hstrat
======

.. currentmodule:: ~hstrat


.. automodule:: hstrat.hstrat


   

   

   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
      
   
   
   
   
      
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
      
   
   
   
   
      
   
   
   
   
   
      
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
      
   
   
   
   
   
      
   
   
   
   
      
   
   
   
   
      
   
   
   
   
      
   
   
   
   
   
   
   
   
   
      
   
   
   
   
   
   
   
      
   
   
   
   
      
   
   
   
   
      
   
   
   
   
      
   
   
   
   
   
   
   
   
   
   
   
   
      
   
   
   
   
      
   
   
   
   
      
   
   
   
   
      
   
   
   
   
      
   
   
   
   
      
   
   
   
   
      
   
   
   
   
   
      
   
   
   
   
   
   
      
   
   
   
   
      
   
   
   
   
   
   
      
   
   
   
   
      
   
   
   
   
   
   
   
      
   
   
   
   
   
   
      
   
   
   
   
   
      
   
   
   
   
      
   
   
   
   
   
   

   

   .. rubric:: Forwarded Modules

   Modules defined elsewhere made available in this namespace for convenience.
   To view documentation for these modules, use the search bar or navigate to the source package manually.

   .. autosummary::
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
      animate
   
   
   
   
      ascii
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
      depth_proportional_resolution_algo
   
   
   
   
      depth_proportional_resolution_tapered_algo
   
   
   
   
   
      descend_template_phylogeny_
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
      estimators
   
   
   
   
   
      fixed_resolution_algo
   
   
   
   
      generate_template_phylogeny
   
   
   
   
      geom_seq_nth_root_algo
   
   
   
   
      geom_seq_nth_root_tapered_algo
   
   
   
   
   
   
   
   
   
      nominal_resolution_algo
   
   
   
   
   
   
   
      pairwise
   
   
   
   
      perfect_resolution_algo
   
   
   
   
      perfect_tracking
   
   
   
   
      plot
   
   
   
   
   
   
   
   
   
   
   
   
      population
   
   
   
   
      priors
   
   
   
   
      provided_stratum_ordered_stores
   
   
   
   
      provided_stratum_retention_algorithms
   
   
   
   
      pseudostochastic_algo
   
   
   
   
      recency_proportional_resolution_algo
   
   
   
   
      recency_proportional_resolution_curbed_algo
   
   
   
   
   
      stochastic_algo
   
   
   
   
   
   
      stratum_ordered_stores
   
   
   
   
      stratum_retention_algorithms
   
   
   
   
   
   
      stratum_retention_policy_evaluators
   
   
   
   
      stratum_retention_policy_parameterizers
   
   
   
   
   
   
   
      surface_build_tree
   
   
   
   
   
   
      surface_unpack_reconstruct
   
   
   
   
   
      tree
   
   
   
   
      trie_postprocess
   
   
   
   
   
   
   

   

   
   
   

   
   
   .. rubric:: Functions

   .. autosummary::
     :toctree:
   
