Index

A

abort_at_alive_count (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) abstract_attribute() (in module phylojunction.pgm.pgm) add_node() (phylojunction.pgm.pgm.DirectedAcyclicGraph method) add_within_hpd_col() (in module phylojunction.plotting.pj_organize) age (phylojunction.data.attribute_transition.AttributeTransition attribute) (phylojunction.data.sampled_ancestor.SampledAncestor attribute) alternative_root_label (phylojunction.data.tree.AnnotatedTree attribute) ANAGENETIC_TRANSITION (phylojunction.calculation.discrete_sse.MacroevolEvent attribute) ANCESTOR_SAMPLING (phylojunction.calculation.discrete_sse.MacroevolEvent attribute) AnnotatedTree (class in phylojunction.data.tree) AnnotatedTreeIncorrectAnnotationError

AnnotatedTreeMissingNodeName AnnotatedTreeMisspecError AnnotatedTreeNodeMissingAttrError arriving_state (phylojunction.calculation.discrete_sse.DiscreteStateDependentRate attribute) ASYM_SPECIATION (phylojunction.calculation.discrete_sse.MacroevolEvent attribute) at_dict (phylojunction.data.tree.AnnotatedTree attribute) at_least (phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError attribute) at_speciation (phylojunction.data.attribute_transition.AttributeTransition attribute) attr_label (phylojunction.data.attribute_transition.AttributeTransition attribute) AttributeTransition (class in phylojunction.data.attribute_transition) autovivify() (in module phylojunction.utility.helper_functions)

B

BaseEnum (class in phylojunction.calculation.math_utils)

brosc_node (phylojunction.data.tree.AnnotatedTree attribute) BW_SPECIATION (phylojunction.calculation.discrete_sse.MacroevolEvent attribute)

C

call_order_idx (phylojunction.pgm.pgm.NodeDAG attribute) check_and_vectorize_if_must() (in module phylojunction.utility.helper_functions) clado_at_dict (phylojunction.data.tree.AnnotatedTree attribute) cmd_line (phylojunction.utility.exception_classes.ScriptSyntaxError attribute) cmdline2dag() (in module phylojunction.interface.cmdbox.cmd_parse) condition_on_obs_both_sides_root (phylojunction.data.tree.AnnotatedTree attribute) (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) condition_on_speciation (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) condition_on_survival (phylojunction.distribution.dn_discrete_sse.DnSSE attribute)

constant_fn (phylojunction.pgm.pgm.StochasticNodeDAG attribute) ConstantFn (class in phylojunction.pgm.pgm) container_name (phylojunction.utility.exception_classes.IncorrectDimensionError attribute) create_ct_fn_obj() (phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar class method) create_det_fn_obj() (phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar class method) create_dn_obj() (phylojunction.interface.grammar.dn_grammar.PJDnGrammar class method) create_str_defaultdict() (in module phylojunction.utility.helper_functions) ct_fn_grammar_dict (phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar attribute) CT_FN_NAME (phylojunction.pgm.pgm.ConstantFn property) ct_fn_name (phylojunction.utility.exception_classes.ParseCtFnInitFailError attribute)

D

dag_obj_to_rev_inference_spec() (in module phylojunction.inference.revbayes.rb_inference) DAGCannotAddNodeError DAGCannotInitialize debug (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) departing_state (phylojunction.calculation.discrete_sse.DiscreteStateDependentRate attribute) det_fn_grammar_dict (phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar attribute) det_fn_name (phylojunction.utility.exception_classes.ParseDetFnInitFailError attribute) det_name (phylojunction.utility.exception_classes.NoPlatingAllowedError attribute) DeterministicNodeDAG (class in phylojunction.pgm.pgm) DimensionalityError DimensionalityWarning DirectedAcyclicGraph (class in phylojunction.pgm.pgm) DiscreteStateDependentParameter (class in phylojunction.calculation.discrete_sse) DiscreteStateDependentParameterManager (class in phylojunction.calculation.discrete_sse) DiscreteStateDependentParameterType (class in phylojunction.calculation.discrete_sse) DiscreteStateDependentProbability (class in phylojunction.calculation.discrete_sse) DiscreteStateDependentProbabilityHandler (class in phylojunction.calculation.discrete_sse) DiscreteStateDependentRate (class in phylojunction.calculation.discrete_sse) DistrForSampling (class in phylojunction.pgm.pgm) dn_grammar_dict (phylojunction.interface.grammar.dn_grammar.PJDnGrammar attribute) DN_NAME (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) (phylojunction.distribution.dn_parametric.DnExponential attribute) (phylojunction.distribution.dn_parametric.DnGamma attribute) (phylojunction.distribution.dn_parametric.DnLogNormal attribute) (phylojunction.distribution.dn_parametric.DnNormal attribute) (phylojunction.distribution.dn_parametric.DnUnif attribute) (phylojunction.pgm.pgm.DistrForSampling property)

