Index

_

__call__() (AssignDestructionTimeYoungestPlusOneTriePostprocessor method), [1], [2], [3], [4], [5] (AssignOriginTimeExpectedValueTriePostprocessor method), [1], [2], [3], [4], [5] (AssignOriginTimeNaiveTriePostprocessor method), [1], [2], [3], [4], [5] (AssignOriginTimeNodeRankTriePostprocessor method), [1], [2], [3], [4], [5] (AssignOriginTimeSampleNaiveTriePostprocessor method), [1], [2], [3], [4], [5] (CalcMrcaUncertaintyAbsExact method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] (CalcMrcaUncertaintyAbsUpperBound method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] (CalcMrcaUncertaintyAbsUpperBoundAtPessimalRank method), [1] (CalcMrcaUncertaintyAbsUpperBoundPessimalRank method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] (CalcMrcaUncertaintyRelUpperBound method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] (CalcMrcaUncertaintyRelUpperBoundAtPessimalRank method), [1] (CalcMrcaUncertaintyRelUpperBoundPessimalRank method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] (CalcNumStrataRetainedExact method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] (CalcNumStrataRetainedUpperBound method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] (CalcRankAtColumnIndex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] (CompoundTriePostprocessor method), [1], [2], [3], [4], [5] (GenDropRanks method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] (IterRetainedRanks method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] (MrcaUncertaintyAbsExactEvaluator method), [1], [2], [3] (MrcaUncertaintyAbsUpperBoundEvaluator method), [1], [2], [3] (MrcaUncertaintyRelExactEvaluator method), [1], [2], [3] (MrcaUncertaintyRelUpperBoundEvaluator method), [1], [2], [3] (NumStrataRetainedExactEvaluator method), [1], [2], [3] (NumStrataRetainedUpperBoundEvaluator method), [1], [2], [3] (PeelBackConjoinedLeavesTriePostprocessor method), [1], [2], [3], [4], [5] (PropertyAtLeastParameterizer method), [1], [2], [3] (PropertyAtMostParameterizer method), [1], [2], [3] (PropertyExactlyParameterizer method), [1], [2], [3] (SampleAncestralRollbacksTriePostprocessor method), [1], [2], [3], [4], [5] __init__() (ArbitraryPrior method), [1], [2] (AssignDestructionTimeYoungestPlusOneTriePostprocessor method), [1], [2], [3], [4], [5], [6], [7], [8], [9] (AssignOriginTimeExpectedValueTriePostprocessor method), [1], [2], [3], [4], [5], [6], [7], [8], [9] (AssignOriginTimeNaiveTriePostprocessor method), [1], [2], [3], [4], [5], [6], [7], [8], [9] (AssignOriginTimeNodeRankTriePostprocessor method), [1], [2], [3], [4], [5], [6], [7], [8], [9] (AssignOriginTimeSampleNaiveTriePostprocessor method), [1], [2], [3], [4], [5], [6], [7], [8], [9] (CalcMrcaUncertaintyAbsExact method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26] (CalcMrcaUncertaintyAbsUpperBound method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] (CalcMrcaUncertaintyAbsUpperBoundAtPessimalRank method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] (CalcMrcaUncertaintyAbsUpperBoundPessimalRank method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32] (CalcMrcaUncertaintyRelExact method), [1], [2], [3], [4], [5], [6], [7] (CalcMrcaUncertaintyRelUpperBound method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] (CalcMrcaUncertaintyRelUpperBoundAtPessimalRank method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] (CalcMrcaUncertaintyRelUpperBoundPessimalRank method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32] (CalcNumStrataRetainedExact method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26] (CalcNumStrataRetainedUpperBound method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28] (CalcRankAtColumnIndex method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26] (CompoundTriePostprocessor method), [1], [2], [3], [4], [5], [6], [7], [8], [9] (DecantingPhyloTracker method), [1], [2], [3], [4], [5], [6] (ExponentialPrior method), [1], [2], [3], [4], [5], [6] (GarbageCollectingPhyloTracker method), [1], [2], [3], [4], [5], [6] (GenDropRanks method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32] (GeometricPrior method), [1], [2], [3], [4], [5], [6] (HereditaryStratigraphicAssemblage method), [1], [2], [3], [4] (HereditaryStratigraphicAssemblageSpecimen method), [1], [2], [3], [4] (HereditaryStratigraphicColumn method), [1], [2], [3], [4] (HereditaryStratigraphicColumnBundle method), [1], [2], [3], [4] (HereditaryStratigraphicSpecimen method), [1], [2], [3], [4] (HereditaryStratum method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreDict method), [1], [2], [3], [4], [5], [6], [7] (HereditaryStratumOrderedStoreList method), [1], [2], [3], [4], [5], [6], [7] (HereditaryStratumOrderedStoreTree method), [1], [2], [3], [4], [5], [6], [7] (IterRetainedRanks method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24] (MrcaUncertaintyAbsExactEvaluator method), [1], [2], [3], [4], [5], [6] (MrcaUncertaintyAbsUpperBoundEvaluator method), [1], [2], [3], [4], [5], [6] (MrcaUncertaintyRelExactEvaluator method), [1], [2], [3], [4], [5], [6] (MrcaUncertaintyRelUpperBoundEvaluator method), [1], [2], [3], [4], [5], [6] (NumStrataRetainedExactEvaluator method), [1], [2], [3], [4], [5], [6] (NumStrataRetainedUpperBoundEvaluator method), [1], [2], [3], [4], [5], [6] (PeelBackConjoinedLeavesTriePostprocessor method), [1], [2], [3] (PerfectBacktrackHandle method), [1], [2], [3], [4], [5], [6] (Policy method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26] (PolicySpec method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28] (PropertyAtLeastParameterizer method), [1], [2], [3], [4], [5], [6] (PropertyAtMostParameterizer method), [1], [2], [3], [4], [5], [6] (PropertyExactlyParameterizer method), [1], [2], [3], [4], [5], [6] (SampleAncestralRollbacksTriePostprocessor method), [1], [2], [3], [4], [5], [6], [7], [8], [9] (UniformPrior method), [1], [2] (UnsatisfiableParameterizationRequestError method), [1], [2]

