plot.ssMCMC: S3 method for plotting ssMCMC objects

In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

S3 method for plotting ssMCMC objects

Description

S3 method for plotting ssMCMC objects

Usage

## S3 method for class 'ssMCMC'
plot(x, ...)

Arguments

x	An 'ssMCMC' object
...	Additional arguments passed to plot

Details

Produces 4 plots. The first 3 plot the prior, reference function and likelihood. Different colors indicate different power posteriors for each. These chains should appear to be well mixed. The final plot shows the sum of the marginal likelihood across each of the steps in the stepping stone algorithm.

Value

No return value, called for side effects. This function generates diagnostic plots for an 'ssMCMC' object, including log-likelihood, log-prior, log-reference function, and cumulative marginal likelihood across power posteriors.

bayou documentation built on June 10, 2025, 5:13 p.m.