dn_name (phylojunction.utility.exception_classes.DimensionalityError attribute) (phylojunction.utility.exception_classes.DimensionalityWarning attribute) (phylojunction.utility.exception_classes.ParseDnInitFailError attribute) DnExponential (class in phylojunction.distribution.dn_parametric) DnGamma (class in phylojunction.distribution.dn_parametric) DnLogNormal (class in phylojunction.distribution.dn_parametric) DnNormal (class in phylojunction.distribution.dn_parametric) DnSSE (class in phylojunction.distribution.dn_discrete_sse) DnUnif (class in phylojunction.distribution.dn_parametric) draw_exp() (phylojunction.distribution.dn_parametric.DnExponential static method) draw_gamma() (phylojunction.distribution.dn_parametric.DnGamma static method) draw_ln() (phylojunction.distribution.dn_parametric.DnLogNormal static method) draw_normal() (phylojunction.distribution.dn_parametric.DnNormal static method) draw_unif() (phylojunction.distribution.dn_parametric.DnUnif static method) dump_pgm_data() (in module phylojunction.readwrite.pj_write) dump_serialized_pgm() (in module phylojunction.readwrite.pj_write) dump_trees_rb_smap_dfs() (in module phylojunction.readwrite.pj_write)

E

epoch_idx (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameter attribute) epsilon (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager attribute) (phylojunction.data.tree.AnnotatedTree attribute) (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) event (phylojunction.calculation.discrete_sse.DiscreteStateDependentRate attribute) events (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) exp_extant_count_bd() (in module phylojunction.calculation.math_utils) exp_len (phylojunction.utility.exception_classes.IncorrectDimensionError attribute) (phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError attribute) exp_rate_parameterization (phylojunction.distribution.dn_parametric.DnExponential attribute) exp_root_height_yule_ntaxa() (in module phylojunction.calculation.math_utils)

exp_scale_or_rate_list (phylojunction.distribution.dn_parametric.DnExponential attribute) EXPONENTIAL (phylojunction.calculation.math_utils.ParametricDistribution attribute) extant_sampled_terminal_nodes_labels (phylojunction.data.tree.AnnotatedTree attribute) extant_terminal_nodes_labels (phylojunction.data.tree.AnnotatedTree attribute) extant_terminal_sampled_state_count_dict (phylojunction.data.tree.AnnotatedTree attribute) extant_terminal_state_count_dict (phylojunction.data.tree.AnnotatedTree attribute) extinct_terminal_nodes_labels (phylojunction.data.tree.AnnotatedTree attribute) extinct_terminal_state_count_dict (phylojunction.data.tree.AnnotatedTree attribute) EXTINCTION (phylojunction.calculation.discrete_sse.MacroevolEvent attribute) extract_reconstructed_tree() (phylojunction.data.tree.AnnotatedTree method) extract_vals_as_str_from_node_dag() (in module phylojunction.pgm.pgm) extract_value_from_dagnodes() (in module phylojunction.pgm.pgm)

F

fn_name (phylojunction.utility.exception_classes.FunctionArgsMismatchError attribute)

from_state (phylojunction.data.attribute_transition.AttributeTransition attribute) FunctionArgsMismatchError

G

GAMMA (phylojunction.calculation.math_utils.ParametricDistribution attribute) gamma_rate_parameterization (phylojunction.distribution.dn_parametric.DnGamma attribute) gamma_scale_or_rate_param_list (phylojunction.distribution.dn_parametric.DnGamma attribute) gamma_shape_param_list (phylojunction.distribution.dn_parametric.DnGamma attribute) generate() (phylojunction.distribution.dn_discrete_sse.DnSSE method) (phylojunction.distribution.dn_parametric.DnExponential method) (phylojunction.distribution.dn_parametric.DnGamma method) (phylojunction.distribution.dn_parametric.DnLogNormal method) (phylojunction.distribution.dn_parametric.DnNormal method) (phylojunction.distribution.dn_parametric.DnUnif method) (phylojunction.pgm.pgm.ValueGenerator method) generate_value() (phylojunction.pgm.pgm.StochasticNodeDAG method) GenerateFailError get_color_map() (in module phylojunction.data.tree) get_covg() (in module phylojunction.utility.helper_functions) get_display_str_by_name() (phylojunction.pgm.pgm.DirectedAcyclicGraph method) get_ellapsed_time_in_seconds() (in module phylojunction.utility.helper_functions) get_exponential_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric) get_gamma_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric) get_ln_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric) get_mcmc_logging_spec_list() (in module phylojunction.inference.revbayes.rb_inference) get_meh() (phylojunction.calculation.discrete_sse.SSEStash method) get_node_dag_by_name() (phylojunction.pgm.pgm.DirectedAcyclicGraph method) get_node_name() (in module phylojunction.data.tree) get_node_stats_str() (phylojunction.pgm.pgm.DeterministicNodeDAG method) (phylojunction.pgm.pgm.NodeDAG method) (phylojunction.pgm.pgm.StochasticNodeDAG method)

