log_normal) LogTransform (class in torchtree.distributions.transforms) loss (torchtree.optim.convergence.VariationalConvergence attribute) (torchtree.optim.optimizer.Optimizer attribute) LOWER (torchtree.cli.utils.CONSTRAINT attribute) lp (torchtree.core.model.CallableModel attribute) lp_needs_update (torchtree.core.model.CallableModel attribute) M main() (in module torchtree.cli.cli) (in module torchtree.torchtree) make_unconstrained() (in module torchtree.cli.utils) mapping (torchtree.evolution.substitution_model.general.GeneralNonSymmetricSubstitutionModel attribute) (torchtree.evolution.substitution_model.general.GeneralSymmetricSubstitutionModel attribute) mass_matrix (torchtree.inference.hmc.adaptation.MassMatrixAdaptor property) (torchtree.inference.hmc.adaptation.WarmupAdaptation property) (torchtree.inference.hmc.operator.HMCOperator property) mass_matrix_adaptor (torchtree.inference.hmc.stan_adaptation.StanWindowedAdaptation attribute) MassMatrixAdaptor (class in torchtree.inference.hmc.adaptation) maximize (torchtree.optim.optimizer.Optimizer attribute) maximum_likelihood() (torchtree.evolution.coalescent.AbstractCoalescentDistribution class method) (torchtree.evolution.coalescent.ConstantCoalescent class method) (torchtree.evolution.coalescent.PiecewiseConstantCoalescent class method) MCMC (class in torchtree.inference.mcmc.mcmc) MCMCOperator (class in torchtree.inference.mcmc.operator) mean() (torchtree.ops.welford.WelfordVariance method) MG94 (class in torchtree.evolution.substitution_model.codon) Model (class in torchtree.core.model) model (torchtree.inference.sampler.Sampler attribute) ModelListener (class in torchtree.core.parametric) models() (torchtree.core.model.Model method) module torchtree torchtree.cli torchtree.cli.advi torchtree.cli.argparse_utils torchtree.cli.cli torchtree.cli.evolution torchtree.cli.hmc torchtree.cli.jacobians torchtree.cli.loggers torchtree.cli.map torchtree.cli.mcmc torchtree.cli.operators torchtree.cli.plugin torchtree.cli.plugin_manager torchtree.cli.priors torchtree.cli.utils torchtree.core torchtree.core.abstractparameter torchtree.core.classproperty_decorator torchtree.core.container torchtree.core.identifiable torchtree.core.logger torchtree.core.model torchtree.core.parameter torchtree.core.parameter_encoder torchtree.core.parameter_utils torchtree.core.parametric torchtree.core.runnable torchtree.core.serializable torchtree.core.utils torchtree.distributions torchtree.distributions.bayesian_bridge torchtree.distributions.ctmc_scale torchtree.distributions.deterministic_normal torchtree.distributions.distributions torchtree.distributions.gmrf torchtree.distributions.gmrf_integrated torchtree.distributions.inverse_gamma torchtree.distributions.joint_distribution torchtree.distributions.log_normal torchtree.distributions.multivariate_normal torchtree.distributions.normal torchtree.distributions.one_on_x torchtree.distributions.scale_mixture torchtree.distributions.transforms torchtree.distributions.tree_prior torchtree.evolution torchtree.evolution.alignment torchtree.evolution.attribute_pattern torchtree.evolution.bdsk torchtree.evolution.birth_death torchtree.evolution.branch_model torchtree.evolution.coalescent torchtree.evolution.datatype torchtree.evolution.io torchtree.evolution.poisson_tree_likelihood torchtree.evolution.rate_transform torchtree.evolution.root_transform torchtree.evolution.site_model torchtree.evolution.site_pattern torchtree.evolution.substitution_model torchtree.evolution.substitution_model.abstract torchtree.evolution.substitution_model.amino_acid torchtree.evolution.substitution_model.codon torchtree.evolution.substitution_model.general torchtree.evolution.substitution_model.nucleotide torchtree.evolution.taxa torchtree.evolution.tree_height_transform torchtree.evolution.tree_likelihood torchtree.evolution.tree_model torchtree.evolution.tree_model_flexible torchtree.evolution.tree_regression torchtree.inference torchtree.inference.hmc torchtree.inference.hmc.adaptation torchtree.inference.hmc.hamiltonian torchtree.inference.hmc.hmc torchtree.inference.hmc.integrator torchtree.inference.hmc.operator torchtree.inference.hmc.stan_adaptation torchtree.inference.mcmc torchtree.inference.mcmc.gmrf_block_updating torchtree.inference.mcmc.mcmc torchtree.inference.mcmc.operator torchtree.inference.sampler torchtree.inference.utils torchtree.nf torchtree.nf.energy_functions torchtree.nf.flow torchtree.nf.planar torchtree.nf.realnvp torchtree.nn torchtree.nn.module torchtree.ops torchtree.ops.dual_averaging torchtree.ops.smooth torchtree.ops.welford torchtree.optim torchtree.optim.convergence torchtree.optim.lr_scheduler torchtree.optim.optimizer torchtree.torchtree torchtree.typing torchtree.variational torchtree.variational.chi torchtree.variational.kl torchtree.variational.renyi Module (class in torchtree.nn.module) module (torchtree.core.parameter.ModuleParameter attribute) (torchtree.nn.module.Module