summarize.posterior: Summarize trends in the posterior
In ACDC: Analysis of Congruent Diversification Classes

Description Usage Arguments Value Examples

Summarize trends in the posterior

1 2	summarize.posterior(posterior, threshold = 0.01, rate_name = "lambda", return_data = FALSE, rm_singleton = FALSE, relative_deltas = FALSE)

`posterior`	a list of ACDC objects, each one representing a sample from the posterior
`threshold`	a threshold for when Δ λ i should be interpreted as decreasing, flat, or increasing
`rate_name`	either "lambda" or "mu" or "delta"
`return_data`	instead of plots, return the plotting dataframes
`rm_singleton`	whether or not to remove singletons. Pass starting at present, going towards ancient
`relative_deltas`	whether to divide Δ λ i by the local lambda value

a ggplot object

data(primates_ebd_log)

posterior <- read.RevBayes(primates_ebd_log, max_t = 65, n_samples = 20)

samples <- sample.congruence.class.posterior(posterior, 
                                             num.samples = 20,
                                             rate.type = "extinction",
                                             rate0.median = 0.1,
                                             model = "MRF",
                                             max.rate = 1.0)

p <- summarize.posterior(samples, threshold = 0.05)