makeplot.autocorr: Make autocorrelation plots of tree topologies from MCMC...

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

Description

This function takes a list of rwty.chain objects, and makes an autocorrelation plot for each chain. Each plot shows the mean phylogenetic distance at a series of sampling intervals. In really well behaved MCMC analyses, the mean distance will stay constant as the sampling interval increases. If there is autocorrelation, the mean distance will increase as the sampling interval increases, and is expected to level off when the autocorrelation decreases to zero. The function calculates path distances, though other distances could also be employed.

Usage

makeplot.autocorr(chains, burnin = 0, max.sampling.interval = NA,
  autocorr.intervals = 40, squared = FALSE, facet = FALSE,
  free_y = FALSE, treedist = "PD", use.all.samples = FALSE)

Arguments

chains	A list of rwty.chain objects.
burnin	The number of trees to eliminate as burnin.
max.sampling.interval	The largest sampling interval for which you want to calculate the mean distance between pairs of trees (default is 10 percent of the length of the chain).
autocorr.intervals	The number of sampling intervals to use. These will be spaced evenly between 1 and the max.sampling.interval
squared	TRUE/FALSE use squared tree distances (necessary to calculate approximate ESS; default FALSE)
facet	TRUE/FALSE to turn facetting of the plot on or off (default FALSE)
free_y	TRUE/FALSE to turn free y scales on the facetted plots on or off (default FALSE). Only works if facet = TRUE.
treedist	the type of tree distance metric to use, can be 'PD' for path distance or 'RF' for Robinson Foulds distance
use.all.samples	(TRUE/FALSE). Whether to calculate autocorrelation from all possible pairs of trees in your chain. The default is FALSE, in which case 500 samples are taken at each sampling interval. This is sufficient to get reasonably accurate estimates of the approximate ESS. Setting this to TRUE will give you slightly more accurate ESS estimates, at the cost of potentially much longer execution times.

Value

A ggplot2 plot object, with one line (facetting off) or facet (facetting on) per rwty.chain object.

Examples

## Not run: 
data(fungus)
makeplot.autocorr(fungus, burnin = 20)

## End(Not run)

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