AssignOriginTimeNaiveTriePostprocessor

class AssignOriginTimeNaiveTriePostprocessor

Functor to assign origin time property to trie nodes calculated as the average of the node’s rank and the minimum rank among its children.

Optionally calculates origin time expected value over this interval for a provided prior distribution.

__init__(prior: ~hstrat.phylogenetic_inference.priors._detail._PriorBase.PriorBase = <hstrat.phylogenetic_inference.priors.ArbitraryPrior object>, assigned_property: str = 'origin_time') → None

Initialize functor instance.

Parameters

priorPriorBase, default ArbitraryPrior()

Prior distribution of ancestor origin times.

Used to calculate interval means.

assigned_propertystr, default “origin_time”

The property name for the assigned origin time.

Methods

__init__(prior: ~hstrat.phylogenetic_inference.priors._detail._PriorBase.PriorBase = <hstrat.phylogenetic_inference.priors.ArbitraryPrior object>, assigned_property: str = 'origin_time') → None

Initialize functor instance.

Parameters

priorPriorBase, default ArbitraryPrior()

Prior distribution of ancestor origin times.

Used to calculate interval means.

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 AssignOriginTimeNaiveTriePostprocessor.<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.

Not used in the current implementation.

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.