__new__() (UnsatisfiableParameterizationRequestError method), [1], [2] __repr__() (MrcaUncertaintyAbsExactEvaluator method), [1], [2], [3] (MrcaUncertaintyAbsUpperBoundEvaluator method), [1], [2], [3] (MrcaUncertaintyRelExactEvaluator method), [1], [2], [3] (MrcaUncertaintyRelUpperBoundEvaluator method), [1], [2], [3] (NumStrataRetainedExactEvaluator method), [1], [2], [3] (NumStrataRetainedUpperBoundEvaluator method), [1], [2], [3] (Policy method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] (PolicySpec method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] (PropertyAtLeastParameterizer method), [1], [2], [3] (PropertyAtMostParameterizer method), [1], [2], [3] (PropertyExactlyParameterizer method), [1], [2], [3] __str__() (MrcaUncertaintyAbsExactEvaluator method), [1], [2], [3] (MrcaUncertaintyAbsUpperBoundEvaluator method), [1], [2], [3] (MrcaUncertaintyRelExactEvaluator method), [1], [2], [3] (MrcaUncertaintyRelUpperBoundEvaluator method), [1], [2], [3] (NumStrataRetainedExactEvaluator method), [1], [2], [3] (NumStrataRetainedUpperBoundEvaluator method), [1], [2], [3] (Policy method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] (PolicySpec method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] (PropertyAtLeastParameterizer method), [1], [2], [3] (PropertyAtMostParameterizer method), [1], [2], [3] (PropertyExactlyParameterizer method), [1], [2], [3]

A

ApplyLocPasteovers() (GarbageCollectingPhyloTracker method), [1], [2], [3] ApplyLocSwaps() (GarbageCollectingPhyloTracker method), [1], [2], [3] ArbitraryPrior (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.priors), [1] assemblage_from_records() (in module hstrat.hstrat) (in module hstrat.serialization), [1] AssignDestructionTimeYoungestPlusOneTriePostprocessor (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.tree), [1] (class in hstrat.phylogenetic_inference.tree.trie_postprocess), [1] AssignOriginTimeExpectedValueTriePostprocessor (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.tree), [1] (class in hstrat.phylogenetic_inference.tree.trie_postprocess), [1]