get_normal_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric) get_prob_handler() (phylojunction.calculation.discrete_sse.SSEStash method) get_rev_inference_spec_info() (phylojunction.distribution.dn_discrete_sse.DnSSE method) (phylojunction.distribution.dn_parametric.DnExponential method) (phylojunction.distribution.dn_parametric.DnGamma method) (phylojunction.distribution.dn_parametric.DnLogNormal method) (phylojunction.distribution.dn_parametric.DnNormal method) (phylojunction.distribution.dn_parametric.DnUnif method) (phylojunction.pgm.pgm.ValueGenerator method) get_rev_str_from_dn_parametric_obj() (in module phylojunction.inference.revbayes.rb_dn_parametric) get_sorted_node_dag_list() (phylojunction.pgm.pgm.DirectedAcyclicGraph method) get_start2end_str() (phylojunction.pgm.pgm.NodeDAG method) get_stats_dict() (phylojunction.data.tree.AnnotatedTree method) get_taxon_states_str() (phylojunction.data.tree.AnnotatedTree method) get_unif_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric) get_write_inference_rev_scripts() (in module phylojunction.readwrite.pj_write) get_x_coord_from_nd_heights() (in module phylojunction.data.tree) get_y_coord_from_n_obs_nodes() (in module phylojunction.data.tree) global_time (phylojunction.data.attribute_transition.AttributeTransition attribute) (phylojunction.data.sampled_ancestor.SampledAncestor attribute) grammar_check() (phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar class method) (phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar class method) (phylojunction.interface.grammar.dn_grammar.PJDnGrammar class method)

I

IncorrectDimensionError InexistentVariableError info (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) init_check_vectorize_sample_size() (phylojunction.distribution.dn_discrete_sse.DnSSE method) (phylojunction.distribution.dn_parametric.DnExponential method) (phylojunction.distribution.dn_parametric.DnGamma method) (phylojunction.distribution.dn_parametric.DnLogNormal method) (phylojunction.distribution.dn_parametric.DnNormal method) (phylojunction.distribution.dn_parametric.DnUnif method) (phylojunction.pgm.pgm.ValueGenerator method) init_return_ann_tr() (phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar class method) init_return_discrete_SSE_dn() (phylojunction.interface.grammar.dn_grammar.PJDnGrammar class method) init_return_parametric_dn() (phylojunction.interface.grammar.dn_grammar.PJDnGrammar class method) init_return_sse_stash() (phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar class method)

init_return_state_dep_prob() (phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar class method) init_return_state_dep_rate() (phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar class method) init_return_tree_mapped_with_attr() (phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar class method) initialize_scalar_dataframe() (in module phylojunction.readwrite.pj_write) initialize_tree_dataframe() (in module phylojunction.readwrite.pj_write) int2set_dict (phylojunction.calculation.discrete_sse.StateIntoPatternConverter attribute) InvalidMCMCChainLength is_clamped (phylojunction.pgm.pgm.NodeDAG attribute) is_csv() (in module phylojunction.readwrite.pj_read) is_deterministic (phylojunction.pgm.pgm.NodeDAG attribute) is_extant_or_sa_on_both_sides_complete_tr_root() (phylojunction.data.tree.AnnotatedTree method) is_sampled (phylojunction.pgm.pgm.NodeDAG attribute) is_tsv() (in module phylojunction.readwrite.pj_read) is_val_in_interval() (in module phylojunction.utility.helper_functions)

J

join_dataframes() (in module phylojunction.plotting.pj_organize)

L

label (phylojunction.data.sampled_ancestor.SampledAncestor attribute) lineage_node_label (phylojunction.data.sampled_ancestor.SampledAncestor attribute) ln_log_space (phylojunction.distribution.dn_parametric.DnLogNormal attribute)

ln_mean_list (phylojunction.distribution.dn_parametric.DnLogNormal attribute) ln_sd_list (phylojunction.distribution.dn_parametric.DnLogNormal attribute) LOGNORMAL (phylojunction.calculation.math_utils.ParametricDistribution attribute)

