phylojunction package
Subpackages
- phylojunction.calculation package
- Submodules
- phylojunction.calculation.discrete_sse module
DiscreteStateDependentParameterDiscreteStateDependentParameterManagerDiscreteStateDependentParameterManager.epsilonDiscreteStateDependentParameterManager.matrix_state_dep_paramsDiscreteStateDependentParameterManager.n_slices_to_ignoreDiscreteStateDependentParameterManager.param_typeDiscreteStateDependentParameterManager.seed_ageDiscreteStateDependentParameterManager.slice_age_endsDiscreteStateDependentParameterManager.slice_t_endsDiscreteStateDependentParameterManager.state_dep_params_at_time()DiscreteStateDependentParameterManager.state_dep_params_dict
DiscreteStateDependentParameterTypeDiscreteStateDependentProbabilityDiscreteStateDependentProbabilityHandlerDiscreteStateDependentProbabilityHandler.n_time_slicesDiscreteStateDependentProbabilityHandler.randomly_decide_taxon_sampling_at_time_at_state()DiscreteStateDependentProbabilityHandler.seed_ageDiscreteStateDependentProbabilityHandler.slice_age_endsDiscreteStateDependentProbabilityHandler.slice_t_endsDiscreteStateDependentProbabilityHandler.state_countDiscreteStateDependentProbabilityHandler.state_dep_prob_managerDiscreteStateDependentProbabilityHandler.str_representation
DiscreteStateDependentRateMacroevolEventMacroevolEventHandlerMacroevolEventHandler.n_time_slicesMacroevolEventHandler.sample_event_sse_rate_param()MacroevolEventHandler.seed_ageMacroevolEventHandler.slice_age_endsMacroevolEventHandler.slice_t_endsMacroevolEventHandler.sse_rate_managerMacroevolEventHandler.state_countMacroevolEventHandler.str_representationMacroevolEventHandler.total_rate()
SSEStashStateIntoPatternConverter
- phylojunction.calculation.math_utils module
- Module contents
- phylojunction.data package
- Submodules
- phylojunction.data.attribute_transition module
AttributeTransitionAttributeTransition.ageAttributeTransition.at_speciationAttributeTransition.attr_labelAttributeTransition.from_stateAttributeTransition.global_timeAttributeTransition.str_representationAttributeTransition.subtending_or_speciating_node_labelAttributeTransition.to_stateAttributeTransition.to_state2AttributeTransition.update_daughter_members()
- phylojunction.data.sampled_ancestor module
- phylojunction.data.tree module
AnnotatedTreeAnnotatedTree.alternative_root_labelAnnotatedTree.at_dictAnnotatedTree.brosc_nodeAnnotatedTree.clado_at_dictAnnotatedTree.condition_on_obs_both_sides_rootAnnotatedTree.epsilonAnnotatedTree.extant_sampled_terminal_nodes_labelsAnnotatedTree.extant_terminal_nodes_labelsAnnotatedTree.extant_terminal_sampled_state_count_dictAnnotatedTree.extant_terminal_state_count_dictAnnotatedTree.extinct_terminal_nodes_labelsAnnotatedTree.extinct_terminal_state_count_dictAnnotatedTree.extract_reconstructed_tree()AnnotatedTree.get_stats_dict()AnnotatedTree.get_taxon_states_str()AnnotatedTree.is_extant_or_sa_on_both_sides_complete_tr_root()AnnotatedTree.max_ageAnnotatedTree.n_extant_sampled_terminal_nodesAnnotatedTree.n_extant_terminal_nodesAnnotatedTree.n_extinct_sampled_terminal_nodesAnnotatedTree.n_extinct_terminal_nodesAnnotatedTree.n_sa_nodesAnnotatedTree.node_ages_dictAnnotatedTree.node_attr_dictAnnotatedTree.node_heights_dictAnnotatedTree.origin_ageAnnotatedTree.origin_edge_lengthAnnotatedTree.origin_nodeAnnotatedTree.plot_node()AnnotatedTree.populate_nd_attr_dict()AnnotatedTree.rec_node_ages_dictAnnotatedTree.rec_node_heights_dictAnnotatedTree.rec_str()AnnotatedTree.rec_tr_at_dictAnnotatedTree.rec_tr_clado_at_dictAnnotatedTree.rec_tr_root_ageAnnotatedTree.rec_tr_root_nodeAnnotatedTree.rec_tr_sa_lineage_dictAnnotatedTree.root_ageAnnotatedTree.root_nodeAnnotatedTree.sa_lineage_dictAnnotatedTree.sa_obs_nodes_labelsAnnotatedTree.seed_ageAnnotatedTree.slice_age_endsAnnotatedTree.slice_t_endsAnnotatedTree.state_countAnnotatedTree.state_count_dictAnnotatedTree.treeAnnotatedTree.tree_diedAnnotatedTree.tree_invalidAnnotatedTree.tree_read_as_newickAnnotatedTree.tree_reconstructedAnnotatedTree.update_rec_tr_at_dict()AnnotatedTree.update_rec_tr_sa_lineage_dict()AnnotatedTree.with_origin
get_color_map()get_node_name()get_x_coord_from_nd_heights()get_y_coord_from_n_obs_nodes()pj_get_name_mrca_obs_terminals()plot_ann_tree()
- Module contents
- phylojunction.distribution package
- Submodules
- phylojunction.distribution.dn_discrete_sse module