AssignOriginTimeNaiveTriePostprocessor (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.tree), [1] (class in hstrat.phylogenetic_inference.tree.trie_postprocess), [1] AssignOriginTimeNodeRankTriePostprocessor (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.tree), [1] (class in hstrat.phylogenetic_inference.tree.trie_postprocess), [1] AssignOriginTimeSampleNaiveTriePostprocessor (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.tree), [1] (class in hstrat.phylogenetic_inference.tree.trie_postprocess), [1]

B

ballpark_patristic_distance_between() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] ballpark_rank_of_mrca_between() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] ballpark_ranks_since_mrca_with() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] build_distance_matrix_biopython() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.population), [1] build_distance_matrix_numpy() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.population), [1]

build_tree() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.tree), [1] build_tree_nj() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.tree), [1] build_tree_trie() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.tree), [1] build_tree_trie_ensemble() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.tree), [1] build_tree_upgma() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.tree), [1] BuildSpecimens() (HereditaryStratigraphicAssemblage method), [1], [2]

C

calc_definitive_max_rank_of_first_retained_disparity_between() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] calc_definitive_max_rank_of_last_retained_commonality_between() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] calc_definitive_min_ranks_since_first_retained_disparity_with() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] calc_definitive_min_ranks_since_last_retained_commonality_with() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] calc_min_implausible_spurious_consecutive_differentia_collisions_between() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] calc_patristic_distance_bounds_between() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] calc_probability_differentia_collision_between() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] calc_rank_of_earliest_detectable_mrca_among() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.population), [1] calc_rank_of_earliest_detectable_mrca_between() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] calc_rank_of_first_retained_disparity_between() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] calc_rank_of_last_retained_commonality_between() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] calc_rank_of_mrca_bounds_among() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.population), [1] calc_rank_of_mrca_bounds_between() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] calc_rank_of_mrca_bounds_provided_confidence_level() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] calc_rank_of_mrca_uncertainty_among() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.population), [1] calc_rank_of_mrca_uncertainty_between() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] calc_ranks_since_earliest_detectable_mrca_with() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] calc_ranks_since_first_retained_disparity_with() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] calc_ranks_since_last_retained_commonality_with() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] calc_ranks_since_mrca_bounds_provided_confidence_level() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] calc_ranks_since_mrca_bounds_with() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] calc_ranks_since_mrca_uncertainty_with() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] CalcIntervalConditionedMean() (ArbitraryPrior method), [1], [2], [3] (ExponentialPrior method), [1], [2], [3] (GeometricPrior method), [1], [2], [3] (UniformPrior method), [1], [2], [3] CalcIntervalProbabilityProxy() (ArbitraryPrior method), [1], [2], [3] (ExponentialPrior method), [1], [2], [3] (GeometricPrior method), [1], [2], [3] (UniformPrior method), [1], [2], [3] CalcMinImplausibleSpuriousConsecutiveDifferentiaCollisions() (HereditaryStratigraphicColumn method), [1], [2] CalcMrcaUncertaintyAbsExact (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] CalcMrcaUncertaintyAbsUpperBound (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo), [1] (in module hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] CalcMrcaUncertaintyAbsUpperBoundAtPessimalRank (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] CalcMrcaUncertaintyAbsUpperBoundPessimalRank (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] CalcMrcaUncertaintyRelExact (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (in module hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17]