property) ModuleParameter (class in torchtree.core.parameter) modules (torchtree.nf.flow.NormalizingFlow attribute) momentum (torchtree.nf.realnvp.BatchNorm attribute) mu (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) (torchtree.evolution.birth_death.BirthDeath attribute) (torchtree.evolution.birth_death.BirthDeathModel attribute) MultivariateNormal (class in torchtree.distributions.multivariate_normal) N n (torchtree.variational.chi.CUBO attribute) name (torchtree.evolution.datatype.CodonDataType attribute) (torchtree.evolution.io.Node attribute) need_update (torchtree.core.parameter.ModuleParameter attribute) (torchtree.core.parameter.TransformedParameter attribute) (torchtree.evolution.root_transform.RootParameter attribute) needs_update (torchtree.evolution.site_model.SiteModel attribute) net (torchtree.nf.realnvp.RealNVP attribute) net_parameters (torchtree.nf.realnvp.RealNVP attribute) newton_raphson() (torchtree.inference.mcmc.gmrf_block_updating.GMRFPiecewiseCoalescentBlockUpdatingOperator method) Node (class in torchtree.evolution.io) node_heights (torchtree.evolution.coalescent.FakeTreeModel property) (torchtree.evolution.tree_model.ReparameterizedTimeTreeModel property) (torchtree.evolution.tree_model.TimeTreeModel property) non_synonymous (torchtree.evolution.substitution_model.codon.MG94 attribute) NonSymmetricSubstitutionModel (class in torchtree.evolution.substitution_model.abstract) norm() (torchtree.evolution.substitution_model.abstract.AbstractSubstitutionModel method) Normal (class in torchtree.distributions.normal) normalize (torchtree.evolution.substitution_model.general.GeneralNonSymmetricSubstitutionModel attribute) NormalizingFlow (class in torchtree.nf.flow) NUCLEOTIDE_AMBIGUITY_STATES (torchtree.evolution.datatype.NucleotideDataType attribute) NUCLEOTIDE_STATES (torchtree.evolution.datatype.NucleotideDataType attribute) NucleotideDataType (class in torchtree.evolution.datatype) NUCLEOTIDES (torchtree.evolution.datatype.NucleotideDataType attribute) num_warmup (torchtree.inference.hmc.stan_adaptation.StanWindowedAdaptation attribute) NUMBER_OF_CODONS (torchtree.evolution.datatype.CodonDataType attribute) O object_hook() (torchtree.core.utils.TensorDecoder method) objs (torchtree.core.logger.CSV attribute) (torchtree.core.logger.Logger attribute) OneOnX (class in torchtree.distributions.one_on_x) Optimizer (class in torchtree.optim.optimizer) optimizer (torchtree.optim.optimizer.Optimizer attribute) OrderedDictType (in module torchtree.typing) origin (torchtree.evolution.bdsk.BDSKModel attribute) (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) (torchtree.evolution.birth_death.BirthDeath attribute) (torchtree.evolution.birth_death.BirthDeathModel attribute) origin_is_root_edge (torchtree.evolution.bdsk.BDSKModel attribute) (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) P p (torchtree.variational.chi.CUBO attribute) (torchtree.variational.kl.ELBO attribute) (torchtree.variational.kl.KLpq attribute) (torchtree.variational.kl.KLpqImportance attribute) (torchtree.variational.kl.SELBO attribute) (torchtree.variational.renyi.VR attribute) p0() (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath method) p_t() (torchtree.evolution.substitution_model.abstract.NonSymmetricSubstitutionModel method) (torchtree.evolution.substitution_model.abstract.SubstitutionModel method) (torchtree.evolution.substitution_model.abstract.SymmetricSubstitutionModel method) (torchtree.evolution.substitution_model.general.EmpiricalSubstitutionModel method) (torchtree.evolution.substitution_model.general.GeneralJC69 method) (torchtree.evolution.substitution_model.nucleotide.JC69 method) p_t_analytical() (torchtree.evolution.substitution_model.nucleotide.HKY method) pack_tensor() (in module torchtree.core.parameter_utils) package_contents() (in module torchtree.core.utils) Parameter (class in torchtree.core.parameter) parameter (torchtree.core.parameter.ViewParameter attribute) Parameter.to() (in module torchtree.core.parameter), [1], [2] ParameterEncoder (class in torchtree.core.parameter_encoder) ParameterListener (class in torchtree.core.parametric) parameters (torchtree.core.logger.Dumper attribute) (torchtree.inference.hmc.hmc.HMC attribute) (torchtree.inference.mcmc.mcmc.MCMC attribute) (torchtree.inference.mcmc.operator.MCMCOperator attribute) (torchtree.optim.optimizer.Optimizer attribute) parameters() (torchtree.core.abstractparameter.AbstractParameter method) (torchtree.core.parameter.ModuleParameter method) (torchtree.core.parameter.TransformedParameter method) (torchtree.core.parametric.Parametric method) (torchtree.evolution.root_transform.RootParameter method) (torchtree.nf.flow.NormalizingFlow method) (torchtree.nf.realnvp.RealNVP method) Parametric (class in torchtree.core.parametric) params() (torchtree.core.container.Container method) parent (torchtree.evolution.io.Node attribute) parse_distribution() (in module