calc_patristic_distance_bounds_between

calc_patristic_distance_bounds_between(first: Union[HereditaryStratigraphicColumn, HereditaryStratigraphicSpecimen], second: Union[HereditaryStratigraphicColumn, HereditaryStratigraphicSpecimen], prior: Literal['arbitrary'], confidence_level: float = 0.95) → Tuple[int, int] | None

What is the total phylogenetic distance along the branch path connecting first and second?

Calculate confidence interval for patristic distance estimate. Branch length here is in terms of number of generations elapsed. So the calculated distance estimates the sum of the number of generations elapsed

Parameters

prior{“arbitrary”}

Prior probability density distribution over possible generations of the MRCA.

Currently only “arbitrary” supported.

confidence_levelfloat, optional

Bounds must capture what probability of containing the true patristic distance? Default 0.95.

Returns

(int, int), optional

Inclusive lower and then exclusive upper bound on patristic distance estimate or None if no common ancestor between first and second can be resolved with sufficient confidence. (Sufficient confidence depends on confidence_level.)

See Also

calc_rank_of_earliest_detectable_mrca_between :

Could any MRCA be detected between first and second? What is the rank of the earliest MRCA that could be reliably detected?

does_definitively_have_no_common_anestor :

Does the hereditary stratigraphic record definitively prove that first and second could not possibly share a common ancestor?

Notes

The true patristic distance is guaranteed to never fall below the returned bounds but may fall above.