M

MacroevolEvent (class in phylojunction.calculation.discrete_sse) MacroevolEventHandler (class in phylojunction.calculation.discrete_sse) make_discrete_SSE_dn() (in module phylojunction.interface.grammar.dn_discrete_sse_makers) make_DiscreteStateDependentProbability() (in module phylojunction.interface.grammar.det_fn_discrete_sse_makers) make_DiscreteStateDependentRate() (in module phylojunction.interface.grammar.det_fn_discrete_sse_makers) make_mapped_ann_tree() (in module phylojunction.interface.grammar.det_fn_map_attribute) make_SSEStash() (in module phylojunction.interface.grammar.det_fn_discrete_sse_makers) make_tree_reader() (in module phylojunction.interface.grammar.ct_fn_treereader_makers) matrix_state_dep_params (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager attribute) max_age (phylojunction.data.tree.AnnotatedTree attribute) max_n_failed_attempts (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) max_param_list (phylojunction.distribution.dn_parametric.DnUnif attribute) max_rec_taxa (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) MaxNFailedAttemptsLimit meh (phylojunction.calculation.discrete_sse.SSEStash attribute) message (phylojunction.utility.exception_classes.AnnotatedTreeIncorrectAnnotationError attribute) (phylojunction.utility.exception_classes.AnnotatedTreeMissingNodeName attribute) (phylojunction.utility.exception_classes.AnnotatedTreeMisspecError attribute) (phylojunction.utility.exception_classes.AnnotatedTreeNodeMissingAttrError attribute) (phylojunction.utility.exception_classes.DAGCannotAddNodeError attribute) (phylojunction.utility.exception_classes.DAGCannotInitialize attribute) (phylojunction.utility.exception_classes.DimensionalityError attribute) (phylojunction.utility.exception_classes.DimensionalityWarning attribute) (phylojunction.utility.exception_classes.FunctionArgsMismatchError attribute) (phylojunction.utility.exception_classes.GenerateFailError attribute) (phylojunction.utility.exception_classes.IncorrectDimensionError attribute) (phylojunction.utility.exception_classes.InexistentVariableError attribute) (phylojunction.utility.exception_classes.InvalidMCMCChainLength attribute) (phylojunction.utility.exception_classes.MissingColumnName attribute) (phylojunction.utility.exception_classes.NodeDAGStatCantFloatError attribute) (phylojunction.utility.exception_classes.NodeInferenceDimensionalityError attribute) (phylojunction.utility.exception_classes.NoPlatingAllowedError attribute) (phylojunction.utility.exception_classes.NotBetweenZeroAndOneError attribute) (phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError attribute) (phylojunction.utility.exception_classes.ObjInitInvalidArgError attribute) (phylojunction.utility.exception_classes.ObjInitMissingParameterError attribute) (phylojunction.utility.exception_classes.ObjInitMissingStateDependentParameterError attribute) (phylojunction.utility.exception_classes.ObjInitRepeatedStateDependentParameterError attribute) (phylojunction.utility.exception_classes.ObjInitRequireNonZeroStateDependentParameterError attribute) (phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError attribute) (phylojunction.utility.exception_classes.ParseCtFnInitFailError attribute) (phylojunction.utility.exception_classes.ParseDetFnInitFailError attribute) (phylojunction.utility.exception_classes.ParseDnInitFailError attribute) (phylojunction.utility.exception_classes.ParseFunctionArgError attribute) (phylojunction.utility.exception_classes.ParseInvalidArgumentError attribute) (phylojunction.utility.exception_classes.ParseInvalidNewickStringError attribute) (phylojunction.utility.exception_classes.ParseMissingArgumentError attribute) (phylojunction.utility.exception_classes.ParseMissingParameterError attribute) (phylojunction.utility.exception_classes.ParseMissingSpecificationError attribute) (phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError attribute) (phylojunction.utility.exception_classes.ParseNotAParameterError attribute) (phylojunction.utility.exception_classes.ParsePathDoesNotExistError attribute) (phylojunction.utility.exception_classes.ParseRequireIntegerError attribute) (phylojunction.utility.exception_classes.ParseRequireNumericError attribute) (phylojunction.utility.exception_classes.ParseRequirePositiveIntegerError attribute) (phylojunction.utility.exception_classes.ParseRequireSingleValueError attribute) (phylojunction.utility.exception_classes.PJCLIInvalidInputError attribute) (phylojunction.utility.exception_classes.ReplicateNumberError attribute) (phylojunction.utility.exception_classes.ScriptSyntaxError attribute) (phylojunction.utility.exception_classes.SSEStashMisspec attribute) (phylojunction.utility.exception_classes.StateDependentParameterMisspec attribute) (phylojunction.utility.exception_classes.VariableAssignmentError attribute) (phylojunction.utility.exception_classes.VariableMisspec attribute)