CalcMrcaUncertaintyRelUpperBound (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo), [1] (in module hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] CalcMrcaUncertaintyRelUpperBoundAtPessimalRank (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] CalcMrcaUncertaintyRelUpperBoundPessimalRank (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] CalcNumStrataRetainedExact (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] CalcNumStrataRetainedUpperBound (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] CalcProbabilityDifferentiaCollision() (HereditaryStratigraphicColumn method), [1], [2] CalcRankAtColumnIndex (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] Clone() (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicColumnBundle method), [1], [2] (HereditaryStratumOrderedStoreDict method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreList method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreTree method), [1], [2], [3], [4] CloneDescendant() (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicColumnBundle method), [1], [2] CloneNthDescendant() (HereditaryStratigraphicColumn method), [1], [2] col_from_int() (in module hstrat.hstrat) (in module hstrat.serialization), [1] col_from_packet() (in module hstrat.hstrat) (in module hstrat.serialization), [1] col_from_packet_buffer() (in module hstrat.hstrat) (in module hstrat.serialization), [1] col_from_records() (in module hstrat.hstrat) (in module hstrat.serialization), [1] col_to_ascii() (in module hstrat.hstrat) (in module hstrat.stratum_retention_viz) (in module hstrat.stratum_retention_viz.ascii), [1] col_to_dataframe() (in module hstrat.hstrat) (in module hstrat.serialization), [1] col_to_int() (in module hstrat.hstrat) (in module hstrat.serialization), [1] col_to_packet() (in module hstrat.hstrat) (in module hstrat.serialization), [1] col_to_records() (in module hstrat.hstrat) (in module hstrat.serialization), [1] col_to_specimen() (in module hstrat.hstrat) (in module hstrat.serialization), [1] compile_perfect_backtrack_phylogeny() (in module hstrat.hstrat) (in module hstrat.test_drive) (in module hstrat.test_drive.perfect_tracking), [1] compile_phylogeny_from_lineage_iters() (in module hstrat.hstrat) (in module hstrat.test_drive) (in module hstrat.test_drive.perfect_tracking), [1] CompilePhylogeny() (DecantingPhyloTracker method), [1], [2], [3] (GarbageCollectingPhyloTracker method), [1], [2], [3] CompoundTriePostprocessor (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.tree), [1] (class in hstrat.phylogenetic_inference.tree.trie_postprocess), [1] CreateDescendant() (PerfectBacktrackHandle method), [1], [2], [3]

D

data (PerfectBacktrackHandle attribute), [1], [2], [3] DecantingPhyloTracker (class in hstrat.hstrat) (class in hstrat.test_drive) (class in hstrat.test_drive.perfect_tracking), [1] DelRanks() (HereditaryStratumOrderedStoreDict method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreList method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreTree method), [1], [2], [3], [4] DepositStrata() (HereditaryStratigraphicColumn method), [1], [2] DepositStratum() (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicColumnBundle method), [1], [2] (HereditaryStratumOrderedStoreDict method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreList method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreTree method), [1], [2], [3], [4] descend_template_phylogeny() (in module hstrat.hstrat) (in module hstrat.test_drive) descend_template_phylogeny_alifestd() (in module hstrat.hstrat) (in module hstrat.test_drive) descend_template_phylogeny_biopython() (in module hstrat.hstrat) (in module hstrat.test_drive) descend_template_phylogeny_dendropy() (in module hstrat.hstrat) (in module hstrat.test_drive)

descend_template_phylogeny_naive() (in module hstrat.hstrat) (in module hstrat.test_drive) descend_template_phylogeny_networkx() (in module hstrat.hstrat) (in module hstrat.test_drive) descend_template_phylogeny_posthoc() (in module hstrat.hstrat) (in module hstrat.test_drive) diff_retained_ranks() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] does_definitively_have_no_common_ancestor() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] does_definitively_share_no_common_ancestor() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.population), [1] does_have_any_common_ancestor() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] does_share_any_common_ancestor() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.population), [1]

E

ElapseGeneration() (DecantingPhyloTracker method), [1], [2], [3] (GarbageCollectingPhyloTracker method), [1], [2], [3] estimate_patristic_distance_between() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] estimate_rank_of_mrca_between() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] estimate_rank_of_mrca_maximum_likelihood() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.estimators), [1] estimate_rank_of_mrca_naive() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.estimators), [1]

estimate_rank_of_mrca_unbiased() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.estimators), [1] estimate_ranks_since_mrca_with() (in module hstrat.hstrat) (in module hstrat.phylogenetic_inference) (in module hstrat.phylogenetic_inference.pairwise), [1] evolve_fitness_trait_population() (in module hstrat.hstrat) (in module hstrat.test_drive) (in module hstrat.test_drive.generate_template_phylogeny), [1] ExponentialPrior (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.priors), [1]

