GeometricPrior
- class GeometricPrior
Enacts a prior expectation that the generation of the most recent common ancestor (MRCA) between extant hereditary stratigraphic columns becomes exponentialy less likely with increasing antiquity.
This prior calculates the exact, discrete geometric distribution of time to MRCA expected under the Wright-Fisher model [1].
Populations. In Mathematical Statistical Physics (pp. 489-545). Elsevier. https://doi.org/10.1016/S0924-8099(06)80048-X
Notes
A static factory function to init an instance with a growth factor calculated from contextual information like population size and the number of generations elapsed since genesis should be made available in the future.
See Also
- GeometricPrior
A continuous approximation of this prior.
Methods
- CalcIntervalConditionedMean(begin_rank: int, end_rank: int) float [source]
Calculate the centriod of prior probability mass within an interval of possible MRCA generations.
Parameters
- begin_rankint
The starting rank of the interval, inclusive.
- end_rankint
The ending rank of the interval, exclusive.
Returns
- float
The prior expected generation of MRCA conditioned on the assumption that the MRCA falls within the given interval.
- CalcIntervalProbabilityProxy(begin_rank: int, end_rank: int) float [source]
Characterize the prior probability of the MRCA generation falling within an interval range.
Parameters
- begin_rankint
The starting rank of the interval, inclusive.
- end_rankint
The ending rank of the interval, exclusive.
Returns
- float
The proxy statistic, proportional to the true estimated interval probability of the MRCA value by a fixed (but unspecified) constant proportion.
- SampleIntervalConditionedValue(begin_rank: int, end_rank: int) int [source]
Sample a generation of the MRCA conditioned on the assumption that the MRCA falls within the given interval.
Parameters
- begin_rankint
The starting rank of the interval, inclusive.
- end_rankint
The ending rank of the interval, exclusive.
Returns
- int
A sampled generation of the MRCA, conditioned on the assumption that the MRCA falls within the given interval.