MetaEnum (class in phylojunction.calculation.math_utils) min_param_list (phylojunction.distribution.dn_parametric.DnUnif attribute) min_rec_taxa (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) MissingColumnName module phylojunction phylojunction.calculation phylojunction.calculation.discrete_sse phylojunction.calculation.math_utils phylojunction.data phylojunction.data.attribute_transition phylojunction.data.sampled_ancestor phylojunction.data.tree phylojunction.distribution phylojunction.distribution.dn_discrete_sse phylojunction.distribution.dn_parametric phylojunction.inference phylojunction.inference.revbayes phylojunction.inference.revbayes.rb_dn_parametric phylojunction.inference.revbayes.rb_inference phylojunction.interface phylojunction.interface.cmdbox phylojunction.interface.cmdbox.cmd_parse phylojunction.interface.cmdbox.cmd_parse_utils phylojunction.interface.grammar phylojunction.interface.grammar.ct_fn_grammar phylojunction.interface.grammar.ct_fn_treereader_makers phylojunction.interface.grammar.det_fn_discrete_sse_makers phylojunction.interface.grammar.det_fn_grammar phylojunction.interface.grammar.det_fn_map_attribute phylojunction.interface.grammar.dn_discrete_sse_makers phylojunction.interface.grammar.dn_grammar phylojunction.interface.pj_sandbox phylojunction.pgm phylojunction.pgm.pgm phylojunction.plotting phylojunction.plotting.pj_draw phylojunction.plotting.pj_organize phylojunction.plotting.pj_seeing_colors phylojunction.plotting.pj_testing_tree_plotting phylojunction.readwrite phylojunction.readwrite.pj_read phylojunction.readwrite.pj_write phylojunction.utility phylojunction.utility.exception_classes phylojunction.utility.helper_functions mutually_exclusive_par_name (phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError attribute)

N

n_char (phylojunction.calculation.discrete_sse.StateIntoPatternConverter attribute) n_diff_par (phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError attribute) n_extant_sampled_terminal_nodes (phylojunction.data.tree.AnnotatedTree attribute) n_extant_terminal_nodes (phylojunction.data.tree.AnnotatedTree attribute) n_extinct_sampled_terminal_nodes (phylojunction.data.tree.AnnotatedTree attribute) n_extinct_terminal_nodes (phylojunction.data.tree.AnnotatedTree attribute) n_nodes (phylojunction.pgm.pgm.DirectedAcyclicGraph attribute) n_repl() (phylojunction.pgm.pgm.ValueGenerator method) n_sa_nodes (phylojunction.data.tree.AnnotatedTree attribute) n_samples() (phylojunction.pgm.pgm.ValueGenerator method) n_sim (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) n_slices_to_ignore (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager attribute) n_states (phylojunction.calculation.discrete_sse.StateIntoPatternConverter attribute) n_states_per_char (phylojunction.calculation.discrete_sse.StateIntoPatternConverter attribute) n_time_slices (phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler attribute) (phylojunction.calculation.discrete_sse.MacroevolEventHandler attribute) (phylojunction.distribution.dn_discrete_sse.DnSSE attribute)

name (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameter attribute) name_node_dict (phylojunction.pgm.pgm.DirectedAcyclicGraph attribute) node_ages_dict (phylojunction.data.tree.AnnotatedTree attribute) node_attr_dict (phylojunction.data.tree.AnnotatedTree attribute) node_dag_name (phylojunction.utility.exception_classes.NoPlatingAllowedError attribute) node_heights_dict (phylojunction.data.tree.AnnotatedTree attribute) node_name (phylojunction.pgm.pgm.NodeDAG attribute) (phylojunction.utility.exception_classes.NodeInferenceDimensionalityError attribute) (phylojunction.utility.exception_classes.ReplicateNumberError attribute) node_val_dict (phylojunction.pgm.pgm.DirectedAcyclicGraph attribute) NodeDAG (class in phylojunction.pgm.pgm) NodeDAGStatCantFloatError NodeInferenceDimensionalityError NoPlatingAllowedError norm_mean_param_list (phylojunction.distribution.dn_parametric.DnNormal attribute) norm_sd_param_list (phylojunction.distribution.dn_parametric.DnNormal attribute) NORMAL (phylojunction.calculation.math_utils.ParametricDistribution attribute) NotBetweenZeroAndOneError

O

obj_name (phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError attribute) (phylojunction.utility.exception_classes.ObjInitInvalidArgError attribute) (phylojunction.utility.exception_classes.ObjInitMissingParameterError attribute) (phylojunction.utility.exception_classes.ObjInitRequireNonZeroStateDependentParameterError attribute) (phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError attribute) (phylojunction.utility.exception_classes.ParseRequireIntegerError attribute) (phylojunction.utility.exception_classes.ParseRequireNumericError attribute) (phylojunction.utility.exception_classes.ParseRequirePositiveIntegerError attribute) (phylojunction.utility.exception_classes.ParseRequireSingleValueError attribute) ObjInitIncorrectDimensionError ObjInitInvalidArgError

