slide.freq: Sliding window measurements of clade split frequencies.

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

Description

This function takes sliding windows of a specified length over an MCMC chain and calculates the split frequency of clades within that window. It allows users to see whether the chain is visiting different areas of treespace.

Usage

slide.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.slide objects, one per chain in the input list of chains. Each rwty.slide object contains the frequencies of clades in the sliding windows, and a translation table that converts clade groupings to factors.

Examples

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

## End(Not run)

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