torchtree.cli.evolution) parse_taxa() (in module torchtree.evolution.io) parse_translate() (in module torchtree.evolution.io) parse_tree() (in module torchtree.evolution.tree_model) parse_trees() (in module torchtree.evolution.io) partial() (torchtree.evolution.datatype.AminoAcidDataType method) (torchtree.evolution.datatype.CodonDataType method) (torchtree.evolution.datatype.DataType method) (torchtree.evolution.datatype.GeneralDataType method) (torchtree.evolution.datatype.NucleotideDataType method) PiecewiseConstantBirthDeath (class in torchtree.evolution.bdsk) PiecewiseConstantCoalescent (class in torchtree.evolution.coalescent) PiecewiseConstantCoalescentGrid (class in torchtree.evolution.coalescent) PiecewiseConstantCoalescentGridModel (class in torchtree.evolution.coalescent) PiecewiseConstantCoalescentModel (class in torchtree.evolution.coalescent) PiecewiseExponentialCoalescentGrid (class in torchtree.evolution.coalescent) PiecewiseExponentialCoalescentGridModel (class in torchtree.evolution.coalescent) PiecewiseLinearCoalescentGrid (class in torchtree.evolution.coalescent) PiecewiseLinearCoalescentGridModel (class in torchtree.evolution.coalescent) PlanarTransform (class in torchtree.nf.planar) Plugin (class in torchtree.cli.plugin) PLUGIN_MANAGER (in module torchtree.cli) PluginManager (class in torchtree.cli.plugin_manager) plugins() (torchtree.cli.plugin_manager.PluginManager method) PoissonTreeLikelihood (class in torchtree.evolution.poisson_tree_likelihood) postorder (torchtree.evolution.tree_model.AbstractTreeModel property) (torchtree.evolution.tree_model.TreeModel property) potential_energy() (torchtree.inference.hmc.hamiltonian.Hamiltonian method) precision (torchtree.distributions.gmrf.GMRF attribute) precision_matrix() (torchtree.distributions.gmrf.GMRF method) print_graph() (in module torchtree.core.utils) probabilities() (torchtree.evolution.site_model.ConstantSiteModel method) (torchtree.evolution.site_model.InvariantSiteModel method) (torchtree.evolution.site_model.SiteModel method) (torchtree.evolution.site_model.UnivariateDiscretizedSiteModel method) process_all() (torchtree.cli.plugin.Plugin method) process_coalescent() (torchtree.cli.plugin.Plugin method) process_data_coalesent() (in module torchtree.evolution.coalescent) process_object() (in module torchtree.core.utils) process_object_number() (in module torchtree.distributions.bayesian_bridge) process_object_with_key() (in module torchtree.core.utils) process_objects() (in module torchtree.core.utils) process_tree_likelihood() (torchtree.cli.plugin.Plugin method) propose_precision() (torchtree.inference.mcmc.gmrf_block_updating.GMRFPiecewiseCoalescentBlockUpdatingOperator method) psi (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) (torchtree.evolution.birth_death.BirthDeath attribute) (torchtree.evolution.birth_death.BirthDeathModel attribute) Q Q (torchtree.evolution.substitution_model.general.EmpiricalSubstitutionModel attribute) q (torchtree.variational.chi.CUBO attribute) (torchtree.variational.kl.ELBO attribute) (torchtree.variational.kl.KLpq attribute) (torchtree.variational.kl.KLpqImportance attribute) (torchtree.variational.renyi.VR attribute) q() (torchtree.evolution.substitution_model.abstract.SubstitutionModel method) (torchtree.evolution.substitution_model.codon.MG94 method) (torchtree.evolution.substitution_model.general.EmpiricalSubstitutionModel method) (torchtree.evolution.substitution_model.general.GeneralJC69 method) (torchtree.evolution.substitution_model.general.GeneralNonSymmetricSubstitutionModel method) (torchtree.evolution.substitution_model.general.GeneralSymmetricSubstitutionModel method) (torchtree.evolution.substitution_model.nucleotide.GTR method) (torchtree.evolution.substitution_model.nucleotide.HKY method) (torchtree.evolution.substitution_model.nucleotide.JC69 method) R R (torchtree.evolution.bdsk.BDSKModel attribute) random_tree_from_heights() (in module torchtree.evolution.io) rate (torchtree.distributions.inverse_gamma.InverseGamma property) (torchtree.distributions.tree_prior.CompoundGammaDirichletPrior attribute) (torchtree.evolution.root_transform.RootParameter attribute) rates (torchtree.evolution.branch_model.BranchModel property) (torchtree.evolution.branch_model.SimpleClockModel property) (torchtree.evolution.branch_model.StrictClockModel property) (torchtree.evolution.substitution_model.abstract.SubstitutionModel property) (torchtree.evolution.substitution_model.amino_acid.LG property) (torchtree.evolution.substitution_model.amino_acid.WAG property) (torchtree.evolution.substitution_model.codon.MG94 property) (torchtree.evolution.substitution_model.general.GeneralJC69 property) (torchtree.evolution.substitution_model.general.GeneralNonSymmetricSubstitutionModel property) (torchtree.evolution.substitution_model.general.GeneralSymmetricSubstitutionModel property) (torchtree.evolution.substitution_model.nucleotide.GTR