plotShiftSummaries: A function to plot a list produced by 'shiftSummaries'

In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Description

A function to plot a list produced by shiftSummaries

Usage

plotShiftSummaries(summaries, pal = rainbow, ask = FALSE,
  single.plot = FALSE, label.pts = TRUE, ...)

Arguments

summaries	A list produced by the function shiftSummaries
pal	A color palette function
ask	Whether to wait for the user between plotting each shift summary
single.plot	A logical indicating whether to summarize all shifts in a single plot.
label.pts	A logical indicating whether to label the scatter plot.
...	Additional parameters passed to the function par(...)

Details

For each shift, this function plots the taxa on the phylogeny that are (usually) in this regime (each taxon is assigned to the specified shifts, thus some descendent taxa may not always be in indicated regime if the shift if they are sometimes in another tipward shift with low posterior probability). The function then plots the distribution of phenotypic states and the predicted regression line, as well as density plots for the intercept and any regression coefficients in the model.

bayou documentation built on May 2, 2019, 2:46 a.m.