phylojunction.distribution.likelihood.ODE package

Submodules

phylojunction.distribution.likelihood.ODE.dn_bisse_ode module

phylojunction.distribution.likelihood.ODE.dn_bisse_ode.bisse_d_eqns(t, ds_es, qs, mus, lambdas)

Return Maddison et al. d/dt D(t) equations.

Parameters:

  • t (float) – Time (not used).

  • ds_es (numpy.ndarray) – Values of Ds for states 0 and 1, followed by values of Es, for states 0 and 1.

  • qs (numpy.ndarray) – Two-dimensional array of values of transition rate parameters for states 0 and 1.

  • mus (numpy.ndarray) – Values of extinction rate parameters for states 0 and 1.

  • lambdas (numpy.ndarray) – Values of birth-rate parameters for states 0 and 1.

Returns
(numpy.ndarray): Values (floats) of D for all states

and of E for all states.

phylojunction.distribution.likelihood.ODE.dn_bisse_ode.bisse_e_eqns(es, qs, mus, lambdas)

Return Maddison et al. d/dt E(t) equations.

Parameters:

  • es (numpy.ndarray) – Values of Es for states 0 and 1.

  • qs (numpy.ndarray) – Two-dimensional array of values of transition rate parameters for states 0 and 1.

  • mus (numpy.ndarray) – Values of extinction rate parameters for states 0 and 1.

  • lambdas (numpy.ndarray) – Two-dimensional array of values of birth-rate parameters for states 0 and 1.

Returns:

Values (floats) of E for states 0 and 1

Return type:

(tuple)

phylojunction.distribution.likelihood.ODE.dn_bisse_ode.solve_bisse_ds_es(ds_es, t_start, t_end, qs, mus, lambdas, verbose: bool | None = False)

phylojunction.distribution.likelihood.ODE.dn_mbt_ode module

phylojunction.distribution.likelihood.ODE.dn_mbt_ode.mbt_bisse_d_eqn(t, ds_es, ds_es_buffer, qs, mus, b)
phylojunction.distribution.likelihood.ODE.dn_mbt_ode.mbt_e_eqn(es, qs, mus, b)
phylojunction.distribution.likelihood.ODE.dn_mbt_ode.solve_mbt_ds_es(ds_es, t_start, t_end, ds_es_buffer, qs, mus, b, verbose: bool | None = False)

Module contents