makeplot.acsf.cumulative: Plot the Change in Split Frequencies (CSF) in sliding windows...

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

Description

This function takes one or more rwty.chain ojects and returns a plot of CSF within each chain as the MCMC progresses. The solid line with points shows the Average Change in Split Frequencies (ACSF; it is average across the changes in split frequencies from all clades in the analysis) between this window and the previous window The grey ribbon shows the upper and lower 95

Usage

makeplot.acsf.cumulative(chains, burnin = 0, window.size = 20,
  facet = 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 to include in each window (note, specified as a number of sampled trees, not a number of generations)
facet	(TRUE/FALSE). TRUE: return a single plot with one facet per chain; FALSE: return a list of individual plots with one plot per chain

Value

output A plof of the CSF between sliding windows over all chains

acsf.plot A ggplot object, or list of ggplot objects

Examples

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

## End(Not run)

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