cumulative.freq: Cumulative means of clade split frequencies.

In danlwarren/RWTY: R We There Yet? Visualizing MCMC Convergence in Phylogenetics

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)

danlwarren/RWTY documentation built on Sept. 5, 2021, 8:35 p.m.