API Documentation¶
An example Python package, illustrating current best-practises.
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kingman.
simulate
(sample_size, random_seed=None)¶ Simulates the Kingman coalescent for the specified sample size and random seed.
Returns a tuple (parent, time) which describes the simulated history of the sample as an oriented forest.
parent
is a list of integers, in which the parent of nodej
isparent[j]
.time
an array of floating point values in which the time at which nodej
was created istime[j]
. See http://jeromekelleher.github.io/ercs/#oriented-trees-and-forests for further information on oriented forests.Time is measured in units of 4Ne generations, following Hudson’s ms.
Parameters: - sample_size (integer) – The sample size; must be >= 2.
- random_seed (integer or None) – The random seed for simulations
Return type: (list, list)