property) (torchtree.evolution.substitution_model.nucleotide.HKY property) (torchtree.evolution.substitution_model.nucleotide.JC69 property) rates() (torchtree.evolution.site_model.ConstantSiteModel method) (torchtree.evolution.site_model.InvariantSiteModel method) (torchtree.evolution.site_model.SiteModel method) (torchtree.evolution.site_model.UnivariateDiscretizedSiteModel method) read_dates_from_csv() (in module torchtree.cli.utils) read_fasta_sequences() (in module torchtree.evolution.alignment) read_tree() (in module torchtree.evolution.io) read_tree_and_alignment() (in module torchtree.evolution.io) RealNVP (class in torchtree.nf.realnvp) register_class() (in module torchtree.core.utils) register_model() (torchtree.core.parametric.Parametric method) register_parameter() (torchtree.core.parametric.Parametric method) REGISTERED_CLASSES (in module torchtree.core.utils) reject() (torchtree.inference.mcmc.operator.MCMCOperator method) rel_difference() (torchtree.optim.convergence.StanVariationalConvergence static method) relative_times (torchtree.evolution.bdsk.BDSKModel attribute) (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) removal_probability (torchtree.evolution.bdsk.BDSKModel attribute) (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) remove_comments() (in module torchtree.core.utils) remove_constraints() (in module torchtree.cli.utils) remove_model_listener() (torchtree.core.model.Model method) remove_parameter_listener() (torchtree.core.model.Model method) remove_sample() (torchtree.ops.welford.WelfordVariance method) ReparameterizedTimeTreeModel (class in torchtree.evolution.tree_model) replace_star_with_str() (in module torchtree.core.utils) replace_wildcard_with_str() (in module torchtree.core.utils) requires_grad (torchtree.core.abstractparameter.AbstractParameter property) (torchtree.core.parameter.CatParameter property) (torchtree.core.parameter.ModuleParameter property) (torchtree.core.parameter.Parameter property) (torchtree.core.parameter.TransformedParameter property) (torchtree.core.parameter.ViewParameter property) rescale (torchtree.distributions.gmrf.GMRF attribute) (torchtree.evolution.tree_likelihood.TreeLikelihoodModel attribute) RescaledRateTransform (class in torchtree.evolution.rate_transform) reset() (torchtree.ops.welford.WelfordVariance method) restart() (torchtree.inference.hmc.adaptation.AdaptiveStepSize method) (torchtree.inference.hmc.adaptation.Adaptor method) (torchtree.inference.hmc.adaptation.DualAveragingStepSize method) (torchtree.inference.hmc.adaptation.MassMatrixAdaptor method) (torchtree.inference.hmc.stan_adaptation.StanWindowedAdaptation method) (torchtree.ops.dual_averaging.DualAveraging method) rho (torchtree.evolution.bdsk.BDSKModel attribute) (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) (torchtree.evolution.birth_death.BirthDeath attribute) (torchtree.evolution.birth_death.BirthDeathModel attribute) RootParameter (class in torchtree.evolution.root_transform) rsample() (torchtree.distributions.deterministic_normal.DeterministicNormal method) (torchtree.distributions.distributions.Distribution method) (torchtree.distributions.distributions.DistributionModel method) (torchtree.distributions.joint_distribution.JointDistributionModel method) (torchtree.distributions.multivariate_normal.MultivariateNormal method) (torchtree.evolution.coalescent.ConstantCoalescent method) (torchtree.nf.flow.NormalizingFlow method) (torchtree.nf.realnvp.RealNVP method) run() (torchtree.core.logger.CSV method) (torchtree.core.logger.Dumper method) (torchtree.core.logger.LoggerInterface method) (torchtree.core.runnable.Runnable method) (torchtree.inference.hmc.hmc.HMC method) (torchtree.inference.mcmc.mcmc.MCMC method) (torchtree.inference.sampler.Sampler method) (torchtree.optim.optimizer.Optimizer method) run_tree_regression() (in module torchtree.cli.evolution) Runnable (class in torchtree.core.runnable) S s (torchtree.evolution.bdsk.BDSKModel attribute) s_net (torchtree.nf.realnvp.LinearMaskedCoupling attribute) sample (torchtree.core.logger.ContainerLogger attribute) (torchtree.core.logger.Logger attribute) (torchtree.core.logger.TreeLogger attribute) sample() (torchtree.distributions.deterministic_normal.DeterministicNormal method) (torchtree.distributions.distributions.Distribution method) (torchtree.distributions.distributions.DistributionModel method) (torchtree.distributions.joint_distribution.JointDistributionModel method) (torchtree.distributions.multivariate_normal.MultivariateNormal method) (torchtree.nf.flow.NormalizingFlow method) (torchtree.nf.realnvp.RealNVP method) sample_momentum() (torchtree.inference.hmc.hamiltonian.Hamiltonian method) (torchtree.inference.hmc.hmc.HMC method) sample_shape (torchtree.core.model.Model property) (torchtree.core.parameter.ModuleParameter property) (torchtree.core.parameter.TransformedParameter property) (torchtree.evolution.coalescent.FakeTreeModel property) Sampler (class in