ObjInitMissingParameterError ObjInitMissingStateDependentParameterError ObjInitRepeatedStateDependentParameterError ObjInitRequireNonZeroStateDependentParameterError ObjInitRequireSameParameterTypeError obs_len (phylojunction.utility.exception_classes.IncorrectDimensionError attribute) (phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError attribute) operator_weight (phylojunction.pgm.pgm.StochasticNodeDAG attribute) origin_age (phylojunction.data.tree.AnnotatedTree attribute) origin_edge_length (phylojunction.data.tree.AnnotatedTree attribute) origin_node (phylojunction.data.tree.AnnotatedTree attribute)

P

par_name (phylojunction.utility.exception_classes.DimensionalityError attribute) (phylojunction.utility.exception_classes.NotBetweenZeroAndOneError attribute) (phylojunction.utility.exception_classes.ParseFunctionArgError attribute) (phylojunction.utility.exception_classes.ParseInvalidArgumentError attribute) (phylojunction.utility.exception_classes.ParseInvalidNewickStringError attribute) (phylojunction.utility.exception_classes.ParseMissingArgumentError attribute) (phylojunction.utility.exception_classes.ParseMissingParameterError attribute) (phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError attribute) (phylojunction.utility.exception_classes.ParseNotAParameterError attribute) (phylojunction.utility.exception_classes.ParsePathDoesNotExistError attribute) (phylojunction.utility.exception_classes.PJCLIInvalidInputError attribute) param_dict (phylojunction.distribution.dn_parametric.DnExponential attribute) (phylojunction.distribution.dn_parametric.DnGamma attribute) (phylojunction.distribution.dn_parametric.DnLogNormal attribute) (phylojunction.distribution.dn_parametric.DnNormal attribute) (phylojunction.distribution.dn_parametric.DnUnif attribute) param_type (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager attribute) ParametricDistribution (class in phylojunction.calculation.math_utils) parent_nd_list (phylojunction.pgm.pgm.NodeDAG attribute) parent_node_tracker (phylojunction.distribution.dn_parametric.DnExponential attribute) (phylojunction.distribution.dn_parametric.DnGamma attribute) (phylojunction.distribution.dn_parametric.DnLogNormal attribute) (phylojunction.distribution.dn_parametric.DnNormal attribute) (phylojunction.distribution.dn_parametric.DnUnif attribute) parse_cli_str_write_fig() (in module phylojunction.readwrite.pj_read) parse_deterministic_function_assignment() (in module phylojunction.interface.cmdbox.cmd_parse) parse_samp_dn_assignment() (in module phylojunction.interface.cmdbox.cmd_parse) parse_spec() (in module phylojunction.interface.cmdbox.cmd_parse_utils) parse_val_vector() (in module phylojunction.interface.cmdbox.cmd_parse_utils) parse_variable_assignment() (in module phylojunction.interface.cmdbox.cmd_parse) ParseCtFnInitFailError ParseDetFnInitFailError ParseDnInitFailError ParseFunctionArgError ParseInvalidArgumentError ParseInvalidNewickStringError ParseMissingArgumentError ParseMissingParameterError ParseMissingSpecificationError ParseMutuallyExclusiveParametersError ParseNotAParameterError ParsePathDoesNotExistError ParseRequireIntegerError ParseRequireNumericError ParseRequirePositiveIntegerError ParseRequireSingleValueError path_str (phylojunction.utility.exception_classes.ParsePathDoesNotExistError attribute) phylojunction module phylojunction.calculation module phylojunction.calculation.discrete_sse module phylojunction.calculation.math_utils module phylojunction.data module phylojunction.data.attribute_transition module phylojunction.data.sampled_ancestor module phylojunction.data.tree module phylojunction.distribution module phylojunction.distribution.dn_discrete_sse module phylojunction.distribution.dn_parametric module phylojunction.inference module phylojunction.inference.revbayes module phylojunction.inference.revbayes.rb_dn_parametric module phylojunction.inference.revbayes.rb_inference module phylojunction.interface module

