estimators

Tools to estimate MRCA generation from shared ranks of commonality and disparity.

Functions

estimate_rank_of_mrca_maximum_likelihood(...)	Estimate the most recent common ancestor (MRCA) at the rank with the highest posterior probability.
estimate_rank_of_mrca_naive(...)	Compute a simple, fast estimate the rank of the most recent common ancestor (MRCA).
estimate_rank_of_mrca_unbiased(...)	Compute an estimate for the rank of the most recent common ancestor (MRCA) that, on average, avoids systematic over- or under-estimation.

estimate_rank_of_mrca_maximum_likelihood(coincident_ranks_from_first_disparity_through_first_commonality: Iterator[int], p_differentia_collision: float, prior: PriorBase) → float | None

Estimate the most recent common ancestor (MRCA) at the rank with the highest posterior probability.

Parameters

coincident_ranks_from_first_disparity_through_first_commonality : typing.Iterator[int]

Iterator of integer values indicating the coincident ranks between two taxa.

Inclusive to first disparity and first commonality.

p_differentia_collisionfloat

The multiplicative inverse of the number of possible differentia.

priorPriorBase

Prior expectation for the distribution of MRCA generation between hereditary stratigraphic columns.

Returns

typing.Optional[float]

Estimated rank of the MRCA, or None if the two hereditary stratigraphic artifacts definitively share no common ancestor.

Notes

The midpoint rank will be estimated for windows of equal posterior probability.

estimate_rank_of_mrca_naive(coincident_ranks_from_first_disparity_through_first_commonality: Iterator[int], p_differentia_collision: float, prior: Literal['arbitrary'] | PriorBase) → float | None

Compute a simple, fast estimate the rank of the most recent common ancestor (MRCA).

Parameters

coincident_ranks_from_first_disparity_through_first_commonality : typing.Iterator[int]

Iterator of integer values indicating the coincident ranks between two taxa.

Inclusive to first disparity and first commonality.

p_differentia_collisionfloat

The multiplicative inverse of the number of possible differentia.

priortyping.Union[typing.Literal[“arbitrary”], PriorBase]

Prior expectation for the distribution of MRCA generation between hereditary stratigraphic columns.

Not used for this calculation.

Returns

typing.Optional[float]

Estimated rank of the MRCA, or None if the two hereditary stratigraphic artifacts definitively share no common ancestor.

Notes

This function estimates the rank of the MRCA by computing the mean of the first retained disparate rank and the last retained common rank, with a correction factor for upper bound exclusivity.

estimate_rank_of_mrca_unbiased(coincident_ranks_from_first_disparity_through_first_commonality: Iterator[int], p_differentia_collision: float, prior: PriorBase) → float | None

Compute an estimate for the rank of the most recent common ancestor (MRCA) that, on average, avoids systematic over- or under-estimation.

Parameters

coincident_ranks_from_first_disparity_through_first_commonalitytyping.Iterator[int]

Iterator of integer values indicating the coincident ranks between two taxa.

Inclusive to first disparity and first commonality.

p_differentia_collisionfloat

The multiplicative inverse of the number of possible differentia.

priorPriorBase

Prior expectation for the distribution of MRCA generation between hereditary stratigraphic columns.

Returns

typing.Optional[float]

Estimated rank of the MRCA, or None if the two hereditary stratigraphic artifacts definitively share no common ancestor.