cumulative.freq: Cumulative means of clade split frequencies.

In rwty: R We There Yet? Visualizing MCMC Convergence in Phylogenetics

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)

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)

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.

Examples

## Not run: 
data(fungus)
cumulative.data <- cumulative.freq(fungus, burnin=20)

## End(Not run)

rwty documentation built on April 3, 2025, 9:20 p.m.