phylojunction.interface.cmdbox module phylojunction.interface.cmdbox.cmd_parse module phylojunction.interface.cmdbox.cmd_parse_utils module phylojunction.interface.grammar module 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 phylojunction.interface.pj_sandbox module phylojunction.pgm module phylojunction.pgm.pgm module phylojunction.plotting module phylojunction.plotting.pj_draw module phylojunction.plotting.pj_organize module phylojunction.plotting.pj_seeing_colors module phylojunction.plotting.pj_testing_tree_plotting module phylojunction.readwrite module phylojunction.readwrite.pj_read module phylojunction.readwrite.pj_write module phylojunction.utility module phylojunction.utility.exception_classes module phylojunction.utility.helper_functions module pj_get_name_mrca_obs_terminals() (in module phylojunction.data.tree) PJCLIInvalidInputError PJCLISampleOutOfRangeError PJCtFnGrammar (class in phylojunction.interface.grammar.ct_fn_grammar) PJDetFnGrammar (class in phylojunction.interface.grammar.det_fn_grammar) PJDnGrammar (class in phylojunction.interface.grammar.dn_grammar) PJIOFileDoesNotExistError plot_ann_tree() (in module phylojunction.data.tree) plot_blank() (in module phylojunction.pgm.pgm) plot_intervals() (in module phylojunction.plotting.pj_draw) plot_node() (phylojunction.data.tree.AnnotatedTree method) (phylojunction.pgm.pgm.DeterministicNodeDAG method) (phylojunction.pgm.pgm.NodeDAG method) (phylojunction.pgm.pgm.StochasticNodeDAG method) plot_node_histogram() (in module phylojunction.pgm.pgm) plot_violins() (in module phylojunction.plotting.pj_draw) populate_nd_attr_dict() (phylojunction.data.tree.AnnotatedTree method) populate_operator_weight() (phylojunction.pgm.pgm.DeterministicNodeDAG method) (phylojunction.pgm.pgm.NodeDAG method) (phylojunction.pgm.pgm.StochasticNodeDAG method) prep_data_df() (in module phylojunction.readwrite.pj_write) prep_data_filepaths_dfs() (in module phylojunction.readwrite.pj_write) prep_trees_rb_smap_dfs() (in module phylojunction.readwrite.pj_write) print_progress() (in module phylojunction.utility.helper_functions) prob_handler (phylojunction.calculation.discrete_sse.SSEStash attribute) (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) PROBABILITY (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterType attribute)

R

random_seed (phylojunction.pgm.pgm.DirectedAcyclicGraph property) randomly_decide_taxon_sampling_at_time_at_state() (phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler method) RATE (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterType attribute) read_csv_tsv_into_dataframe() (in module phylojunction.readwrite.pj_read) read_node_attr_update_tree() (in module phylojunction.readwrite.pj_read) read_nwk_tree_str() (in module phylojunction.readwrite.pj_read) read_serialized_pgm() (in module phylojunction.readwrite.pj_read) read_text_file() (in module phylojunction.readwrite.pj_read) rec_node_ages_dict (phylojunction.data.tree.AnnotatedTree attribute) rec_node_heights_dict (phylojunction.data.tree.AnnotatedTree attribute) rec_str() (phylojunction.data.tree.AnnotatedTree method) rec_tr_at_dict (phylojunction.data.tree.AnnotatedTree attribute) rec_tr_clado_at_dict (phylojunction.data.tree.AnnotatedTree attribute) rec_tr_root_age (phylojunction.data.tree.AnnotatedTree attribute) rec_tr_root_node (phylojunction.data.tree.AnnotatedTree attribute) rec_tr_sa_lineage_dict (phylojunction.data.tree.AnnotatedTree attribute) repl_size (phylojunction.pgm.pgm.NodeDAG property)

ReplicateNumberError rng_seed (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) root_age (phylojunction.data.tree.AnnotatedTree attribute) root_is_born (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) root_node (phylojunction.data.tree.AnnotatedTree attribute) run_example_geosse_file() (in module phylojunction.interface.pj_sandbox) run_example_manual_incomplete_sampling_bisse() (in module phylojunction.interface.pj_sandbox) run_example_manual_tree_building() (in module phylojunction.interface.pj_sandbox) run_example_map_attr() (in module phylojunction.interface.pj_sandbox) run_example_read_tree_function() (in module phylojunction.interface.pj_sandbox) run_example_yule_string() (in module phylojunction.interface.pj_sandbox) runtime_limit (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) RunTimeLimit rv_name (phylojunction.utility.exception_classes.DimensionalityWarning attribute) (phylojunction.utility.exception_classes.InexistentVariableError attribute) (phylojunction.utility.exception_classes.VariableAssignmentError attribute) (phylojunction.utility.exception_classes.VariableMisspec attribute)

S

sa_lineage_dict (phylojunction.data.tree.AnnotatedTree attribute) sa_obs_nodes_labels (phylojunction.data.tree.AnnotatedTree attribute) sample_event_sse_rate_param() (phylojunction.calculation.discrete_sse.MacroevolEventHandler method) sample_size (phylojunction.pgm.pgm.DirectedAcyclicGraph attribute) (phylojunction.pgm.pgm.NodeDAG property) SampledAncestor (class in phylojunction.data.sampled_ancestor) sampling_dn (phylojunction.pgm.pgm.StochasticNodeDAG attribute) script2dag() (in module phylojunction.interface.cmdbox.cmd_parse) ScriptSyntaxError seed_age (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager attribute) (phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler attribute) (phylojunction.calculation.discrete_sse.MacroevolEventHandler attribute) (phylojunction.data.tree.AnnotatedTree attribute) (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) set2int_dict (phylojunction.calculation.discrete_sse.StateIntoPatternConverter attribute) simulate() (phylojunction.distribution.dn_discrete_sse.DnSSE method) slice_age_ends (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager attribute) (phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler attribute) (phylojunction.calculation.discrete_sse.MacroevolEventHandler attribute) (phylojunction.data.tree.AnnotatedTree attribute) slice_t_ends (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager attribute) (phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler attribute) (phylojunction.calculation.discrete_sse.MacroevolEventHandler attribute) (phylojunction.data.tree.AnnotatedTree attribute) (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) sse_rate_manager (phylojunction.calculation.discrete_sse.MacroevolEventHandler attribute) sse_stash (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) SSEStash (class in phylojunction.calculation.discrete_sse)