      ~assemblage_from_dstream_df
      ~assemblage_from_records
      ~assemblage_to_ascii
      ~ballpark_patristic_distance_between
      ~ballpark_rank_of_mrca_between
      ~ballpark_ranks_since_mrca_with
      ~build_distance_matrix_biopython
      ~build_distance_matrix_numpy
      ~build_tree
      ~build_tree_nj
      ~build_tree_searchtable
      ~build_tree_trie
      ~build_tree_trie_ensemble
      ~build_tree_upgma
      ~calc_definitive_max_rank_of_first_retained_disparity_between
      ~calc_definitive_max_rank_of_last_retained_commonality_between
      ~calc_definitive_min_ranks_since_first_retained_disparity_with
      ~calc_definitive_min_ranks_since_last_retained_commonality_with
      ~calc_min_implausible_spurious_consecutive_differentia_collisions_between
      ~calc_patristic_distance_bounds_between
      ~calc_probability_differentia_collision_between
      ~calc_rank_of_earliest_detectable_mrca_among
      ~calc_rank_of_earliest_detectable_mrca_between
      ~calc_rank_of_first_retained_disparity_between
      ~calc_rank_of_last_retained_commonality_between
      ~calc_rank_of_mrca_bounds_among
      ~calc_rank_of_mrca_bounds_between
      ~calc_rank_of_mrca_bounds_provided_confidence_level
      ~calc_rank_of_mrca_uncertainty_among
      ~calc_rank_of_mrca_uncertainty_between
      ~calc_ranks_since_earliest_detectable_mrca_with
      ~calc_ranks_since_first_retained_disparity_with
      ~calc_ranks_since_last_retained_commonality_with
      ~calc_ranks_since_mrca_bounds_provided_confidence_level
      ~calc_ranks_since_mrca_bounds_with
      ~calc_ranks_since_mrca_uncertainty_with
      ~col_from_int
      ~col_from_packet
      ~col_from_packet_buffer
      ~col_from_records
      ~col_to_ascii
      ~col_to_dataframe
      ~col_to_int
      ~col_to_packet
      ~col_to_records
      ~col_to_specimen
      ~compile_perfect_backtrack_phylogeny
      ~compile_phylogeny_from_lineage_iters
      ~descend_template_phylogeny
      ~descend_template_phylogeny_alifestd
      ~descend_template_phylogeny_biopython
      ~descend_template_phylogeny_dendropy
      ~descend_template_phylogeny_naive
      ~descend_template_phylogeny_networkx
      ~descend_template_phylogeny_posthoc
      ~diff_retained_ranks
      ~does_definitively_have_no_common_ancestor
      ~does_definitively_share_no_common_ancestor
      ~does_have_any_common_ancestor
      ~does_share_any_common_ancestor
      ~estimate_patristic_distance_between
      ~estimate_rank_of_mrca_between
      ~estimate_rank_of_mrca_maximum_likelihood
      ~estimate_rank_of_mrca_naive
      ~estimate_rank_of_mrca_unbiased
      ~estimate_ranks_since_mrca_with
      ~evolve_fitness_trait_population
      ~get_last_common_stratum_between
      ~get_nth_common_rank_between
      ~iter_perfect_backtrack_lineage
      ~mrca_uncertainty_absolute_barplot
      ~mrca_uncertainty_relative_barplot
      ~pack_differentiae
      ~pack_differentiae_bytes
      ~pack_differentiae_str
      ~policy_from_records
      ~policy_panel_animate
      ~policy_panel_plot
      ~policy_to_records
      ~pop_from_records
      ~pop_to_assemblage
      ~pop_to_dataframe
      ~pop_to_records
      ~specimen_from_records
      ~strata_retained_frac_lineplot
      ~strata_retained_num_lineplot
      ~stratum_retention_animate
      ~stratum_retention_dripplot
      ~surf_from_hex
      ~surf_to_hex
      ~surf_to_specimen
      ~surface_postprocess_trie
      ~surface_test_drive
      ~surface_validate_trie
      ~unassemblage_from_records
      ~unpack_differentiae
      ~unpack_differentiae_bytes
      ~unpack_differentiae_str
   
   

   
   
   .. rubric:: Classes

   .. autosummary::
     :toctree:
   
      ~ArbitraryPrior
      ~AssignDestructionTimeYoungestPlusOneTriePostprocessor
      ~AssignOriginTimeExpectedValueTriePostprocessor
      ~AssignOriginTimeNaiveTriePostprocessor
      ~AssignOriginTimeNodeRankTriePostprocessor
      ~AssignOriginTimeSampleNaiveTriePostprocessor
      ~CompoundTriePostprocessor
      ~DecantingPhyloTracker
      ~ExponentialPrior
      ~GarbageCollectingPhyloTracker
      ~GeometricPrior
      ~HereditaryStratigraphicAssemblage
      ~HereditaryStratigraphicAssemblageSpecimen
      ~HereditaryStratigraphicColumn
      ~HereditaryStratigraphicColumnBundle
      ~HereditaryStratigraphicSpecimen
      ~HereditaryStratigraphicSurface
      ~HereditaryStratum
      ~HereditaryStratumOrderedStoreDict
      ~HereditaryStratumOrderedStoreList
      ~HereditaryStratumOrderedStoreTree
      ~MrcaUncertaintyAbsExactEvaluator
      ~MrcaUncertaintyAbsUpperBoundEvaluator
      ~MrcaUncertaintyRelExactEvaluator
      ~MrcaUncertaintyRelUpperBoundEvaluator
      ~NopTriePostprocessor
      ~NumStrataRetainedExactEvaluator
      ~NumStrataRetainedUpperBoundEvaluator
      ~PeelBackConjoinedLeavesTriePostprocessor
      ~PerfectBacktrackHandle
      ~PropertyAtLeastParameterizer
      ~PropertyAtMostParameterizer
      ~PropertyExactlyParameterizer
      ~SampleAncestralRollbacksTriePostprocessor
      ~UniformPrior
   
   

   
   
   .. rubric:: Exceptions

   .. autosummary::
     :toctree:
   
      ~UnsatisfiableParameterizationRequestError