phylojunction.data.attribute_transition module
- -class phylojunction.data.attribute_transition.AttributeTransition(attr_label: str, subtending_node_label: str, global_time: float, from_state: int, to_state: int, to_state2: int | None = None, at_speciation: bool = False) +class phylojunction.data.attribute_transition.AttributeTransition(attr_label: str, subtending_node_label: str, global_time: float, from_state: int, to_state: int, age: float | None = None, to_state2: int | None = None, at_speciation: bool = False)
Bases:
+object-
+
- +age: float +
- at_speciation: bool | None @@ -160,7 +165,7 @@
- -class phylojunction.data.sampled_ancestor.SampledAncestor(label: str, lineage_node_label: str, global_time: float, age: float = None, state: int = 0, time_to_lineage_node: float = -1.0) +class phylojunction.data.sampled_ancestor.SampledAncestor(label: str, lineage_node_label: str, global_time: float, age: float | None = None, state: int = 0, time_to_lineage_node: float = -1.0)
Bases:
+object-
+
- +rec_tr_clado_at_dict: Dict[str, AttributeTransition] | None +
- rec_tr_root_age: float @@ -714,12 +724,15 @@
- update_rec_tr_at_dict(rec_tree_root_nd: Node) None -
Update ‘rec_tr_at_dict’ member.
+Update ‘rec_tr_at_dict’ and ‘rec_clado-at_dict’ members.
The ‘at_dict’ member of the AnnotatedTree, when defined, will by default host the state transitions of every node of the complete -tree. This method initializes ‘rec_trat_dict’ so that it reflects the -reconstructed tree – it is only called when necessary, -by the ‘extract_reconstructed_tree’ method.
+tree. This method initializes ‘rec_tr_at_dict’ so that it +reflects the reconstructed tree – it is only called when +necessary, by the ‘extract_reconstructed_tree’ method. +Member ‘rec_tr_clado_at_dict’ is also updated. Internal nodes +undergoing cladogenetic changes that are in the complete tree +but not in the reconstructed tree are removed.
Submodules
-
diff --git a/docs/build/html/phylojunction.distribution.html b/docs/build/html/phylojunction.distribution.html
index eec51d6..4bcf87b 100644
--- a/docs/build/html/phylojunction.distribution.html
+++ b/docs/build/html/phylojunction.distribution.html
@@ -106,7 +106,7 @@
- -class phylojunction.distribution.dn_discrete_sse.DnSSE(sse_stash: SSEStash, n: int = 1, n_replicates: int = 1, origin: bool = True, start_states_list: List[int] = [], stop: str = '', stop_value: List[float] = [], condition_on_speciation: bool = False, condition_on_survival: bool = True, condition_on_obs_both_sides_root: bool = False, min_rec_taxa: int = 0, max_rec_taxa: int = 1000000000000, abort_at_alive_count: int = 1000000000000, epsilon: float = 1e-12, runtime_limit: int = 5, max_n_failed_attempts: int = 200, rng_seed: int | None = None, debug: bool | None = False, info: bool | None = False) +class phylojunction.distribution.dn_discrete_sse.DnSSE(sse_stash: SSEStash, n: int = 1, n_replicates: int = 1, origin: bool = True, start_states_list: List[int] = [], stop: str = '', stop_value: List[float] = [], condition_on_speciation: bool = False, condition_on_survival: bool = True, condition_on_obs_both_sides_root: bool = False, min_rec_taxa: int = 0, max_rec_taxa: int = 1000000000000, abort_at_alive_count: int = 1000000000000, epsilon: float = 1e-12, runtime_limit: int = 300, max_n_failed_attempts: int = 200, rng_seed: int | None = None, debug: bool | None = False, info: bool | None = False)
Bases:
DistrForSamplingDiscrete SSE distribution.
Class for the discrete state-dependent speciation and extinction @@ -190,9 +190,9 @@
SubmodulesSubmodules
- phylojunction.data.attribute_transition module
create_str_defaultdict()get_covg()get_ellapsed_time_in_minutes()get_ellapsed_time_in_seconds()is_val_in_interval()print_progress()symmetric_difference()Submodules
- -dn_grammar_dict: Dict[str, Tuple[str, ...]] = {'discrete_sse': ('n', 'nr', 'stop', 'stop_value', 'origin', 'stash', 'start_state', 'eps', 'runtime_limit', 'max_n_attempts', 'cond_spn', 'cond_surv', 'cond_obs_both_sides', 'min_rec_taxa', 'max_rec_taxa', 'abort_at_alive_count'), 'exponential': ('n', 'nr', 'rate', 'rate_parameterization'), 'gamma': ('n', 'nr', 'shape', 'scale', 'rate_parameterization'), 'lognormal': ('n', 'nr', 'mean', 'sd', 'log_space'), 'normal': ('n', 'nr', 'mean', 'sd'), 'unif': ('n', 'nr', 'min', 'max')}
+dn_grammar_dict: Dict[str, Tuple[str, ...]] = {'discrete_sse': ('n', 'nr', 'stop', 'stop_value', 'origin', 'stash', 'start_state', 'eps', 'runtime_limit', 'max_n_attempts', 'cond_spn', 'cond_surv', 'cond_obs_both_sides', 'min_rec_taxa', 'max_rec_taxa', 'abort_at_alive_count'), 'exponential': ('n', 'nr', 'rate', 'rate_parameterization'), 'gamma': ('n', 'nr', 'shape', 'scale', 'rate_parameterization'), 'lognormal': ('n', 'nr', 'meanlog', 'sdlog', 'log_space'), 'normal': ('n', 'nr', 'mean', 'sd'), 'unif': ('n', 'nr', 'min', 'max')}- -plot_node(axes: Axes, sample_idx: int | None = 0, repl_idx: int | None = 0, repl_size: int | None = 1, branch_attr: str | None = 'state') None +plot_node(axes: Axes, sample_idx: int | None = 0, repl_idx: int | None = 0, repl_size: int | None = 1, branch_attr: str | None = 'state', draw_reconstructed: bool | None = False) None
- +phylojunction.readwrite.pj_write.dump_trees_rb_smap_dfs(dir_string: str, dag_obj: DirectedAcyclicGraph, tr_dag_node_name_list: List[str], mapped_attr_name: str, prefix: str = '') None +
- phylojunction.readwrite.pj_write.get_write_inference_rev_scripts(all_sims_model_spec_list: List[str], all_sims_mcmc_logging_spec_list: List[str], dir_list: List[str], prefix: str = '', write2file: bool = False) List[str] @@ -436,12 +441,40 @@
- -phylojunction.readwrite.pj_write.prep_trees_rb_smap_dfs(dag_obj: DirectedAcyclicGraph) DataFrame +phylojunction.readwrite.pj_write.prep_trees_rb_smap_dfs(dag_obj: DirectedAcyclicGraph, tree_dag_node_name_list: List[str], mapped_attr_name: str) Tuple[Dict[str, List[DataFrame]], Dict[str, List[str]]]
Initialize pandas DataFrame’s for holding stochastic maps.
Each dataframe will hold stochastic maps for all nodes for all (replicate) trees in a single sample. Each iteration will correspond to a single replicate.
-Returns:
+-
+
- Parameters: +
-
+
dag_obj (DirectedAcyclicGraph) – Instance of DAG class, holding +the model.
+tree_dag_node_name_list (list) – List with names of the DAG nodes +tree random variables along which attributes have +transitioned and for which we are producing a stochastic +mapping dataframe.
+mapped_attr_name (str) – Name of the attribute being +stochastically mapped. E.g., ‘state’.
+
+- Returns: +
-
+
- A tuple with two dictionaries. The keys of both
dictionaries are DAG node names. The values are lists. +Inside the lists of one are pandas DataFrame instances +with all replicates per sample in a single dataframes +(and one dataframe per sample). In the lists of the other +dictionary’s values are lists of strings with the contents +of the dataframes (used for unit testing).
+
+
+- Return type: +
(tuple)
+
+
None
-
Submodules
phylojunction.distribution.dn_discrete_sse module
-
diff --git a/docs/build/html/phylojunction.pgm.html b/docs/build/html/phylojunction.pgm.html
index 70e1c59..273bc3e 100644
--- a/docs/build/html/phylojunction.pgm.html
+++ b/docs/build/html/phylojunction.pgm.html
@@ -133,7 +133,7 @@
Submodules
-
diff --git a/docs/build/html/phylojunction.readwrite.html b/docs/build/html/phylojunction.readwrite.html
index b1dda2f..69e5cfc 100644
--- a/docs/build/html/phylojunction.readwrite.html
+++ b/docs/build/html/phylojunction.readwrite.html
@@ -292,6 +292,11 @@
Submodules +
Submodules
-
@@ -454,12 +487,10 @@
SubmodulesReturns: -
- -phylojunction.utility.helper_functions.get_ellapsed_time_in_minutes(start: float, end: float) int -
Calculate ellapsed time
+- +phylojunction.utility.helper_functions.get_ellapsed_time_in_seconds(start: float, end: float) int +
Calculate ellapsed time in seconds.