SSEStashMisspec start_states (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) state (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameter attribute) (phylojunction.data.sampled_ancestor.SampledAncestor attribute) state_count (phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler attribute) (phylojunction.calculation.discrete_sse.MacroevolEventHandler attribute) (phylojunction.data.tree.AnnotatedTree attribute) (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) state_count_dict (phylojunction.data.tree.AnnotatedTree attribute) state_dep_params_at_time() (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager method) state_dep_params_dict (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager attribute) state_dep_prob_manager (phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler attribute) state_representation (phylojunction.calculation.discrete_sse.DiscreteStateDependentProbability attribute) state_tuple (phylojunction.calculation.discrete_sse.DiscreteStateDependentRate attribute) StateDependentParameterMisspec StateIntoPatternConverter (class in phylojunction.calculation.discrete_sse) StochasticNodeDAG (class in phylojunction.pgm.pgm) stop (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) stop_val (phylojunction.distribution.dn_discrete_sse.DnSSE attribute) str_representation (phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler attribute) (phylojunction.calculation.discrete_sse.DiscreteStateDependentRate attribute) (phylojunction.calculation.discrete_sse.MacroevolEventHandler attribute) (phylojunction.calculation.discrete_sse.SSEStash attribute) (phylojunction.data.attribute_transition.AttributeTransition attribute) (phylojunction.data.sampled_ancestor.SampledAncestor attribute) subtending_or_speciating_node_label (phylojunction.data.attribute_transition.AttributeTransition attribute) symmetric_diff_str (phylojunction.utility.exception_classes.ObjInitMissingStateDependentParameterError attribute) symmetric_difference() (in module phylojunction.utility.helper_functions)

T

time_to_lineage_node (phylojunction.data.sampled_ancestor.SampledAncestor attribute) to_state (phylojunction.data.attribute_transition.AttributeTransition attribute) to_state2 (phylojunction.data.attribute_transition.AttributeTransition attribute) tokenize_fn_spec() (in module phylojunction.interface.cmdbox.cmd_parse_utils) total_rate() (phylojunction.calculation.discrete_sse.MacroevolEventHandler method)

tree (phylojunction.data.tree.AnnotatedTree attribute) tree_died (phylojunction.data.tree.AnnotatedTree attribute) tree_invalid (phylojunction.data.tree.AnnotatedTree attribute) tree_read_as_newick (phylojunction.data.tree.AnnotatedTree attribute) tree_reconstructed (phylojunction.data.tree.AnnotatedTree attribute) truncate_colormap() (in module phylojunction.plotting.pj_seeing_colors)

U

UNDEFINED (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterType attribute) UNIFORM (phylojunction.calculation.math_utils.ParametricDistribution attribute)

update_daughter_members() (phylojunction.data.attribute_transition.AttributeTransition method) update_rec_tr_at_dict() (phylojunction.data.tree.AnnotatedTree method) update_rec_tr_sa_lineage_dict() (phylojunction.data.tree.AnnotatedTree method)

V

val_or_obj() (in module phylojunction.interface.cmdbox.cmd_parse_utils) value (phylojunction.calculation.discrete_sse.DiscreteStateDependentParameter attribute) (phylojunction.pgm.pgm.NodeDAG property) ValueGenerator (class in phylojunction.pgm.pgm) VariableAssignmentError

VariableMisspec vectorized_params (phylojunction.distribution.dn_parametric.DnExponential attribute) (phylojunction.distribution.dn_parametric.DnGamma attribute) (phylojunction.distribution.dn_parametric.DnLogNormal attribute) (phylojunction.distribution.dn_parametric.DnNormal attribute) (phylojunction.distribution.dn_parametric.DnUnif attribute)

W

W_SPECIATION (phylojunction.calculation.discrete_sse.MacroevolEvent attribute) with_origin (phylojunction.data.tree.AnnotatedTree attribute) (phylojunction.distribution.dn_discrete_sse.DnSSE attribute)

write_data_df() (in module phylojunction.readwrite.pj_write) write_fig_to_file() (in module phylojunction.readwrite.pj_write) write_str_list() (in module phylojunction.readwrite.pj_write)