makeplot.asdsf: Plot the Standard Deviation of Split Frequencies over the...

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

Plot the Standard Deviation of Split Frequencies over the course of an MCMC.

Description

This function takes two or more rwty.chain ojects and returns a plot of ASDSF as the run progresses. The solid line with points shows the Average Standard Deviation of Split Frequences at the current generation The grey ribbon shows the upper and lower 95

Usage

makeplot.asdsf(
  chains,
  burnin = 0,
  window.size = 20,
  min.freq = 0,
  log.y = TRUE
)

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 between each point at which the ASDSFs is calculated (note, specified as a number of sampled trees, not a number of generations)
min.freq	The minimum frequency for a node to be used for calculating ASDSF.
log.y	Controls whether they Y axis is plotted on a log scale or not. Which scale is more useful depends largely on the amount of disagreement between your chains. Attempting to make an asdsf plot with a log Y axis for chains that include standard deviations of zero will result in warning messages.

Value

output A cumulative plot of ASDSF across all chains

Examples

## Not run: 
data(fungus)
p <- makeplot.asdsf(fungus, burnin = 20)
p

## End(Not run)

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