- Parameters:
-
@@ -961,7 +961,7 @@
Ellapsed time in minutes in time window
+Ellapsed time in seconds in time window
- Return type:
int
diff --git a/docs/build/html/pjdoc/index.html b/docs/build/html/pjdoc/index.html index 013521c..1056fb9 100644 --- a/docs/build/html/pjdoc/index.html +++ b/docs/build/html/pjdoc/index.html @@ -282,7 +282,7 @@Specifying a model (an example) -
+
Figure 2. Factor graph representing the time-homogenous birth-death model specified in example script 1.
Parametric distributions
Uniform
-The function for assigning a uniform (
+uniform) distribution to a variable has four parameters:The function for assigning a uniform (
uniform) distribution to a random variable has four parameters:@@ -534,7 +534,7 @@n(integer, optional): Number of samples to draw (samples are i.i.d.). Defaults to 1.Uniform
Exponential
-The function for assigning a exponential (
+exponential) distribution to a variable has four parameters:The function for assigning a exponential (
exponential) distribution to a random variable has four parameters:@@ -552,7 +552,7 @@n(integer, optional): Number of samples to draw (samples are i.i.d.). Defaults to 1.Exponential
Gamma
-The function for assigning a gamma (
+gamma) distribution to a variable has five parameters:The function for assigning a gamma (
gamma) distribution to a random variable has five parameters:diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js index 5b4f4c0..e69caf4 100644 --- a/docs/build/html/searchindex.js +++ b/docs/build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["index", "installing", "modules", "phylojunction", "phylojunction.calculation", "phylojunction.data", "phylojunction.distribution", "phylojunction.inference", "phylojunction.inference.revbayes", "phylojunction.interface", "phylojunction.interface.cmdbox", "phylojunction.interface.grammar", "phylojunction.pgm", "phylojunction.plotting", "phylojunction.readwrite", "phylojunction.utility", "pjdoc/index", "pjdoc/parametric", "pjdoc/treedists"], "filenames": ["index.rst", "installing.rst", "modules.rst", "phylojunction.rst", "phylojunction.calculation.rst", "phylojunction.data.rst", "phylojunction.distribution.rst", "phylojunction.inference.rst", "phylojunction.inference.revbayes.rst", 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"phylojunction.distribution.dn_parametric.DnUnif.vectorized_params"]], "with_origin (phylojunction.distribution.dn_discrete_sse.dnsse attribute)": [[6, "phylojunction.distribution.dn_discrete_sse.DnSSE.with_origin"]], "phylojunction.inference": [[7, "module-phylojunction.inference"]], "dag_obj_to_rev_inference_spec() (in module phylojunction.inference.revbayes.rb_inference)": [[8, "phylojunction.inference.revbayes.rb_inference.dag_obj_to_rev_inference_spec"]], "get_exponential_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_exponential_rev_inference_spec_info"]], "get_gamma_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_gamma_rev_inference_spec_info"]], "get_ln_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_ln_rev_inference_spec_info"]], "get_mcmc_logging_spec_list() (in module phylojunction.inference.revbayes.rb_inference)": [[8, "phylojunction.inference.revbayes.rb_inference.get_mcmc_logging_spec_list"]], "get_normal_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_normal_rev_inference_spec_info"]], "get_rev_str_from_dn_parametric_obj() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_rev_str_from_dn_parametric_obj"]], "get_unif_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric)": [[8, "phylojunction.inference.revbayes.rb_dn_parametric.get_unif_rev_inference_spec_info"]], "phylojunction.inference.revbayes": [[8, "module-phylojunction.inference.revbayes"]], "phylojunction.inference.revbayes.rb_dn_parametric": [[8, "module-phylojunction.inference.revbayes.rb_dn_parametric"]], "phylojunction.inference.revbayes.rb_inference": [[8, "module-phylojunction.inference.revbayes.rb_inference"]], "phylojunction.interface": [[9, "module-phylojunction.interface"]], "phylojunction.interface.pj_sandbox": [[9, "module-phylojunction.interface.pj_sandbox"]], "run_example_geosse_file() (in module phylojunction.interface.pj_sandbox)": [[9, "phylojunction.interface.pj_sandbox.run_example_geosse_file"]], "run_example_manual_incomplete_sampling_bisse() (in module phylojunction.interface.pj_sandbox)": [[9, "phylojunction.interface.pj_sandbox.run_example_manual_incomplete_sampling_bisse"]], "run_example_manual_tree_building() (in module phylojunction.interface.pj_sandbox)": [[9, "phylojunction.interface.pj_sandbox.run_example_manual_tree_building"]], "run_example_map_attr() (in module phylojunction.interface.pj_sandbox)": [[9, "phylojunction.interface.pj_sandbox.run_example_map_attr"]], "run_example_read_tree_function() (in module phylojunction.interface.pj_sandbox)": [[9, "phylojunction.interface.pj_sandbox.run_example_read_tree_function"]], "run_example_yule_string() (in module phylojunction.interface.pj_sandbox)": [[9, "phylojunction.interface.pj_sandbox.run_example_yule_string"]], "cmdline2dag() (in module phylojunction.interface.cmdbox.cmd_parse)": [[10, "phylojunction.interface.cmdbox.cmd_parse.cmdline2dag"]], "parse_deterministic_function_assignment() (in module phylojunction.interface.cmdbox.cmd_parse)": [[10, "phylojunction.interface.cmdbox.cmd_parse.parse_deterministic_function_assignment"]], "parse_samp_dn_assignment() (in module phylojunction.interface.cmdbox.cmd_parse)": [[10, "phylojunction.interface.cmdbox.cmd_parse.parse_samp_dn_assignment"]], "parse_spec() (in module phylojunction.interface.cmdbox.cmd_parse_utils)": [[10, "phylojunction.interface.cmdbox.cmd_parse_utils.parse_spec"]], "parse_val_vector() (in module phylojunction.interface.cmdbox.cmd_parse_utils)": [[10, "phylojunction.interface.cmdbox.cmd_parse_utils.parse_val_vector"]], "parse_variable_assignment() (in module phylojunction.interface.cmdbox.cmd_parse)": [[10, "phylojunction.interface.cmdbox.cmd_parse.parse_variable_assignment"]], "phylojunction.interface.cmdbox": [[10, "module-phylojunction.interface.cmdbox"]], "phylojunction.interface.cmdbox.cmd_parse": [[10, "module-phylojunction.interface.cmdbox.cmd_parse"]], "phylojunction.interface.cmdbox.cmd_parse_utils": [[10, "module-phylojunction.interface.cmdbox.cmd_parse_utils"]], "script2dag() (in module phylojunction.interface.cmdbox.cmd_parse)": [[10, "phylojunction.interface.cmdbox.cmd_parse.script2dag"]], "tokenize_fn_spec() (in module phylojunction.interface.cmdbox.cmd_parse_utils)": [[10, "phylojunction.interface.cmdbox.cmd_parse_utils.tokenize_fn_spec"]], "val_or_obj() (in module phylojunction.interface.cmdbox.cmd_parse_utils)": [[10, "phylojunction.interface.cmdbox.cmd_parse_utils.val_or_obj"]], "pjctfngrammar (class in phylojunction.interface.grammar.ct_fn_grammar)": [[11, "phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar"]], "pjdetfngrammar (class in phylojunction.interface.grammar.det_fn_grammar)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar"]], "pjdngrammar (class in phylojunction.interface.grammar.dn_grammar)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar"]], "create_ct_fn_obj() (phylojunction.interface.grammar.ct_fn_grammar.pjctfngrammar class method)": [[11, "phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar.create_ct_fn_obj"]], "create_det_fn_obj() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.create_det_fn_obj"]], "create_dn_obj() (phylojunction.interface.grammar.dn_grammar.pjdngrammar class method)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.create_dn_obj"]], "ct_fn_grammar_dict (phylojunction.interface.grammar.ct_fn_grammar.pjctfngrammar attribute)": [[11, "phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar.ct_fn_grammar_dict"]], "det_fn_grammar_dict (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar attribute)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.det_fn_grammar_dict"]], "dn_grammar_dict (phylojunction.interface.grammar.dn_grammar.pjdngrammar attribute)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.dn_grammar_dict"]], "grammar_check() (phylojunction.interface.grammar.ct_fn_grammar.pjctfngrammar class method)": [[11, "phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar.grammar_check"]], "grammar_check() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.grammar_check"]], "grammar_check() (phylojunction.interface.grammar.dn_grammar.pjdngrammar class method)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.grammar_check"]], "init_return_ann_tr() (phylojunction.interface.grammar.ct_fn_grammar.pjctfngrammar class method)": [[11, "phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar.init_return_ann_tr"]], "init_return_discrete_sse_dn() (phylojunction.interface.grammar.dn_grammar.pjdngrammar