make.beta: Make beta values for marginal likelihood calculation

In dosreislab/mcmc3r: Tools to work with MCMCtree

Make beta values for marginal likelihood calculation

Description

Make appropriate beta values

Usage

make.beta(n, method = c("step-stones", "gauss-quad"), a = 5)

Arguments

n	numeric, number of beta points
method	character, the method to choose the beta points, see details
a	numeric, exponent for stepping stones beta generation, see details

Details

If method = "step-stones", the beta values are given by the formula

\beta_{i}=\left(\frac{i-1}{n}\right)^{a}.

Values of a between 5 to 8 appear appropriate. Large a values produce beta values close to zero.

If method = "gauss-quad", the beta values are calculated according to the n Gauss-Legendre quadrature rule (see Rannala and Yang, 2017).

Value

Numeric vector with n beta values

Author(s)

Mario dos Reis

References

Rannala B and Yang Z (2017) Efficient Bayesian species tree inference under the multispecies coalescent. Systematic Biology, 66: 823–842.

See Also

The generated beta values are suitable input for make.bfctlf.

dosreislab/mcmc3r documentation built on March 29, 2024, 6:45 p.m.