torchtree.inference.sampler) samples (torchtree.inference.sampler.Sampler attribute) (torchtree.ops.welford.WelfordVariance attribute) (torchtree.optim.convergence.VariationalConvergence attribute) (torchtree.variational.chi.CUBO attribute) (torchtree.variational.kl.ELBO attribute) (torchtree.variational.kl.KLpq attribute) (torchtree.variational.kl.KLpqImportance attribute) (torchtree.variational.kl.SELBO attribute) (torchtree.variational.renyi.VR attribute) sampling_times (torchtree.evolution.tree_model.TimeTreeModel attribute) save_full_state() (torchtree.inference.mcmc.mcmc.MCMC method) (torchtree.optim.optimizer.Optimizer method) save_parameters() (in module torchtree.core.parameter_utils) scale (torchtree.distributions.bayesian_bridge.BayesianBridge attribute) (torchtree.distributions.deterministic_normal.DeterministicNormal attribute) ScaleMixtureNormal (class in torchtree.distributions.scale_mixture) ScalerOperator (class in torchtree.inference.mcmc.operator) Scheduler (class in torchtree.optim.lr_scheduler) scheduler (torchtree.optim.lr_scheduler.Scheduler attribute) (torchtree.optim.optimizer.Optimizer attribute) score (torchtree.variational.kl.ELBO attribute) SELBO (class in torchtree.variational.kl) Sequence (in module torchtree.evolution.alignment) sequence_size (torchtree.evolution.alignment.Alignment property) set_adaptable_parameter() (torchtree.inference.hmc.operator.HMCOperator method) (torchtree.inference.mcmc.gmrf_block_updating.GMRFPiecewiseCoalescentBlockUpdatingOperator method) (torchtree.inference.mcmc.operator.DirichletOperator method) (torchtree.inference.mcmc.operator.MCMCOperator method) (torchtree.inference.mcmc.operator.ScalerOperator method) (torchtree.inference.mcmc.operator.SlidingWindowOperator method) set_tensor() (in module torchtree.inference.hmc.integrator) setup_dates() (in module torchtree.evolution.tree_model) setup_indexes() (in module torchtree.evolution.tree_model) shape (torchtree.core.abstractparameter.AbstractParameter property) (torchtree.core.parameter.ModuleParameter property) (torchtree.core.parameter.TransformedParameter property) (torchtree.core.parameter.ViewParameter property) (torchtree.distributions.ctmc_scale.CTMCScale attribute) (torchtree.distributions.tree_prior.CompoundGammaDirichletPrior attribute) (torchtree.evolution.site_model.WeibullSiteModel property) shift (torchtree.evolution.root_transform.RootParameter attribute) sign (torchtree.distributions.transforms.CumSumExpTransform attribute) (torchtree.distributions.transforms.CumSumSoftPlusTransform attribute) (torchtree.distributions.transforms.CumSumTransform attribute) (torchtree.distributions.transforms.LogTransform attribute) (torchtree.distributions.transforms.SoftPlusTransform attribute) (torchtree.distributions.transforms.TrilExpDiagonalTransform attribute) (torchtree.evolution.rate_transform.LogDifferenceRateTransform attribute) (torchtree.evolution.rate_transform.RescaledRateTransform attribute) (torchtree.evolution.tree_height_transform.DifferenceNodeHeightTransform attribute) (torchtree.evolution.tree_height_transform.GeneralNodeHeightTransform attribute) SignalHandler (class in torchtree.core.utils) SimpleClockModel (class in torchtree.evolution.branch_model) SIMPLEX (torchtree.cli.utils.CONSTRAINT attribute) site_model (torchtree.evolution.tree_likelihood.TreeLikelihoodModel attribute) site_pattern (torchtree.evolution.tree_likelihood.TreeLikelihoodModel attribute) SiteModel (class in torchtree.evolution.site_model) SitePattern (class in torchtree.evolution.site_pattern) size (torchtree.evolution.datatype.AbstractDataType property) (torchtree.evolution.datatype.DataType property) size() (torchtree.core.parameter.Parameter method) slab (torchtree.distributions.bayesian_bridge.BayesianBridge attribute) (torchtree.distributions.scale_mixture.ScaleMixtureNormal attribute) SlidingWindowOperator (class in torchtree.inference.mcmc.operator) smooth_max() (in module torchtree.ops.smooth) smoothed_acceptance_rate() (torchtree.inference.mcmc.operator.MCMCOperator method) soft_searchsorted() (in module torchtree.ops.smooth) soft_sort() (in module torchtree.ops.smooth) SoftPiecewiseConstantCoalescentGrid (class in torchtree.evolution.coalescent) SoftPlusTransform (class in torchtree.distributions.transforms) sort_indices() (torchtree.evolution.tree_height_transform.GeneralNodeHeightTransform method) split_newick() (in module torchtree.evolution.io) sqrt_mass_matrix (torchtree.inference.hmc.adaptation.WarmupAdaptation property) sqrt_pi (torchtree.evolution.substitution_model.general.EmpiricalSubstitutionModel attribute) sqrt_pi_inv (torchtree.evolution.substitution_model.general.EmpiricalSubstitutionModel attribute) StanVariationalConvergence (class in torchtree.optim.convergence) StanWindowedAdaptation (class in torchtree.inference.hmc.stan_adaptation) start (torchtree.optim.convergence.VariationalConvergence attribute) state_count (torchtree.evolution.datatype.AbstractDataType property) (torchtree.evolution.datatype.DataType property) (torchtree.evolution.substitution_model.general.GeneralJC69 attribute) (torchtree.evolution.substitution_model.general.GeneralNonSymmetricSubstitutionModel attribute) (torchtree.evolution.substitution_model.general.GeneralSymmetricSubstitutionModel attribute) state_dict() (torchtree.inference.hmc.adaptation.Adaptor method) (torchtree.inference.hmc.integrator.Integrator method) (torchtree.inference.mcmc.mcmc.MCMC method) (torchtree.inference.mcmc.operator.MCMCOperator method) (torchtree.optim.lr_scheduler.Scheduler method) (torchtree.optim.optimizer.Optimizer method) states (torchtree.evolution.datatype.AbstractDataType property) (torchtree.evolution.datatype.DataType property) step() (torchtree.inference.mcmc.operator.MCMCOperator method) (torchtree.ops.dual_averaging.DualAveraging method) (torchtree.optim.lr_scheduler.Scheduler method) step_size (torchtree.inference.hmc.adaptation.WarmupAdaptation property) (torchtree.inference.hmc.integrator.LeapfrogIntegrator attribute) step_size_adaptor (torchtree.inference.hmc.stan_adaptation.StanWindowedAdaptation attribute) steps (torchtree.inference.hmc.integrator.LeapfrogIntegrator attribute) stop (torchtree.core.utils.SignalHandler attribute) stop_count (torchtree.evolution.datatype.CodonDataType attribute) str_or_float() (in module torchtree.cli.argparse_utils) StrictClockModel (class in torchtree.evolution.branch_model) string_to_list_index() (in module torchtree.core.utils) subst_model (torchtree.evolution.tree_likelihood.TreeLikelihoodModel attribute) SubstitutionModel (class in torchtree.evolution.substitution_model.abstract) sufficient_statistics() (torchtree.evolution.coalescent.PiecewiseConstantCoalescent method) (torchtree.evolution.coalescent.PiecewiseConstantCoalescentGrid method) sum_log_abs_det_jacobians (torchtree.nf.flow.NormalizingFlow attribute) (torchtree.nf.realnvp.RealNVP attribute) support (torchtree.distributions.inverse_gamma.InverseGamma attribute) (torchtree.distributions.one_on_x.OneOnX attribute) (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) (torchtree.evolution.coalescent.AbstractCoalescentDistribution attribute) (torchtree.evolution.coalescent.ConstantCoalescentIntegrated attribute) (torchtree.evolution.coalescent.ExponentialCoalescent attribute) (torchtree.evolution.coalescent.PiecewiseExponentialCoalescentGrid attribute) (torchtree.evolution.coalescent.PiecewiseLinearCoalescentGrid attribute) survival (torchtree.evolution.bdsk.BDSKModel attribute) (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) (torchtree.evolution.birth_death.BirthDeath attribute) (torchtree.evolution.birth_death.BirthDeathModel attribute) SymmetricSubstitutionModel (class in torchtree.evolution.substitution_model.abstract) synonymous (torchtree.evolution.substitution_model.codon.MG94 attribute) T t_net (torchtree.nf.realnvp.LinearMaskedCoupling attribute) table (torchtree.evolution.datatype.CodonDataType attribute) tag (torchtree.core.model.Model property) target_acceptance_probability (torchtree.inference.hmc.adaptation.AdaptiveStepSize attribute) (torchtree.inference.mcmc.operator.MCMCOperator attribute) Taxa (class in torchtree.evolution.taxa) taxa (torchtree.evolution.alignment.Alignment property) (torchtree.evolution.attribute_pattern.AttributePattern attribute) (torchtree.evolution.tree_model.AbstractTreeModel property) (torchtree.evolution.tree_model.TreeModel property) taxa_count (torchtree.evolution.tree_height_transform.DifferenceNodeHeightTransform attribute) (torchtree.evolution.tree_height_transform.GeneralNodeHeightTransform attribute) (torchtree.evolution.tree_model.AbstractTreeModel attribute) (torchtree.evolution.tree_model.TimeTreeModel attribute) Taxon (class in torchtree.evolution.taxa) temperature (torchtree.evolution.coalescent.PiecewiseConstantCoalescentGridModel attribute) (torchtree.evolution.coalescent.SoftPiecewiseConstantCoalescentGrid attribute) tensor (torchtree.core.abstractparameter.AbstractParameter property) (torchtree.core.parameter.CatParameter property) (torchtree.core.parameter.ModuleParameter property) (torchtree.core.parameter.Parameter property) (torchtree.core.parameter.TransformedParameter property) (torchtree.core.parameter.ViewParameter property) (torchtree.evolution.root_transform.RootParameter property) tensor_rand() (in module torchtree.core.utils) TensorDecoder (class in torchtree.core.utils) TensorEncoder (class in torchtree.core.utils) theta (torchtree.evolution.coalescent.AbstractCoalescentDistribution attribute) (torchtree.evolution.coalescent.AbstractCoalescentModel attribute) (torchtree.evolution.coalescent.ExponentialCoalescent attribute) (torchtree.evolution.coalescent.PiecewiseExponentialCoalescentGrid attribute) (torchtree.evolution.coalescent.PiecewiseLinearCoalescentGrid attribute) threshold (torchtree.evolution.tree_likelihood.TreeLikelihoodModel attribute) times (torchtree.evolution.bdsk.BDSKModel attribute) (torchtree.evolution.bdsk.PiecewiseConstantBirthDeath attribute) TimeTreeModel (class in torchtree.evolution.tree_model) to() (torchtree.core.abstractparameter.Device method) (torchtree.core.model.Model method) (torchtree.core.parameter.CatParameter method) (torchtree.core.parameter.ModuleParameter method) (torchtree.core.parameter.Parameter method) (torchtree.core.parameter.TransformedParameter method) (torchtree.core.parameter.ViewParameter method) (torchtree.distributions.ctmc_scale.CTMCScale method) (torchtree.evolution.site_model.ConstantSiteModel method) (torchtree.evolution.site_model.InvariantSiteModel method) (torchtree.evolution.site_model.UnivariateDiscretizedSiteModel method) (torchtree.nf.flow.NormalizingFlow method) (torchtree.nn.module.Module method) to_nexus() (in module torchtree.evolution.io) tol_rel_obj (torchtree.optim.convergence.StanVariationalConvergence attribute) torchtree module torchtree.cli module torchtree.cli.advi module torchtree.cli.argparse_utils module torchtree.cli.cli module torchtree.cli.evolution module torchtree.cli.hmc module torchtree.cli.jacobians module torchtree.cli.loggers module torchtree.cli.map module torchtree.cli.mcmc module torchtree.cli.operators module torchtree.cli.plugin module torchtree.cli.plugin_manager module torchtree.cli.priors module torchtree.cli.utils module torchtree.core module torchtree.core.abstractparameter module torchtree.core.classproperty_decorator module torchtree.core.container module torchtree.core.identifiable module torchtree.core.logger module torchtree.core.model module torchtree.core.parameter module torchtree.core.parameter_encoder module torchtree.core.parameter_utils module torchtree.core.parametric module torchtree.core.runnable module torchtree.core.serializable module torchtree.core.utils module torchtree.distributions module torchtree.distributions.bayesian_bridge module torchtree.distributions.ctmc_scale module torchtree.distributions.deterministic_normal module torchtree.distributions.distributions module torchtree.distributions.gmrf module torchtree.distributions.gmrf_integrated module torchtree.distributions.inverse_gamma module torchtree.distributions.joint_distribution module torchtree.distributions.log_normal module torchtree.distributions.multivariate_normal module torchtree.distributions.normal module torchtree.distributions.one_on_x module torchtree.distributions.scale_mixture module torchtree.distributions.transforms module torchtree.distributions.tree_prior module torchtree.evolution module torchtree.evolution.alignment module torchtree.evolution.attribute_pattern module torchtree.evolution.bdsk module torchtree.evolution.birth_death module torchtree.evolution.branch_model module torchtree.evolution.coalescent module torchtree.evolution.datatype module torchtree.evolution.io module torchtree.evolution.poisson_tree_likelihood module torchtree.evolution.rate_transform module torchtree.evolution.root_transform module torchtree.evolution.site_model module torchtree.evolution.site_pattern module torchtree.evolution.substitution_model module torchtree.evolution.substitution_model.abstract module torchtree.evolution.substitution_model.amino_acid module torchtree.evolution.substitution_model.codon module torchtree.evolution.substitution_model.general module torchtree.evolution.substitution_model.nucleotide module torchtree.evolution.taxa module torchtree.evolution.tree_height_transform module torchtree.evolution.tree_likelihood module torchtree.evolution.tree_model module torchtree.evolution.tree_model_flexible module torchtree.evolution.tree_regression module torchtree.inference module torchtree.inference.hmc module torchtree.inference.hmc.adaptation module torchtree.inference.hmc.hamiltonian module torchtree.inference.hmc.hmc module torchtree.inference.hmc.integrator module torchtree.inference.hmc.operator module torchtree.inference.hmc.stan_adaptation module torchtree.inference.mcmc module torchtree.inference.mcmc.gmrf_block_updating module torchtree.inference.mcmc.mcmc module torchtree.inference.mcmc.operator module torchtree.inference.sampler module torchtree.inference.utils module torchtree.nf module torchtree.nf.energy_functions module torchtree.nf.flow module torchtree.nf.planar module torchtree.nf.realnvp module torchtree.nn module torchtree.nn.module module torchtree.ops module torchtree.ops.dual_averaging module torchtree.ops.smooth module torchtree.ops.welford module torchtree.optim module torchtree.optim.convergence module torchtree.optim.lr_scheduler module torchtree.optim.optimizer module torchtree.torchtree module torchtree.typing module torchtree.variational module torchtree.variational.chi module torchtree.variational.kl module torchtree.variational.renyi module transform (torchtree.core.parameter.TransformedParameter attribute) transform() (torchtree.evolution.root_transform.RootParameter