class method)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.init_return_discrete_SSE_dn"]], "init_return_parametric_dn() (phylojunction.interface.grammar.dn_grammar.pjdngrammar class method)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.init_return_parametric_dn"]], "init_return_sse_stash() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_sse_stash"]], "init_return_state_dep_prob() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_state_dep_prob"]], "init_return_state_dep_rate() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_state_dep_rate"]], "init_return_tree_mapped_with_attr() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_tree_mapped_with_attr"]], "make_discretestatedependentprobability() (in module phylojunction.interface.grammar.det_fn_discrete_sse_makers)": [[11, "phylojunction.interface.grammar.det_fn_discrete_sse_makers.make_DiscreteStateDependentProbability"]], "make_discretestatedependentrate() (in module phylojunction.interface.grammar.det_fn_discrete_sse_makers)": [[11, "phylojunction.interface.grammar.det_fn_discrete_sse_makers.make_DiscreteStateDependentRate"]], "make_ssestash() (in module phylojunction.interface.grammar.det_fn_discrete_sse_makers)": [[11, "phylojunction.interface.grammar.det_fn_discrete_sse_makers.make_SSEStash"]], "make_discrete_sse_dn() (in module phylojunction.interface.grammar.dn_discrete_sse_makers)": [[11, "phylojunction.interface.grammar.dn_discrete_sse_makers.make_discrete_SSE_dn"]], "make_mapped_ann_tree() (in module phylojunction.interface.grammar.det_fn_map_attribute)": [[11, "phylojunction.interface.grammar.det_fn_map_attribute.make_mapped_ann_tree"]], "make_tree_reader() (in module phylojunction.interface.grammar.ct_fn_treereader_makers)": [[11, "phylojunction.interface.grammar.ct_fn_treereader_makers.make_tree_reader"]], "phylojunction.interface.grammar": [[11, "module-phylojunction.interface.grammar"]], "phylojunction.interface.grammar.ct_fn_grammar": [[11, "module-phylojunction.interface.grammar.ct_fn_grammar"]], "phylojunction.interface.grammar.ct_fn_treereader_makers": [[11, "module-phylojunction.interface.grammar.ct_fn_treereader_makers"]], "phylojunction.interface.grammar.det_fn_discrete_sse_makers": [[11, "module-phylojunction.interface.grammar.det_fn_discrete_sse_makers"]], "phylojunction.interface.grammar.det_fn_grammar": [[11, "module-phylojunction.interface.grammar.det_fn_grammar"]], "phylojunction.interface.grammar.det_fn_map_attribute": [[11, "module-phylojunction.interface.grammar.det_fn_map_attribute"]], "phylojunction.interface.grammar.dn_discrete_sse_makers": [[11, "module-phylojunction.interface.grammar.dn_discrete_sse_makers"]], "phylojunction.interface.grammar.dn_grammar": [[11, "module-phylojunction.interface.grammar.dn_grammar"]], "ct_fn_name (phylojunction.pgm.pgm.constantfn property)": [[12, "phylojunction.pgm.pgm.ConstantFn.CT_FN_NAME"]], "constantfn (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.ConstantFn"]], "dn_name (phylojunction.pgm.pgm.distrforsampling property)": [[12, "phylojunction.pgm.pgm.DistrForSampling.DN_NAME"]], "deterministicnodedag (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG"]], "directedacyclicgraph (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph"]], "distrforsampling (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.DistrForSampling"]], "nodedag (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.NodeDAG"]], "stochasticnodedag (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG"]], "valuegenerator (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.ValueGenerator"]], "abstract_attribute() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.abstract_attribute"]], "add_node() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.add_node"]], "call_order_idx (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.call_order_idx"]], "constant_fn (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.constant_fn"]], "extract_vals_as_str_from_node_dag() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.extract_vals_as_str_from_node_dag"]], "extract_value_from_dagnodes() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.extract_value_from_dagnodes"]], "generate() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.generate"]], "generate_value() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.generate_value"]], "get_display_str_by_name() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_display_str_by_name"]], "get_node_dag_by_name() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_node_dag_by_name"]], "get_node_stats_str() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.get_node_stats_str"]], "get_node_stats_str() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.get_node_stats_str"]], "get_node_stats_str() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.get_node_stats_str"]], "get_rev_inference_spec_info() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.get_rev_inference_spec_info"]], "get_sorted_node_dag_list() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_sorted_node_dag_list"]], "get_start2end_str() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.get_start2end_str"]], "init_check_vectorize_sample_size() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.init_check_vectorize_sample_size"]], "is_clamped (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_clamped"]], "is_deterministic (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_deterministic"]], "is_sampled (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_sampled"]], "n_nodes (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.n_nodes"]], "n_repl() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.n_repl"]], "n_samples() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.n_samples"]], "name_node_dict (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.name_node_dict"]], "node_name (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.node_name"]], "node_val_dict (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.node_val_dict"]], "operator_weight (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.operator_weight"]], "parent_nd_list (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.parent_nd_list"]], "phylojunction.pgm": [[12, "module-phylojunction.pgm"]], "phylojunction.pgm.pgm": [[12, "module-phylojunction.pgm.pgm"]], "plot_blank() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.plot_blank"]], "plot_node() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.plot_node"]], "plot_node() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.plot_node"]], "plot_node() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.plot_node"]], "plot_node_histogram() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.plot_node_histogram"]], "populate_operator_weight() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.populate_operator_weight"]], "populate_operator_weight() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.populate_operator_weight"]], "populate_operator_weight() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.populate_operator_weight"]], "random_seed (phylojunction.pgm.pgm.directedacyclicgraph property)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.random_seed"]], "repl_size (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.repl_size"]], "sample_size (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.sample_size"]], "sample_size (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.sample_size"]], "sampling_dn (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.sampling_dn"]], "value (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.value"]], "add_within_hpd_col() (in module phylojunction.plotting.pj_organize)": [[13, "phylojunction.plotting.pj_organize.add_within_hpd_col"]], "join_dataframes() (in module phylojunction.plotting.pj_organize)": [[13, "phylojunction.plotting.pj_organize.join_dataframes"]], "phylojunction.plotting": [[13, "module-phylojunction.plotting"]], "phylojunction.plotting.pj_draw": [[13, "module-phylojunction.plotting.pj_draw"]], "phylojunction.plotting.pj_organize": [[13, "module-phylojunction.plotting.pj_organize"]], "phylojunction.plotting.pj_seeing_colors": [[13, "module-phylojunction.plotting.pj_seeing_colors"]], "phylojunction.plotting.pj_testing_tree_plotting": [[13, "module-phylojunction.plotting.pj_testing_tree_plotting"]], "plot_intervals() (in module phylojunction.plotting.pj_draw)": [[13, "phylojunction.plotting.pj_draw.plot_intervals"]], "plot_violins() (in module phylojunction.plotting.pj_draw)": [[13, "phylojunction.plotting.pj_draw.plot_violins"]], "truncate_colormap() (in module