G

GarbageCollectingPhyloTracker (class in hstrat.hstrat) (class in hstrat.test_drive) (class in hstrat.test_drive.perfect_tracking), [1] GenDropRanks (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] GeometricPrior (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.priors), [1] get_hstrat_version() (in module hstrat.hstrat) get_last_common_stratum_between() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] get_nth_common_rank_between() (in module hstrat.hstrat) (in module hstrat.juxtaposition), [1] GetAlgoIdentifier() (PolicySpec static method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] GetAlgoTitle() (PolicySpec static method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] GetAnnotation() (HereditaryStratum method), [1], [2] GetColumnIndexOfRank() (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratumOrderedStoreDict method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreList method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreTree method), [1], [2], [3], [4] GetData() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2] GetDegree() (PolicySpec method), [1], [2], [3] GetDepositionRank() (HereditaryStratum method), [1], [2] GetDepthProportionalResolution() (PolicySpec method), [1], [2], [3] GetDifferentia() (HereditaryStratum method), [1], [2] GetDifferentiaVals() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2]

GetEvalCtor() (Policy method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] (PolicySpec method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] GetFixedResolution() (PolicySpec method), [1] GetHashSalt() (PolicySpec method), [1] GetInterspersal() (PolicySpec method), [1], [2], [3] GetNumDiscardedStrata() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2] GetNumStrataDeposited() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicColumnBundle method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2] GetNumStrataRetained() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2] (HereditaryStratumOrderedStoreDict method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreList method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreTree method), [1], [2], [3], [4] GetRankAtColumnIndex() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2] (HereditaryStratumOrderedStoreDict method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreList method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreTree method), [1], [2], [3], [4] GetRankIndex() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2] GetRecencyProportionalResolution() (PolicySpec method), [1] GetRetentionProbability() (PolicySpec method), [1] GetSizeCurb() (PolicySpec method), [1] GetSpec() (Policy method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] GetStratumAtColumnIndex() (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratumOrderedStoreDict method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreList method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreTree method), [1], [2], [3], [4] GetStratumAtRank() (HereditaryStratigraphicColumn method), [1], [2] GetStratumDifferentiaBitWidth() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2] GetStratumMask() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2]

H

HasAnyAnnotations() (HereditaryStratigraphicColumn method), [1], [2] HasDiscardedStrata() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2] hash_salt (PolicySpec attribute), [1] HereditaryStratigraphicAssemblage (class in hstrat.frozen_instrumentation), [1] (class in hstrat.hstrat) HereditaryStratigraphicAssemblageSpecimen (class in hstrat.frozen_instrumentation), [1] (class in hstrat.hstrat) HereditaryStratigraphicColumn (class in hstrat.genome_instrumentation), [1] (class in hstrat.hstrat) HereditaryStratigraphicColumnBundle (class in hstrat.genome_instrumentation), [1] (class in hstrat.hstrat) HereditaryStratigraphicSpecimen (class in hstrat.frozen_instrumentation), [1] (class in hstrat.hstrat) HereditaryStratum (class in hstrat.genome_instrumentation), [1] (class in hstrat.hstrat) HereditaryStratumOrderedStoreDict (class in hstrat.genome_instrumentation), [1] (class in hstrat.genome_instrumentation.stratum_ordered_stores), [1] (class in hstrat.hstrat) HereditaryStratumOrderedStoreList (class in hstrat.genome_instrumentation), [1] (class in hstrat.genome_instrumentation.stratum_ordered_stores), [1] (class in hstrat.hstrat) HereditaryStratumOrderedStoreTree (class in hstrat.genome_instrumentation), [1] (class in hstrat.genome_instrumentation.stratum_ordered_stores), [1] (class in hstrat.hstrat) hstrat module hstrat.frozen_instrumentation module hstrat.genome_instrumentation module hstrat.genome_instrumentation.stratum_ordered_stores module hstrat.hstrat module hstrat.juxtaposition module hstrat.phylogenetic_inference module hstrat.phylogenetic_inference.estimators module hstrat.phylogenetic_inference.pairwise module hstrat.phylogenetic_inference.population module hstrat.phylogenetic_inference.priors module hstrat.phylogenetic_inference.tree module

hstrat.phylogenetic_inference.tree.trie_postprocess module hstrat.serialization module hstrat.stratum_retention_strategy module hstrat.stratum_retention_strategy.stratum_retention_algorithms module hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo module hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo module hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo module hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo module hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo module hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo module hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo module hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo module hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo module hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo module hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo module hstrat.stratum_retention_strategy.stratum_retention_policy_evaluators module hstrat.stratum_retention_strategy.stratum_retention_policy_parameterizers module hstrat.stratum_retention_viz module hstrat.stratum_retention_viz.animate module hstrat.stratum_retention_viz.ascii module hstrat.stratum_retention_viz.plot module hstrat.test_drive module hstrat.test_drive.generate_template_phylogeny module hstrat.test_drive.perfect_tracking module