DnSSEDnSSE.DN_NAMEDnSSE.abort_at_alive_countDnSSE.condition_on_obs_both_sides_rootDnSSE.condition_on_speciationDnSSE.condition_on_survivalDnSSE.debugDnSSE.epsilonDnSSE.eventsDnSSE.generate()DnSSE.get_rev_inference_spec_info()DnSSE.infoDnSSE.init_check_vectorize_sample_size()DnSSE.max_n_failed_attemptsDnSSE.max_rec_taxaDnSSE.min_rec_taxaDnSSE.n_simDnSSE.n_time_slicesDnSSE.prob_handlerDnSSE.rng_seedDnSSE.root_is_bornDnSSE.runtime_limitDnSSE.seed_ageDnSSE.simulate()DnSSE.slice_t_endsDnSSE.sse_stashDnSSE.start_statesDnSSE.state_countDnSSE.stopDnSSE.stop_valDnSSE.with_origin
- phylojunction.distribution.dn_parametric module
DnExponentialDnExponential.DN_NAMEDnExponential.draw_exp()DnExponential.exp_rate_parameterizationDnExponential.exp_scale_or_rate_listDnExponential.generate()DnExponential.get_rev_inference_spec_info()DnExponential.init_check_vectorize_sample_size()DnExponential.param_dictDnExponential.parent_node_trackerDnExponential.vectorized_params
DnGammaDnGamma.DN_NAMEDnGamma.draw_gamma()DnGamma.gamma_rate_parameterizationDnGamma.gamma_scale_or_rate_param_listDnGamma.gamma_shape_param_listDnGamma.generate()DnGamma.get_rev_inference_spec_info()DnGamma.init_check_vectorize_sample_size()DnGamma.param_dictDnGamma.parent_node_trackerDnGamma.vectorized_params
DnLogNormalDnLogNormal.DN_NAMEDnLogNormal.draw_ln()DnLogNormal.generate()DnLogNormal.get_rev_inference_spec_info()DnLogNormal.init_check_vectorize_sample_size()DnLogNormal.ln_log_spaceDnLogNormal.ln_mean_listDnLogNormal.ln_sd_listDnLogNormal.param_dictDnLogNormal.parent_node_trackerDnLogNormal.vectorized_params
DnNormalDnUnif
- Module contents
- phylojunction.inference package
- phylojunction.interface package
- Subpackages
- phylojunction.interface.cmdbox package
- phylojunction.interface.grammar package
- Submodules
- phylojunction.interface.grammar.ct_fn_grammar module
- phylojunction.interface.grammar.ct_fn_treereader_makers module
- phylojunction.interface.grammar.det_fn_discrete_sse_makers module
- phylojunction.interface.grammar.det_fn_grammar module
- phylojunction.interface.grammar.det_fn_map_attribute module
- phylojunction.interface.grammar.dn_discrete_sse_makers module
- phylojunction.interface.grammar.dn_grammar module
- Module contents
- Submodules
- phylojunction.interface.pj_sandbox module
- Module contents
- Subpackages
- phylojunction.pgm package
- Submodules
- phylojunction.pgm.pgm module
ConstantFnDeterministicNodeDAGDirectedAcyclicGraphDirectedAcyclicGraph.add_node()DirectedAcyclicGraph.get_display_str_by_name()DirectedAcyclicGraph.get_node_dag_by_name()DirectedAcyclicGraph.get_sorted_node_dag_list()DirectedAcyclicGraph.n_nodesDirectedAcyclicGraph.name_node_dictDirectedAcyclicGraph.node_val_dictDirectedAcyclicGraph.random_seedDirectedAcyclicGraph.sample_size
DistrForSamplingNodeDAGStochasticNodeDAGValueGeneratorabstract_attribute()extract_vals_as_str_from_node_dag()extract_value_from_dagnodes()plot_blank()plot_node_histogram()
- Module contents
- phylojunction.plotting package
- phylojunction.readwrite package
- phylojunction.utility package
- Submodules
- phylojunction.utility.exception_classes module
AnnotatedTreeIncorrectAnnotationErrorAnnotatedTreeMissingNodeNameAnnotatedTreeMisspecErrorAnnotatedTreeNodeMissingAttrErrorDAGCannotAddNodeErrorDAGCannotInitializeDimensionalityErrorDimensionalityWarningFunctionArgsMismatchErrorGenerateFailErrorIncorrectDimensionErrorInexistentVariableErrorInvalidMCMCChainLengthMaxNFailedAttemptsLimitMissingColumnNameNoPlatingAllowedErrorNodeDAGStatCantFloatErrorNodeInferenceDimensionalityErrorNotBetweenZeroAndOneErrorObjInitIncorrectDimensionErrorObjInitInvalidArgErrorObjInitMissingParameterErrorObjInitMissingStateDependentParameterErrorObjInitRepeatedStateDependentParameterErrorObjInitRequireNonZeroStateDependentParameterErrorObjInitRequireSameParameterTypeErrorPJCLIInvalidInputErrorPJCLISampleOutOfRangeErrorPJIOFileDoesNotExistErrorParseCtFnInitFailErrorParseDetFnInitFailErrorParseDnInitFailErrorParseFunctionArgErrorParseInvalidArgumentErrorParseInvalidNewickStringErrorParseMissingArgumentErrorParseMissingParameterErrorParseMissingSpecificationErrorParseMutuallyExclusiveParametersErrorParseNotAParameterErrorParsePathDoesNotExistErrorParseRequireIntegerErrorParseRequireNumericErrorParseRequirePositiveIntegerErrorParseRequireSingleValueErrorReplicateNumberErrorRunTimeLimitSSEStashMisspecScriptSyntaxErrorStateDependentParameterMisspecVariableAssignmentErrorVariableMisspec
- phylojunction.utility.helper_functions module
- Module contents