phylojunction.plotting.pj_seeing_colors)": [[13, "phylojunction.plotting.pj_seeing_colors.truncate_colormap"]], "dump_pgm_data() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.dump_pgm_data"]], "dump_serialized_pgm() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.dump_serialized_pgm"]], "get_write_inference_rev_scripts() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.get_write_inference_rev_scripts"]], "initialize_scalar_dataframe() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.initialize_scalar_dataframe"]], "initialize_tree_dataframe() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.initialize_tree_dataframe"]], "is_csv() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.is_csv"]], "is_tsv() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.is_tsv"]], "parse_cli_str_write_fig() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.parse_cli_str_write_fig"]], "phylojunction.readwrite": [[14, "module-phylojunction.readwrite"]], "phylojunction.readwrite.pj_read": [[14, "module-phylojunction.readwrite.pj_read"]], "phylojunction.readwrite.pj_write": [[14, "module-phylojunction.readwrite.pj_write"]], "prep_data_df() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.prep_data_df"]], "prep_data_filepaths_dfs() (in module phylojunction.readwrite.pj_write)": 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(phylojunction.calculation.discrete_sse.macroevolevent attribute)": [[4, "phylojunction.calculation.discrete_sse.MacroevolEvent.W_SPECIATION"]], "arriving_state (phylojunction.calculation.discrete_sse.discretestatedependentrate attribute)": [[4, "phylojunction.calculation.discrete_sse.DiscreteStateDependentRate.arriving_state"]], "departing_state (phylojunction.calculation.discrete_sse.discretestatedependentrate attribute)": [[4, "phylojunction.calculation.discrete_sse.DiscreteStateDependentRate.departing_state"]], "epoch_idx (phylojunction.calculation.discrete_sse.discretestatedependentparameter attribute)": [[4, "phylojunction.calculation.discrete_sse.DiscreteStateDependentParameter.epoch_idx"]], "epsilon (phylojunction.calculation.discrete_sse.discretestatedependentparametermanager attribute)": [[4, "phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager.epsilon"]], "event (phylojunction.calculation.discrete_sse.discretestatedependentrate attribute)": [[4, 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"n_time_slices (phylojunction.calculation.discrete_sse.discretestatedependentprobabilityhandler attribute)": [[4, "phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler.n_time_slices"]], "n_time_slices (phylojunction.calculation.discrete_sse.macroevoleventhandler attribute)": [[4, "phylojunction.calculation.discrete_sse.MacroevolEventHandler.n_time_slices"]], "name (phylojunction.calculation.discrete_sse.discretestatedependentparameter attribute)": [[4, "phylojunction.calculation.discrete_sse.DiscreteStateDependentParameter.name"]], "param_type (phylojunction.calculation.discrete_sse.discretestatedependentparametermanager attribute)": [[4, "phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager.param_type"]], "phylojunction.calculation": [[4, "module-phylojunction.calculation"]], "phylojunction.calculation.discrete_sse": [[4, "module-phylojunction.calculation.discrete_sse"]], "phylojunction.calculation.math_utils": [[4, 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"phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler.seed_age"]], "seed_age (phylojunction.calculation.discrete_sse.macroevoleventhandler attribute)": [[4, "phylojunction.calculation.discrete_sse.MacroevolEventHandler.seed_age"]], "set2int_dict (phylojunction.calculation.discrete_sse.stateintopatternconverter attribute)": [[4, "phylojunction.calculation.discrete_sse.StateIntoPatternConverter.set2int_dict"]], "slice_age_ends (phylojunction.calculation.discrete_sse.discretestatedependentparametermanager attribute)": [[4, "phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager.slice_age_ends"]], "slice_age_ends (phylojunction.calculation.discrete_sse.discretestatedependentprobabilityhandler attribute)": [[4, "phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler.slice_age_ends"]], "slice_age_ends (phylojunction.calculation.discrete_sse.macroevoleventhandler attribute)": [[4, "phylojunction.calculation.discrete_sse.MacroevolEventHandler.slice_age_ends"]], "slice_t_ends (phylojunction.calculation.discrete_sse.discretestatedependentparametermanager attribute)": [[4, "phylojunction.calculation.discrete_sse.DiscreteStateDependentParameterManager.slice_t_ends"]], "slice_t_ends (phylojunction.calculation.discrete_sse.discretestatedependentprobabilityhandler attribute)": [[4, "phylojunction.calculation.discrete_sse.DiscreteStateDependentProbabilityHandler.slice_t_ends"]], "slice_t_ends (phylojunction.calculation.discrete_sse.macroevoleventhandler attribute)": [[4, "phylojunction.calculation.discrete_sse.MacroevolEventHandler.slice_t_ends"]], "sse_rate_manager (phylojunction.calculation.discrete_sse.macroevoleventhandler attribute)": [[4, "phylojunction.calculation.discrete_sse.MacroevolEventHandler.sse_rate_manager"]], "state (phylojunction.calculation.discrete_sse.discretestatedependentparameter attribute)": [[4, 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attribute)": [[5, "phylojunction.data.attribute_transition.AttributeTransition.attr_label"]], "brosc_node (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.brosc_node"]], "clado_at_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.clado_at_dict"]], "condition_on_obs_both_sides_root (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.condition_on_obs_both_sides_root"]], "epsilon (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.epsilon"]], "extant_sampled_terminal_nodes_labels (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.extant_sampled_terminal_nodes_labels"]], "extant_terminal_nodes_labels (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.extant_terminal_nodes_labels"]], "extant_terminal_sampled_state_count_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.extant_terminal_sampled_state_count_dict"]], "extant_terminal_state_count_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.extant_terminal_state_count_dict"]], "extinct_terminal_nodes_labels (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.extinct_terminal_nodes_labels"]], "extinct_terminal_state_count_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.extinct_terminal_state_count_dict"]], "extract_reconstructed_tree() (phylojunction.data.tree.annotatedtree method)": [[5, "phylojunction.data.tree.AnnotatedTree.extract_reconstructed_tree"]], "from_state (phylojunction.data.attribute_transition.attributetransition attribute)": [[5, "phylojunction.data.attribute_transition.AttributeTransition.from_state"]], 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"phylojunction.data.sampled_ancestor.SampledAncestor.global_time"]], "is_extant_or_sa_on_both_sides_complete_tr_root() (phylojunction.data.tree.annotatedtree method)": [[5, "phylojunction.data.tree.AnnotatedTree.is_extant_or_sa_on_both_sides_complete_tr_root"]], "label (phylojunction.data.sampled_ancestor.sampledancestor attribute)": [[5, "phylojunction.data.sampled_ancestor.SampledAncestor.label"]], "lineage_node_label (phylojunction.data.sampled_ancestor.sampledancestor attribute)": [[5, "phylojunction.data.sampled_ancestor.SampledAncestor.lineage_node_label"]], "max_age (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.max_age"]], "n_extant_sampled_terminal_nodes (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.n_extant_sampled_terminal_nodes"]], "n_extant_terminal_nodes (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.n_extant_terminal_nodes"]], "n_extinct_sampled_terminal_nodes (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.n_extinct_sampled_terminal_nodes"]], "n_extinct_terminal_nodes (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.n_extinct_terminal_nodes"]], "n_sa_nodes (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.n_sa_nodes"]], "node_ages_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.node_ages_dict"]], "node_attr_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.node_attr_dict"]], "node_heights_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.node_heights_dict"]], "origin_age (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.origin_age"]], "origin_edge_length (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.origin_edge_length"]], "origin_node (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.origin_node"]], "phylojunction.data": [[5, "module-phylojunction.data"]], "phylojunction.data.attribute_transition": [[5, "module-phylojunction.data.attribute_transition"]], "phylojunction.data.sampled_ancestor": [[5, "module-phylojunction.data.sampled_ancestor"]], "phylojunction.data.tree": [[5, "module-phylojunction.data.tree"]], "pj_get_name_mrca_obs_terminals() (in