spDemography.stepping_stone_2d

spDemography.stepping_stone_2d(d, rate, scale=True, timesteps=None)

Create a 2D stepping stone model, either for a single time step or for multiple time steps of deme size change.

Parameters

Name	Type	Description	Default
d	numpy.ndarray	The demography matrix representing the population sizes.	required
rate	float or numpy.ndarray	The migration rate(s) between populations. If a float, it represents a constant migration rate for all populations. If a numpy.ndarray, it represents a migration matrix with shape (T, N, N), where N is the total number of populations and T is the number of time steps - 1, if T > 1.	required
scale	bool	Whether to scale the migration rate matrix. Default is True.	True
timesteps	Union[int, List[int]]	The list of timesteps representing the amount of time passing between each demographic event, in generations. If a single integer is provided, the function assumes that the time steps are equal.	None

Returns

Type	Description
msprime.Demography	The constructed 2d stepping stone model as an msprime.Demography object.

Notes

The demography matrix d should have shape (n, m) or (k, n, m), where n is the number of rows and m is the number of columns for a 2D array and k is the number of layers in a 3D array. The migration rate matrix rate should have shape (N, N), where N is the total number of populations. If there are multiple time steps of population size change, the add_landscape_change function is called to modify the model accordingly.