I

iter_perfect_backtrack_lineage() (in module hstrat.hstrat) (in module hstrat.test_drive) (in module hstrat.test_drive.perfect_tracking), [1] IterRankDifferentiaZip() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2] (HereditaryStratumOrderedStoreDict method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreList method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreTree method), [1], [2], [3], [4] IterRetainedDifferentia() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2] IterRetainedRanks (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17]

IterRetainedRanks() (HereditaryStratigraphicAssemblageSpecimen method), [1], [2] (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratigraphicSpecimen method), [1], [2] (HereditaryStratumOrderedStoreDict method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreList method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreTree method), [1], [2], [3], [4] IterRetainedStrata() (HereditaryStratigraphicColumn method), [1], [2] (HereditaryStratumOrderedStoreDict method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreList method), [1], [2], [3], [4] (HereditaryStratumOrderedStoreTree method), [1], [2], [3], [4]

M

module hstrat hstrat.frozen_instrumentation hstrat.genome_instrumentation hstrat.genome_instrumentation.stratum_ordered_stores hstrat.hstrat hstrat.juxtaposition hstrat.phylogenetic_inference hstrat.phylogenetic_inference.estimators hstrat.phylogenetic_inference.pairwise hstrat.phylogenetic_inference.population hstrat.phylogenetic_inference.priors hstrat.phylogenetic_inference.tree hstrat.phylogenetic_inference.tree.trie_postprocess hstrat.serialization hstrat.stratum_retention_strategy hstrat.stratum_retention_strategy.stratum_retention_algorithms hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo hstrat.stratum_retention_strategy.stratum_retention_policy_evaluators hstrat.stratum_retention_strategy.stratum_retention_policy_parameterizers hstrat.stratum_retention_viz hstrat.stratum_retention_viz.animate hstrat.stratum_retention_viz.ascii hstrat.stratum_retention_viz.plot hstrat.test_drive hstrat.test_drive.generate_template_phylogeny hstrat.test_drive.perfect_tracking

mrca_uncertainty_absolute_barplot() (in module hstrat.hstrat) (in module hstrat.stratum_retention_viz) (in module hstrat.stratum_retention_viz.plot), [1] mrca_uncertainty_relative_barplot() (in module hstrat.hstrat) (in module hstrat.stratum_retention_viz) (in module hstrat.stratum_retention_viz.plot), [1] MrcaUncertaintyAbsExactEvaluator (class in hstrat.hstrat) (class in hstrat.stratum_retention_strategy) (class in hstrat.stratum_retention_strategy.stratum_retention_policy_evaluators), [1] MrcaUncertaintyAbsUpperBoundEvaluator (class in hstrat.hstrat) (class in hstrat.stratum_retention_strategy) (class in hstrat.stratum_retention_strategy.stratum_retention_policy_evaluators), [1] MrcaUncertaintyRelExactEvaluator (class in hstrat.hstrat) (class in hstrat.stratum_retention_strategy) (class in hstrat.stratum_retention_strategy.stratum_retention_policy_evaluators), [1] MrcaUncertaintyRelUpperBoundEvaluator (class in hstrat.hstrat) (class in hstrat.stratum_retention_strategy) (class in hstrat.stratum_retention_strategy.stratum_retention_policy_evaluators), [1]

N

NumStrataRetainedExactEvaluator (class in hstrat.hstrat) (class in hstrat.stratum_retention_strategy) (class in hstrat.stratum_retention_strategy.stratum_retention_policy_evaluators), [1]

NumStrataRetainedUpperBoundEvaluator (class in hstrat.hstrat) (class in hstrat.stratum_retention_strategy) (class in hstrat.stratum_retention_strategy.stratum_retention_policy_evaluators), [1]