module phylojunction.data.tree)": [[5, "phylojunction.data.tree.pj_get_name_mrca_obs_terminals"]], "plot_ann_tree() (in module phylojunction.data.tree)": [[5, "phylojunction.data.tree.plot_ann_tree"]], "plot_node() (phylojunction.data.tree.annotatedtree method)": [[5, "phylojunction.data.tree.AnnotatedTree.plot_node"]], "populate_nd_attr_dict() (phylojunction.data.tree.annotatedtree method)": [[5, "phylojunction.data.tree.AnnotatedTree.populate_nd_attr_dict"]], "rec_node_ages_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.rec_node_ages_dict"]], "rec_node_heights_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.rec_node_heights_dict"]], "rec_str() (phylojunction.data.tree.annotatedtree method)": [[5, "phylojunction.data.tree.AnnotatedTree.rec_str"]], "rec_tr_at_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.rec_tr_at_dict"]], "rec_tr_clado_at_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.rec_tr_clado_at_dict"]], "rec_tr_root_age (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.rec_tr_root_age"]], "rec_tr_root_node (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.rec_tr_root_node"]], "rec_tr_sa_lineage_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.rec_tr_sa_lineage_dict"]], "root_age (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.root_age"]], "root_node (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.root_node"]], "sa_lineage_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.sa_lineage_dict"]], "sa_obs_nodes_labels (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.sa_obs_nodes_labels"]], "seed_age (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.seed_age"]], "slice_age_ends (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.slice_age_ends"]], "slice_t_ends (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.slice_t_ends"]], "state (phylojunction.data.sampled_ancestor.sampledancestor attribute)": [[5, "phylojunction.data.sampled_ancestor.SampledAncestor.state"]], "state_count (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.state_count"]], "state_count_dict (phylojunction.data.tree.annotatedtree attribute)": [[5, "phylojunction.data.tree.AnnotatedTree.state_count_dict"]], "str_representation (phylojunction.data.attribute_transition.attributetransition attribute)": [[5, "phylojunction.data.attribute_transition.AttributeTransition.str_representation"]], "str_representation (phylojunction.data.sampled_ancestor.sampledancestor attribute)": [[5, "phylojunction.data.sampled_ancestor.SampledAncestor.str_representation"]], "subtending_or_speciating_node_label 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(phylojunction.interface.grammar.dn_grammar.pjdngrammar class method)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.grammar_check"]], "init_return_ann_tr() (phylojunction.interface.grammar.ct_fn_grammar.pjctfngrammar class method)": [[11, "phylojunction.interface.grammar.ct_fn_grammar.PJCtFnGrammar.init_return_ann_tr"]], "init_return_discrete_sse_dn() (phylojunction.interface.grammar.dn_grammar.pjdngrammar class method)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.init_return_discrete_SSE_dn"]], "init_return_parametric_dn() (phylojunction.interface.grammar.dn_grammar.pjdngrammar class method)": [[11, "phylojunction.interface.grammar.dn_grammar.PJDnGrammar.init_return_parametric_dn"]], "init_return_sse_stash() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_sse_stash"]], "init_return_state_dep_prob() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_state_dep_prob"]], "init_return_state_dep_rate() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_state_dep_rate"]], "init_return_tree_mapped_with_attr() (phylojunction.interface.grammar.det_fn_grammar.pjdetfngrammar class method)": [[11, "phylojunction.interface.grammar.det_fn_grammar.PJDetFnGrammar.init_return_tree_mapped_with_attr"]], "make_discretestatedependentprobability() (in module phylojunction.interface.grammar.det_fn_discrete_sse_makers)": [[11, "phylojunction.interface.grammar.det_fn_discrete_sse_makers.make_DiscreteStateDependentProbability"]], "make_discretestatedependentrate() (in module phylojunction.interface.grammar.det_fn_discrete_sse_makers)": [[11, "phylojunction.interface.grammar.det_fn_discrete_sse_makers.make_DiscreteStateDependentRate"]], "make_ssestash() (in module phylojunction.interface.grammar.det_fn_discrete_sse_makers)": [[11, "phylojunction.interface.grammar.det_fn_discrete_sse_makers.make_SSEStash"]], "make_discrete_sse_dn() (in module phylojunction.interface.grammar.dn_discrete_sse_makers)": [[11, "phylojunction.interface.grammar.dn_discrete_sse_makers.make_discrete_SSE_dn"]], "make_mapped_ann_tree() (in module phylojunction.interface.grammar.det_fn_map_attribute)": [[11, "phylojunction.interface.grammar.det_fn_map_attribute.make_mapped_ann_tree"]], "make_tree_reader() (in module phylojunction.interface.grammar.ct_fn_treereader_makers)": [[11, "phylojunction.interface.grammar.ct_fn_treereader_makers.make_tree_reader"]], "phylojunction.interface.grammar": [[11, "module-phylojunction.interface.grammar"]], "phylojunction.interface.grammar.ct_fn_grammar": [[11, "module-phylojunction.interface.grammar.ct_fn_grammar"]], "phylojunction.interface.grammar.ct_fn_treereader_makers": [[11, "module-phylojunction.interface.grammar.ct_fn_treereader_makers"]], "phylojunction.interface.grammar.det_fn_discrete_sse_makers": [[11, "module-phylojunction.interface.grammar.det_fn_discrete_sse_makers"]], "phylojunction.interface.grammar.det_fn_grammar": [[11, "module-phylojunction.interface.grammar.det_fn_grammar"]], "phylojunction.interface.grammar.det_fn_map_attribute": [[11, "module-phylojunction.interface.grammar.det_fn_map_attribute"]], "phylojunction.interface.grammar.dn_discrete_sse_makers": [[11, "module-phylojunction.interface.grammar.dn_discrete_sse_makers"]], "phylojunction.interface.grammar.dn_grammar": [[11, "module-phylojunction.interface.grammar.dn_grammar"]], "ct_fn_name (phylojunction.pgm.pgm.constantfn property)": [[12, "phylojunction.pgm.pgm.ConstantFn.CT_FN_NAME"]], "constantfn (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.ConstantFn"]], "dn_name (phylojunction.pgm.pgm.distrforsampling property)": [[12, "phylojunction.pgm.pgm.DistrForSampling.DN_NAME"]], "deterministicnodedag (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG"]], "directedacyclicgraph (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph"]], "distrforsampling (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.DistrForSampling"]], "nodedag (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.NodeDAG"]], "stochasticnodedag (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG"]], "valuegenerator (class in phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.ValueGenerator"]], "abstract_attribute() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.abstract_attribute"]], "add_node() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.add_node"]], "call_order_idx (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.call_order_idx"]], "constant_fn (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.constant_fn"]], "extract_vals_as_str_from_node_dag() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.extract_vals_as_str_from_node_dag"]], "extract_value_from_dagnodes() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.extract_value_from_dagnodes"]], "generate() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.generate"]], "generate_value() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.generate_value"]], "get_display_str_by_name() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_display_str_by_name"]], "get_node_dag_by_name() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_node_dag_by_name"]], "get_node_stats_str() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.get_node_stats_str"]], "get_node_stats_str() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.get_node_stats_str"]], "get_node_stats_str() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.get_node_stats_str"]], "get_rev_inference_spec_info() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.get_rev_inference_spec_info"]], "get_sorted_node_dag_list() (phylojunction.pgm.pgm.directedacyclicgraph method)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.get_sorted_node_dag_list"]], "get_start2end_str() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.get_start2end_str"]], "init_check_vectorize_sample_size() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.init_check_vectorize_sample_size"]], "is_clamped (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_clamped"]], "is_deterministic (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_deterministic"]], "is_sampled (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.is_sampled"]], "n_nodes (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.n_nodes"]], "n_repl() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.n_repl"]], "n_samples() (phylojunction.pgm.pgm.valuegenerator method)": [[12, "phylojunction.pgm.pgm.ValueGenerator.n_samples"]], "name_node_dict (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.name_node_dict"]], "node_name (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.node_name"]], "node_val_dict (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.node_val_dict"]], "operator_weight (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.operator_weight"]], "parent_nd_list (phylojunction.pgm.pgm.nodedag attribute)": [[12, "phylojunction.pgm.pgm.NodeDAG.parent_nd_list"]], "phylojunction.pgm": [[12, "module-phylojunction.pgm"]], "phylojunction.pgm.pgm": [[12, "module-phylojunction.pgm.pgm"]], "plot_blank() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.plot_blank"]], "plot_node() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.plot_node"]], "plot_node() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.plot_node"]], "plot_node() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.plot_node"]], "plot_node_histogram() (in module phylojunction.pgm.pgm)": [[12, "phylojunction.pgm.pgm.plot_node_histogram"]], "populate_operator_weight() (phylojunction.pgm.pgm.deterministicnodedag method)": [[12, "phylojunction.pgm.pgm.DeterministicNodeDAG.populate_operator_weight"]], "populate_operator_weight() (phylojunction.pgm.pgm.nodedag method)": [[12, "phylojunction.pgm.pgm.NodeDAG.populate_operator_weight"]], "populate_operator_weight() (phylojunction.pgm.pgm.stochasticnodedag method)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.populate_operator_weight"]], "random_seed (phylojunction.pgm.pgm.directedacyclicgraph property)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.random_seed"]], "repl_size (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.repl_size"]], "sample_size (phylojunction.pgm.pgm.directedacyclicgraph attribute)": [[12, "phylojunction.pgm.pgm.DirectedAcyclicGraph.sample_size"]], "sample_size (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.sample_size"]], "sampling_dn (phylojunction.pgm.pgm.stochasticnodedag attribute)": [[12, "phylojunction.pgm.pgm.StochasticNodeDAG.sampling_dn"]], "value (phylojunction.pgm.pgm.nodedag property)": [[12, "phylojunction.pgm.pgm.NodeDAG.value"]], "add_within_hpd_col() (in module phylojunction.plotting.pj_organize)": [[13, "phylojunction.plotting.pj_organize.add_within_hpd_col"]], "join_dataframes() (in module phylojunction.plotting.pj_organize)": [[13, "phylojunction.plotting.pj_organize.join_dataframes"]], "phylojunction.plotting": [[13, "module-phylojunction.plotting"]], "phylojunction.plotting.pj_draw": [[13, "module-phylojunction.plotting.pj_draw"]], "phylojunction.plotting.pj_organize": [[13, "module-phylojunction.plotting.pj_organize"]], "phylojunction.plotting.pj_seeing_colors": [[13, "module-phylojunction.plotting.pj_seeing_colors"]], "phylojunction.plotting.pj_testing_tree_plotting": [[13, "module-phylojunction.plotting.pj_testing_tree_plotting"]], "plot_intervals() (in module phylojunction.plotting.pj_draw)": [[13, "phylojunction.plotting.pj_draw.plot_intervals"]], "plot_violins() (in module phylojunction.plotting.pj_draw)": [[13, "phylojunction.plotting.pj_draw.plot_violins"]], "truncate_colormap() (in module phylojunction.plotting.pj_seeing_colors)": [[13, "phylojunction.plotting.pj_seeing_colors.truncate_colormap"]], "dump_pgm_data() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.dump_pgm_data"]], "dump_serialized_pgm() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.dump_serialized_pgm"]], "dump_trees_rb_smap_dfs() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.dump_trees_rb_smap_dfs"]], "get_write_inference_rev_scripts() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.get_write_inference_rev_scripts"]], "initialize_scalar_dataframe() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.initialize_scalar_dataframe"]], "initialize_tree_dataframe() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.initialize_tree_dataframe"]], "is_csv() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.is_csv"]], "is_tsv() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.is_tsv"]], "parse_cli_str_write_fig() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.parse_cli_str_write_fig"]], "phylojunction.readwrite": [[14, "module-phylojunction.readwrite"]], "phylojunction.readwrite.pj_read": [[14, "module-phylojunction.readwrite.pj_read"]], "phylojunction.readwrite.pj_write": [[14, "module-phylojunction.readwrite.pj_write"]], "prep_data_df() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.prep_data_df"]], "prep_data_filepaths_dfs() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.prep_data_filepaths_dfs"]], "prep_trees_rb_smap_dfs() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.prep_trees_rb_smap_dfs"]], "read_csv_tsv_into_dataframe() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_csv_tsv_into_dataframe"]], "read_node_attr_update_tree() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_node_attr_update_tree"]], "read_nwk_tree_str() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_nwk_tree_str"]], "read_serialized_pgm() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_serialized_pgm"]], "read_text_file() (in module phylojunction.readwrite.pj_read)": [[14, "phylojunction.readwrite.pj_read.read_text_file"]], "write_data_df() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.write_data_df"]], "write_fig_to_file() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.write_fig_to_file"]], "write_str_list() (in module phylojunction.readwrite.pj_write)": [[14, "phylojunction.readwrite.pj_write.write_str_list"]], "annotatedtreeincorrectannotationerror": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeIncorrectAnnotationError"]], "annotatedtreemissingnodename": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeMissingNodeName"]], "annotatedtreemisspecerror": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeMisspecError"]], "annotatedtreenodemissingattrerror": [[15, "phylojunction.utility.exception_classes.AnnotatedTreeNodeMissingAttrError"]], "dagcannotaddnodeerror": [[15, "phylojunction.utility.exception_classes.DAGCannotAddNodeError"]], "dagcannotinitialize": [[15, "phylojunction.utility.exception_classes.DAGCannotInitialize"]], "dimensionalityerror": [[15, "phylojunction.utility.exception_classes.DimensionalityError"]], "dimensionalitywarning": [[15, "phylojunction.utility.exception_classes.DimensionalityWarning"]], "functionargsmismatcherror": [[15, "phylojunction.utility.exception_classes.FunctionArgsMismatchError"]], "generatefailerror": [[15, "phylojunction.utility.exception_classes.GenerateFailError"]], "incorrectdimensionerror": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError"]], "inexistentvariableerror": [[15, "phylojunction.utility.exception_classes.InexistentVariableError"]], "invalidmcmcchainlength": [[15, "phylojunction.utility.exception_classes.InvalidMCMCChainLength"]], "maxnfailedattemptslimit": [[15, "phylojunction.utility.exception_classes.MaxNFailedAttemptsLimit"]], "missingcolumnname": [[15, "phylojunction.utility.exception_classes.MissingColumnName"]], "noplatingallowederror": [[15, "phylojunction.utility.exception_classes.NoPlatingAllowedError"]], "nodedagstatcantfloaterror": [[15, "phylojunction.utility.exception_classes.NodeDAGStatCantFloatError"]], "nodeinferencedimensionalityerror": [[15, "phylojunction.utility.exception_classes.NodeInferenceDimensionalityError"]], "notbetweenzeroandoneerror": [[15, "phylojunction.utility.exception_classes.NotBetweenZeroAndOneError"]], "objinitincorrectdimensionerror": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError"]], "objinitinvalidargerror": [[15, "phylojunction.utility.exception_classes.ObjInitInvalidArgError"]], "objinitmissingparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitMissingParameterError"]], "objinitmissingstatedependentparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitMissingStateDependentParameterError"]], "objinitrepeatedstatedependentparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitRepeatedStateDependentParameterError"]], "objinitrequirenonzerostatedependentparametererror": [[15, "phylojunction.utility.exception_classes.ObjInitRequireNonZeroStateDependentParameterError"]], "objinitrequiresameparametertypeerror": [[15, "phylojunction.utility.exception_classes.ObjInitRequireSameParameterTypeError"]], "pjcliinvalidinputerror": [[15, "phylojunction.utility