rwty (version 1.0.3)

cumulative.freq: Cumulative means of clade split frequencies.

Description

This function calculates the cumulative mean split frequencies of clades as an MCMC progresses.

Usage

cumulative.freq(chains, burnin = 0, window.size = 20)

Value

A list of rwty.cumulative objects, one per chain in the input list of chains. Each rwty.cumulative object contains the cumulative mean split frequencies of clades at sp windows, and a translation table that converts clade groupings to factors.

Arguments

chains

A list of rwty.chain objects.

burnin

The number of trees to eliminate as burnin. Defaults to zero.

window.size

The number of trees to include in each window (note, specified as a number of sampled trees, not a number of generations)

Examples

if (FALSE) {
data(fungus)
cumulative.data <- cumulative.freq(fungus, burnin=20)
}