ExponentialPrior
- class ExponentialPrior
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 provides a continuous approximation of the 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
An exact, discrete analog 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.