P

pack_differentiae() (in module hstrat.hstrat) (in module hstrat.serialization), [1] pack_differentiae_bytes() (in module hstrat.hstrat) (in module hstrat.serialization), [1] pack_differentiae_str() (in module hstrat.hstrat) (in module hstrat.serialization), [1] parent (PerfectBacktrackHandle attribute), [1], [2], [3] PeelBackConjoinedLeavesTriePostprocessor (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.tree), [1] (class in hstrat.phylogenetic_inference.tree.trie_postprocess), [1] PerfectBacktrackHandle (class in hstrat.hstrat) (class in hstrat.test_drive) (class in hstrat.test_drive.perfect_tracking), [1] Policy (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo), [1] (in module hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (in module hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] policy_from_records() (in module hstrat.hstrat) (in module hstrat.serialization), [1] policy_panel_animate() (in module hstrat.hstrat) (in module hstrat.stratum_retention_viz) (in module hstrat.stratum_retention_viz.animate), [1] policy_panel_plot() (in module hstrat.hstrat) (in module hstrat.stratum_retention_viz) (in module hstrat.stratum_retention_viz.plot), [1]

policy_spec_t (Policy attribute), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] policy_to_records() (in module hstrat.hstrat) (in module hstrat.serialization), [1] PolicySpec (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.depth_proportional_resolution_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.fixed_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.geom_seq_nth_root_tapered_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.nominal_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.perfect_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.pseudostochastic_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.recency_proportional_resolution_curbed_algo), [1] (class in hstrat.stratum_retention_strategy.stratum_retention_algorithms.stochastic_algo), [1] pop_from_records() (in module hstrat.hstrat) (in module hstrat.serialization), [1] pop_to_assemblage() (in module hstrat.hstrat) (in module hstrat.serialization), [1] pop_to_dataframe() (in module hstrat.hstrat) (in module hstrat.serialization), [1] pop_to_records() (in module hstrat.hstrat) (in module hstrat.serialization), [1] PropertyAtLeastParameterizer (class in hstrat.hstrat) (class in hstrat.stratum_retention_strategy) (class in hstrat.stratum_retention_strategy.stratum_retention_policy_parameterizers), [1] PropertyAtMostParameterizer (class in hstrat.hstrat) (class in hstrat.stratum_retention_strategy) (class in hstrat.stratum_retention_strategy.stratum_retention_policy_parameterizers), [1] PropertyExactlyParameterizer (class in hstrat.hstrat) (class in hstrat.stratum_retention_strategy) (class in hstrat.stratum_retention_strategy.stratum_retention_policy_parameterizers), [1]

S

SampleAncestralRollbacksTriePostprocessor (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.tree), [1] (class in hstrat.phylogenetic_inference.tree.trie_postprocess), [1] SampleIntervalConditionedValue() (ArbitraryPrior method), [1], [2], [3] (ExponentialPrior method), [1], [2], [3] (GeometricPrior method), [1], [2], [3] (UniformPrior method), [1], [2], [3] specimen_from_records() (in module hstrat.hstrat) (in module hstrat.serialization), [1] strata_retained_frac_lineplot() (in module hstrat.hstrat) (in module hstrat.stratum_retention_viz) (in module hstrat.stratum_retention_viz.plot), [1]

strata_retained_num_lineplot() (in module hstrat.hstrat) (in module hstrat.stratum_retention_viz) (in module hstrat.stratum_retention_viz.plot), [1] stratum_retention_animate() (in module hstrat.hstrat) (in module hstrat.stratum_retention_viz) (in module hstrat.stratum_retention_viz.animate), [1] stratum_retention_dripplot() (in module hstrat.hstrat) (in module hstrat.stratum_retention_viz) (in module hstrat.stratum_retention_viz.plot), [1]

U

unassemblage_from_records() (in module hstrat.hstrat) (in module hstrat.serialization), [1] UniformPrior (class in hstrat.hstrat) (class in hstrat.phylogenetic_inference) (class in hstrat.phylogenetic_inference.priors), [1] unpack_differentiae() (in module hstrat.hstrat) (in module hstrat.serialization), [1]

unpack_differentiae_bytes() (in module hstrat.hstrat) (in module hstrat.serialization), [1] unpack_differentiae_str() (in module hstrat.hstrat) (in module hstrat.serialization), [1] UnsatisfiableParameterizationRequestError, [1], [2], [3]

W

WithoutCalcRankAtColumnIndex() (Policy method), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17]