Classes

Top level classes.

kSFS([X, mutation_types, file, n])

Primary class for working with SFS data to infer demography \(\eta(t)\equiv 2N(t)\), or with \(k\)-SFS data to infer demography and mutation spectrum history \(\boldsymbol\mu(t)\).

eta(change_points, y)

Demographic history \(\eta(t)\).

mu(change_points, Z, mutation_types)

Mutation spectrum history (MuSH) \(\boldsymbol\mu(t)\).

Submodules

Submodules that the main classes rely on, and may be of interest to some users

optimization

Optimization algorithms.

histories

History objects for representing demography \(\eta(t)\) and MuSH \(\boldsymbol\mu(t)\).

loss_functions

Loss functions for measuring goodness of fit.

utils

Utility functions.

composition

Functions for compositional data analysis.