method) TransformedParameter (class in torchtree.core.parameter) transitions (torchtree.evolution.substitution_model.codon.MG94 attribute) tree (torchtree.evolution.branch_model.AbstractClockModel attribute) (torchtree.evolution.tree_height_transform.DifferenceNodeHeightTransform attribute) (torchtree.evolution.tree_height_transform.GeneralNodeHeightTransform attribute) (torchtree.evolution.tree_model.AbstractTreeModel attribute) tree_model (torchtree.core.logger.TreeLogger attribute) (torchtree.distributions.ctmc_scale.CTMCScale attribute) (torchtree.distributions.gmrf.GMRF attribute) (torchtree.distributions.gmrf_integrated.GMRFGammaIntegrated attribute) (torchtree.distributions.tree_prior.CompoundGammaDirichletPrior attribute) (torchtree.evolution.bdsk.BDSKModel attribute) (torchtree.evolution.birth_death.BirthDeathModel attribute) (torchtree.evolution.coalescent.AbstractCoalescentModel attribute) (torchtree.evolution.coalescent.ConstantCoalescentIntegratedModel attribute) (torchtree.evolution.poisson_tree_likelihood.PoissonTreeLikelihood attribute) (torchtree.evolution.tree_likelihood.TreeLikelihoodModel attribute) TreeLikelihoodModel (class in torchtree.evolution.tree_likelihood) TreeLogger (class in torchtree.core.logger) TreeModel (class in torchtree.evolution.tree_model) TrilExpDiagonalTransform (class in torchtree.distributions.transforms) triplets (torchtree.evolution.datatype.CodonDataType attribute) tune() (torchtree.inference.hmc.operator.HMCOperator method) (torchtree.inference.mcmc.operator.MCMCOperator method) tuning_parameter (torchtree.inference.hmc.operator.HMCOperator property) (torchtree.inference.mcmc.gmrf_block_updating.GMRFPiecewiseCoalescentBlockUpdatingOperator property) (torchtree.inference.mcmc.operator.DirichletOperator property) (torchtree.inference.mcmc.operator.MCMCOperator property) (torchtree.inference.mcmc.operator.ScalerOperator property) (torchtree.inference.mcmc.operator.SlidingWindowOperator property) U u (torchtree.nf.planar.PlanarTransform attribute) u_hat() (torchtree.nf.planar.PlanarTransform method) UnivariateDiscretizedSiteModel (class in torchtree.evolution.site_model) UnRootedTreeModel (class in torchtree.evolution.tree_model) update() (torchtree.core.parameter.CatParameter method) update_bounds() (torchtree.evolution.tree_height_transform.GeneralNodeHeightTransform method) update_leaf_heights() (torchtree.evolution.tree_model.TimeTreeModel method) update_mass_matrices() (torchtree.inference.hmc.operator.HMCOperator method) update_node_heights() (torchtree.evolution.tree_model.ReparameterizedTimeTreeModel method) update_parameters() (in module torchtree.core.utils) update_rates() (torchtree.evolution.site_model.UnivariateDiscretizedSiteModel method) update_rates_probs() (torchtree.evolution.site_model.InvariantSiteModel method) update_traversals() (torchtree.evolution.tree_model.AbstractTreeModel method) (torchtree.evolution.tree_model.TimeTreeModel method) UPPER (torchtree.cli.utils.CONSTRAINT attribute) use_tip_states (torchtree.evolution.tree_likelihood.TreeLikelihoodModel attribute) V validate() (in module torchtree.core.utils) variance() (torchtree.ops.welford.WelfordVariance method) variance_estimator (torchtree.inference.hmc.adaptation.MassMatrixAdaptor attribute) variance_estimator2 (torchtree.inference.hmc.adaptation.MassMatrixAdaptor attribute) VariationalConvergence (class in torchtree.optim.convergence) ViewParameter (class in torchtree.core.parameter) VR (class in torchtree.variational.renyi) W w (torchtree.nf.planar.PlanarTransform attribute) w1() (in module torchtree.nf.energy_functions) w2() (in module torchtree.nf.energy_functions) w3() (in module torchtree.nf.energy_functions) WAG (class in torchtree.evolution.substitution_model.amino_acid) warmup_adaptor (torchtree.inference.hmc.hmc.HMC attribute) WarmupAdaptation (class in torchtree.inference.hmc.adaptation) WeibullSiteModel (class in torchtree.evolution.site_model) weight (torchtree.distributions.transforms.LinearTransform attribute) (torchtree.inference.mcmc.operator.MCMCOperator attribute) weights (torchtree.distributions.gmrf.GMRF attribute) (torchtree.variational.kl.SELBO attribute) WelfordVariance (class in torchtree.ops.welford) wrapper() (torchtree.core.utils.AlternativeAttributeError class method) write_newick() (torchtree.evolution.tree_model.AbstractTreeModel method) (torchtree.evolution.tree_model.TreeModel method) writer (torchtree.core.logger.Logger attribute) X x (torchtree.distributions.bayesian_bridge.BayesianBridge attribute) (torchtree.distributions.ctmc_scale.CTMCScale attribute) (torchtree.distributions.scale_mixture.ScaleMixtureNormal attribute) (torchtree.nf.energy_functions.EnergyFunctionModel attribute) (torchtree.nf.flow.NormalizingFlow attribute) (torchtree.nf.realnvp.RealNVP attribute) (torchtree.nn.module.Module attribute) (torchtree.ops.dual_averaging.DualAveraging attribute) Z zero_or_path() (in module torchtree.cli.argparse_utils)