.exception_classes.PJCLIInvalidInputError"]], "pjclisampleoutofrangeerror": [[15, "phylojunction.utility.exception_classes.PJCLISampleOutOfRangeError"]], "pjiofiledoesnotexisterror": [[15, "phylojunction.utility.exception_classes.PJIOFileDoesNotExistError"]], "parsectfninitfailerror": [[15, "phylojunction.utility.exception_classes.ParseCtFnInitFailError"]], "parsedetfninitfailerror": [[15, "phylojunction.utility.exception_classes.ParseDetFnInitFailError"]], "parsedninitfailerror": [[15, "phylojunction.utility.exception_classes.ParseDnInitFailError"]], "parsefunctionargerror": [[15, "phylojunction.utility.exception_classes.ParseFunctionArgError"]], "parseinvalidargumenterror": [[15, "phylojunction.utility.exception_classes.ParseInvalidArgumentError"]], "parseinvalidnewickstringerror": [[15, "phylojunction.utility.exception_classes.ParseInvalidNewickStringError"]], "parsemissingargumenterror": [[15, "phylojunction.utility.exception_classes.ParseMissingArgumentError"]], "parsemissingparametererror": [[15, "phylojunction.utility.exception_classes.ParseMissingParameterError"]], "parsemissingspecificationerror": [[15, "phylojunction.utility.exception_classes.ParseMissingSpecificationError"]], "parsemutuallyexclusiveparameterserror": [[15, "phylojunction.utility.exception_classes.ParseMutuallyExclusiveParametersError"]], "parsenotaparametererror": [[15, "phylojunction.utility.exception_classes.ParseNotAParameterError"]], "parsepathdoesnotexisterror": [[15, "phylojunction.utility.exception_classes.ParsePathDoesNotExistError"]], "parserequireintegererror": [[15, "phylojunction.utility.exception_classes.ParseRequireIntegerError"]], "parserequirenumericerror": [[15, "phylojunction.utility.exception_classes.ParseRequireNumericError"]], "parserequirepositiveintegererror": [[15, "phylojunction.utility.exception_classes.ParseRequirePositiveIntegerError"]], "parserequiresinglevalueerror": [[15, "phylojunction.utility.exception_classes.ParseRequireSingleValueError"]], "replicatenumbererror": [[15, "phylojunction.utility.exception_classes.ReplicateNumberError"]], "runtimelimit": [[15, "phylojunction.utility.exception_classes.RunTimeLimit"]], "ssestashmisspec": [[15, "phylojunction.utility.exception_classes.SSEStashMisspec"]], "scriptsyntaxerror": [[15, "phylojunction.utility.exception_classes.ScriptSyntaxError"]], "statedependentparametermisspec": [[15, "phylojunction.utility.exception_classes.StateDependentParameterMisspec"]], "variableassignmenterror": [[15, "phylojunction.utility.exception_classes.VariableAssignmentError"]], "variablemisspec": [[15, "phylojunction.utility.exception_classes.VariableMisspec"]], "at_least (phylojunction.utility.exception_classes.objinitincorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.ObjInitIncorrectDimensionError.at_least"]], "autovivify() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.autovivify"]], "check_and_vectorize_if_must() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.check_and_vectorize_if_must"]], "cmd_line (phylojunction.utility.exception_classes.scriptsyntaxerror attribute)": [[15, "phylojunction.utility.exception_classes.ScriptSyntaxError.cmd_line"]], "container_name (phylojunction.utility.exception_classes.incorrectdimensionerror attribute)": [[15, "phylojunction.utility.exception_classes.IncorrectDimensionError.container_name"]], "create_str_defaultdict() (in module phylojunction.utility.helper_functions)": [[15, "phylojunction.utility.helper_functions.create_str_defaultdict"]], "ct_fn_name (phylojunction.utility.exception_classes.parsectfninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseCtFnInitFailError.ct_fn_name"]], "det_fn_name (phylojunction.utility.exception_classes.parsedetfninitfailerror attribute)": [[15, "phylojunction.utility.exception_classes.ParseDetFnInitFailError.det_fn_name"]], "det_name (phylojunction.utility.exception_classes.noplatingallowederror attribute)": [[15, "phylojunction.utility.exception_classes.NoPlatingAllowedError.det_name"]], "dn_name (phylojunction.utility.exception_classes.dimensionalityerror attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityError.dn_name"]], "dn_name (phylojunction.utility.exception_classes.dimensionalitywarning attribute)": [[15, "phylojunction.utility.exception_classes.DimensionalityWarning.dn_name"]], "dn_name 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--- a/examples/parametric.pj +++ b/examples/parametric.pj @@ -1,4 +1,4 @@ # stochastic-node variables ('rv1') assignment ln_mean ~ exponential(n=5, rate=1.5) ln_sd ~ unif(n=5, min=0.05, max=0.15) -ln_rv ~ lognormal(n=5, nr=2, mean=ln_mean, sd=ln_sd) +ln_rv ~ lognormal(n=5, nr=2, meanlog=ln_mean, sdlog=ln_sd) diff --git a/src/phylojunction/distribution/dn_discrete_sse.py b/src/phylojunction/distribution/dn_discrete_sse.py index 47364b6..3195d92 100644 --- a/src/phylojunction/distribution/dn_discrete_sse.py +++ b/src/phylojunction/distribution/dn_discrete_sse.py @@ -101,9 +101,9 @@ class DnSSE(pgm.DistrForSampling): other words, if the difference between a tiny value 'x' and 0.0 is smaller than epsilon, then 'x' is set to 0.0. Defaults to 1e-12. - runtime_limit (int, optional): Runtime ceiling (in minutes) + runtime_limit (int, optional): Runtime ceiling (in seconds) for obtaining the 'n' tree samples. If this limit is met, - the sampling procedure is aborted. Defaults to 5. + the sampling procedure is aborted. Defaults to 300. max_n_failed_attempts (int, optional): Maximum number of failed tree sampling attempts (replicates included) before PhyloJunction quits. Defaults to 200. @@ -174,7 +174,7 @@ def __init__(self, max_rec_taxa: int = int(1e12), abort_at_alive_count: int = int(1e12), epsilon: float = 1e-12, - runtime_limit: int = 5, + runtime_limit: int = 300, max_n_failed_attempts: int = 200, rng_seed: ty.Optional[int] = None, debug: ty.Optional[bool] = False, @@ -2180,7 +2180,7 @@ def generate(self) -> ty.List[AnnotatedTree]: while repl_size < self.n_repl: # abort due to runtime limit ellapsed_time = \ - pjh.get_ellapsed_time_in_minutes(start_time, time.time()) + pjh.get_ellapsed_time_in_seconds(start_time, time.time()) if ellapsed_time >= self.runtime_limit: raise ec.RunTimeLimit(self.runtime_limit) diff --git a/src/phylojunction/distribution/dn_discrete_sse.pyi b/src/phylojunction/distribution/dn_discrete_sse.pyi index 7a7482f..bae4a0a 100644 --- a/src/phylojunction/distribution/dn_discrete_sse.pyi +++ b/src/phylojunction/distribution/dn_discrete_sse.pyi @@ -54,7 +54,7 @@ class DnSSE(pgm.DistrForSampling): max_rec_taxa: int = int(1e12), abort_at_alive_count: int = int(1e12), epsilon: float = 1e-12, - runtime_limit: int = 5, + runtime_limit: int = 300, max_n_failed_attempts: int = 100, rng_seed: ty.Optional[int] = None, debug: ty.Optional[bool] = False, diff --git a/src/phylojunction/interface/grammar/dn_grammar.py b/src/phylojunction/interface/grammar/dn_grammar.py index e6d716f..a33386c 100644 --- a/src/phylojunction/interface/grammar/dn_grammar.py +++ b/src/phylojunction/interface/grammar/dn_grammar.py @@ -20,7 +20,7 @@ class PJDnGrammar(): dn_grammar_dict: ty.Dict[str, ty.Tuple[str, ...]] = \ { "lognormal": - tuple(["n", "nr", "mean", "sd", "log_space"]), + tuple(["n", "nr", "meanlog", "sdlog", "log_space"]), "normal": tuple(["n", "nr", "mean", "sd"]), "exponential": @@ -131,7 +131,7 @@ def init_return_parametric_dn( raise ec.ParseRequireIntegerError( dnpar.DnNormal.DN_NAME, arg) - elif arg == "mean": + elif arg == "meanlog": try: ln_mean = [float(v) for v in extracted_val_list] @@ -139,7 +139,7 @@ def init_return_parametric_dn( raise ec.ParseRequireNumericError( dnpar.DnNormal.DN_NAME, arg) - elif arg == "sd": + elif arg == "sdlog": try: ln_sd = [float(v) for v in extracted_val_list] @@ -157,7 +157,7 @@ def init_return_parametric_dn( ln_log_space = False # making sure essential parameters of distribution have been specified - for par_obj, par_name in ((ln_mean, "mean"), (ln_sd, "sd")): + for par_obj, par_name in ((ln_mean, "meanlog"), (ln_sd, "sdlog")): if not par_obj: raise ec.ParseMissingParameterError(par_name) diff --git a/src/phylojunction/utility/helper_functions.py b/src/phylojunction/utility/helper_functions.py index 62df7b9..2d599a6 100644 --- a/src/phylojunction/utility/helper_functions.py +++ b/src/phylojunction/utility/helper_functions.py @@ -152,21 +152,21 @@ def check_and_vectorize_if_must( return vectorized_param_list -def get_ellapsed_time_in_minutes(start: float, end: float) -> int: - """Calculate ellapsed time +def get_ellapsed_time_in_seconds(start: float, end: float) -> int: + """Calculate ellapsed time in seconds. Args: start (float): Start of time window end (float): End of time window Returns: - int: Ellapsed time in minutes in time window + int: Ellapsed time in seconds