calc_ranks_since_mrca_bounds_with

calc_ranks_since_mrca_bounds_with(focal: Union[HereditaryStratigraphicColumn, HereditaryStratigraphicSpecimen], other: Union[HereditaryStratigraphicColumn, HereditaryStratigraphicSpecimen], prior: Literal['arbitrary'], confidence_level: float = 0.95) → Tuple[int, int] | None

How many generations have elapsed since MRCA?

Calculate bounds on estimate for the number of depositions elapsed along focal column’s line of descent since the most recent common ancestor with other.

Parameters

prior{“arbitrary”}

Prior probability density distribution over possible generations of the MRCA.

Currently only “arbitrary” supported.

confidence_levelfloat, optional

With what probability should the true rank of the MRCA fall within the calculated bounds? Default 0.95.

Returns

(int, int), optional

Inclusive lower bound and then exclusive upper bound on estimate or None if no common ancestor between focal and other can be resolved with sufficient confidence. (Sufficient confidence depends on bound_type.)

See Also

calc_ranks_since_mrca_uncertainty_between :

Wrapper to report uncertainty of calculated bounds.

calc_ranks_since_earliest_detectable_mrca_between :

Could any MRCA be detected between focal and other? How many ranks have elapsed since the earliest MRCA that could be reliably detected?

calc_ranks_since_mrca_bounds_provided_confidence_level :

With what actual confidence (i.e., more than requested) is the true rank of the MRCA captured within the calculated bounds?

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 number of ranks since the MRCA is guaranteed to never fall below the bounds but may fall above.

An alternate approach could be to construct the bounds such that the true number of ranks since the MRCA will fall above or below the bounds with equal probability. This would involve setting the confidence level for calculating the first disparity with other to significance_level/2 and the confidence level for calculaing the last comonality with other to 1 - significance_level/2. This means the confidence level applied to calculating the first disparity with other would always be <= 0.5. However, shifting the calculated first disparity with other above the definitive min first retained disparity requires confidence level >= 0.5. So, in practice such a symmetric approach would only result in the upper bound being shifted upward. For this reason, it is no longer provided as an option.

In the absence of evidence to the contrary (i.e., more common strata than spurious differentia collisions alone could plausibly cause), this method assumes no common ancestry between focal and other, returning None. This means that if few enough common ranks are shared between focal and other (and the differentia bit with is small enough), it may not be possible to detect any common ancestry after accounting for the possibility of spurious differentia collisions (even if common ancestry did exist). So, calls to this method would always return None. Likewise, MRCAs at very early ranks may not be able to be reliably detected due to insufficient evidence. This can lead to cases where columns with true common ancestry have MRCA bounds estimated as None at much higher than the expected failure rate at the given confidence level. Note that with sufficient differentia bit width (i.e., so that even one collision is implausible at the given confidence level) this issue does not occur. Use CalcRanksSinceEarliestDetectableMrcaWith to determine the earliest rank at which an MRCA could be reliably detected between focal and other.