AssignOriginTimeExpectedValueTriePostprocessor

class AssignOriginTimeExpectedValueTriePostprocessor

Functor to assign origin time property to trie nodes using expected values over the distribution of possible differentia collisions.

Computes the origin time of trie nodes based on the expected value, taking into account the probability of differentia collision and the prior distribution expected for ancestor origin times.

__init__(prior: PriorBase, assigned_property: str = 'origin_time') → None

Initialize functor instance.

Parameters

priorPriorBase

The prior distribution used to calculate expected values.

assigned_propertystr, default “origin_time”

The property name for the assigned origin time.

Methods

__init__(prior: PriorBase, assigned_property: str = 'origin_time') → None

Initialize functor instance.

Parameters

priorPriorBase

The prior distribution used to calculate expected values.

assigned_propertystr, default “origin_time”

The property name for the assigned origin time.

__call__(trie: ~hstrat.phylogenetic_inference.tree._impl._TrieInnerNode.TrieInnerNode, p_differentia_collision: float, mutate: bool = False, progress_wrap: ~typing.Callable = <function AssignOriginTimeExpectedValueTriePostprocessor.<lambda>>) → TrieInnerNode

Assign origin times to trie nodes.

Parameters

trieTrieInnerNode

The input trie to be postprocessed.

p_differentia_collisionfloat

Probability of a randomly-generated differentia matching an existing differentia.

mutatebool, default False

Are side effects on the input argument trie allowed?

progress_wraptyping.Callable, optional

Pass tqdm or equivalent to report progress.

Returns

TrieInnerNode

The postprocessed trie with assigned origin times.