in time window """ # returns (min, sec) ellapsed_minutes, ellapsed_secs = divmod(end - start, 60) - # return int(ellapsed_minutes * 60 + ellapsed_secs) # in seconds - return int(ellapsed_minutes) + return int(ellapsed_minutes * 60 + ellapsed_secs) # in seconds + # return int(ellapsed_minutes) def is_val_in_interval( @@ -251,4 +251,4 @@ def symmetric_difference( print_progress(49, 100) - print(get_ellapsed_time_in_minutes(0.0, 125)) # 2 minutes (and 5 seconds) + print(get_ellapsed_time_in_seconds(0.0, 125)) # 2 minutes (and 5 seconds) diff --git a/src/phylojunction/utility/helper_functions.pyi b/src/phylojunction/utility/helper_functions.pyi index a4b17a7..c09ac08 100644 --- a/src/phylojunction/utility/helper_functions.pyi +++ b/src/phylojunction/utility/helper_functions.pyi @@ -5,5 +5,5 @@ def print_progress(idx: int, iterator_len: int) -> None: ... def create_str_defaultdict() -> defaultdict: ... def autovivify(levels: int = ..., final=...) -> ty.DefaultDict: ... def check_and_vectorize_if_must(param_list: ty.Union[int, float, str, ty.List[ty.Union[int, float, str]]], dn_name: str, size_to_grow: int = 1) -> ty.List[ty.List[ty.Union[int, float, str]]]: ... -def get_ellapsed_time_in_minutes(start: float, end: float) -> int: ... +def get_ellapsed_time_in_seconds(start: float, end: float) -> int: ... def symmetric_difference(set1: ty.Set[ty.Any], set2: ty.Set[ty.Any]) -> ty.Set[ty.Any]: ... \ No newline at end of file diff --git a/tests/interface/test_cmd_parametric_sampling_dn_assignment.py b/tests/interface/test_cmd_parametric_sampling_dn_assignment.py index c33e83d..8f3a644 100644 --- a/tests/interface/test_cmd_parametric_sampling_dn_assignment.py +++ b/tests/interface/test_cmd_parametric_sampling_dn_assignment.py @@ -35,7 +35,6 @@ def test_sampling_unif_assignment(self): self.assertGreater(1.0, max(a_node_dag.value)) self.assertEqual(1, dag_obj.n_nodes) - def test_sampling_unif_vectorized_assignment(self): """ Test if uniform (with vectorized inputs) sampling distribution @@ -65,7 +64,6 @@ def test_sampling_unif_vectorized_assignment(self): self.assertTrue(tup[0] <= a_node_dag.value[idx * 2] < tup[1]) self.assertTrue(tup[0] <= a_node_dag.value[idx * 2 + 1] < tup[1]) self.assertEqual(2, dag_obj.n_nodes) - def test_sampling_exp_assignment(self): """ @@ -115,7 +113,6 @@ def test_sampling_exp_assignment(self): self.assertAlmostEqual(0.5, mean(a_node_dag2.value), delta=0.05) self.assertEqual(2, dag_obj.n_nodes) - def test_sampling_gamma_assignment(self): """ Test if gamma sampling distribution assignments are correctly @@ -165,7 +162,6 @@ def test_sampling_gamma_assignment(self): self.assertAlmostEqual(1.0, mean(a_node_dag2.value), delta=0.05) self.assertEqual(2, dag_obj.n_nodes) - def test_sampling_normal_assignment(self): """ Test if normal sampling distribution assignments are correctly @@ -192,7 +188,6 @@ def test_sampling_normal_assignment(self): self.assertAlmostEqual(0.5, mean(a_node_dag.value), delta=0.1) self.assertEqual(1, dag_obj.n_nodes) - def test_sampling_ln_assignment(self): """ Test if log-normal sampling distribution assignments are @@ -205,7 +200,7 @@ def test_sampling_ln_assignment(self): ################################### dag_obj = pgm.DirectedAcyclicGraph() - cmd_line1 = "ln1 ~ lognormal(n=100000, mean=-3.25, sd=0.25)" + cmd_line1 = "ln1 ~ lognormal(n=100000, meanlog=-3.25, sdlog=0.25)" stoch_node_name, _, stoch_node_spec = \ re.split(cmdu.sampled_as_regex, cmd_line1) @@ -228,8 +223,8 @@ def test_sampling_ln_assignment(self): ########################## exp_mean = str(math.exp(-3.25)) - cmd_line2 = "ln2 ~ lognormal(n=100000, mean=" + exp_mean \ - + ", sd=0.25, log_space=\"false\")" + cmd_line2 = "ln2 ~ lognormal(n=100000, meanlog=" + exp_mean \ + + ", sdlog=0.25, log_space=\"false\")" stoch_node_name, _, stoch_node_spec = \ re.split(cmdu.sampled_as_regex, cmd_line2) @@ -247,7 +242,6 @@ def test_sampling_ln_assignment(self): self.assertAlmostEqual(0.01, stdev(a_node_dag.value), delta=0.1) self.assertEqual(2, dag_obj.n_nodes) - def test_unif_misspec(self): """ Test uniform sampling distribution assignment throws exception @@ -321,7 +315,6 @@ def test_unif_misspec(self): "the name of a distribution (e.g., \'normal\') or its " "specification (e.g., \'(mean=0.0, sd=1.0)\'), or both.")) - def test_exp_misspec(self): """ Test exponential sampling distribution assignment throws @@ -381,7 +374,6 @@ def test_exp_misspec(self): "the name of a distribution (e.g., \'normal\') or its " "specification (e.g., \'(mean=0.0, sd=1.0)\'), or both.")) - def test_gamma_misspec(self): """ Test gamma sampling distribution assignment throws exception @@ -431,7 +423,6 @@ def test_gamma_misspec(self): "the name of a distribution (e.g., \'normal\') or its " "specification (e.g., \'(mean=0.0, sd=1.0)\'), or both.")) - def test_normal_misspec(self): """ Test normal sampling distribution assignment throws exception @@ -487,7 +478,7 @@ def test_ln_misspec(self): dag_obj = pgm.DirectedAcyclicGraph() - cmd_line1 = "ln ~ lognormal(n=1, nr=1, sd=0.25)" + cmd_line1 = "ln ~ lognormal(n=1, nr=1, sdlog=0.25)" stoch_node_name, _, stoch_node_spec = \ re.split(cmdu.sampled_as_regex, cmd_line1) @@ -498,7 +489,7 @@ def test_ln_misspec(self): self.assertEqual(str(exc_inner.exception), "Parsing the specification of \'lognormal\' failed. " \ - "Parameter \'mean\' is missing.") + "Parameter \'meanlog\' is missing.") cmd_line2 = "ln ~ lognormal(n=1, rate=1.0)" diff --git a/tests/readwrite/test_data_dump.py b/tests/readwrite/test_data_dump.py index a5034ec..a7addba 100644 --- a/tests/readwrite/test_data_dump.py +++ b/tests/readwrite/test_data_dump.py @@ -555,14 +555,14 @@ def test_bisse_data_dump_tree_nd_states_table(self): # exist -- don't forget to export it! # # Then you can do: - # $ python3 tests/readwrite/test_data_dump.py + # $ python3.11 tests/readwrite/test_data_dump.py # # or # - # $ python3 -m tests.readwrite.test_data_dump + # $ python3.11 -m tests.readwrite.test_data_dump # # or # - # $ python3 -m unittest tests.readwrite.test_data_dump.TestDataDump.test_bisse_data_dump_file_names + # $ python3.11 -m unittest tests.readwrite.test_data_dump.TestDataDump.test_bisse_data_dump_file_names unittest.main() \ No newline at end of file@@ -571,7 +571,7 @@n(integer, optional): Number of samples to draw (samples are i.i.d.). Defaults to 1.Gamma
Normal
-The function for assigning a normal (
+normal) distribution to a variable has four parameters:The function for assigning a normal (
normal) distribution to a random variable has four parameters:@@ -589,13 +589,13 @@n(integer, optional): Number of samples to draw (samples are i.i.d.). Defaults to 1.Normal<
Log-normal
-The function for assigning a log-normal (
+lognormal) distribution to a variable has five parameters:The function for assigning a log-normal (
lognormal) distribution to a random variable has five parameters:
@@ -716,7 +716,7 @@n(integer, optional): Number of samples to draw (samples are i.i.d.). Defaults to 1.-nr(integer, optional): Number of replicates to draw per sample. Defaults to 1.-mean(real, required): Mean (location) of distribution.+sd(positive real, required): Standard deviation (scale) of distribution.+meanlog(real, required): Mean (location) of distribution over the logarithm of the random variable.sdlog(positive real, required): Standard deviation (scale) of distribution over the logarithm of the random variable.log_space(string boolean, optional): Whether the value ofmeanis in log-space. Defaults to “true”.Discrete SSE
min_rec_taxa(positive integer, optional): Minimum number of sampled (extant and sampled ancestors) nodes the tree should have. Defaults to 0.max_rec_taxa(positive integer, optional): Maximum number of sampled (extant and sampled ancestors) nodes the tree should have. Defaults to 1e12.-abort_at_alive_count(positive integer, optional): The count of a tree’s living nodes (irrespective of node sampling) at which point the tree is considered too large for simulation to continue. Trees can grow out of control whenstop="age"and one of the rates allows it to grow too big before the stopping condition is met. This parameter can be used to throw away such trees and preventing PhyloJunction from crashing. Defaults to 1e12.+runtime_limit(positive integer, optional): Maximum number of minutes to wait until all samples are drawn. Sampling is aborted at this point. Defaults to 5.runtime_limit(positive integer, optional): Maximum number of seconds to wait until all samples are drawn. Sampling is aborted at this point. Defaults to 300.max_n_attempts(positive integer, optional): Maximum number of (failed) attempts before sampling is aborted. Defaults to 200.
SubmodulesReturns: -
Submodules
phylojunction.data.sampled_ancestor module
Submodules -