makeplot.param: Plotting parameters

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

Plotting parameters

Description

Plots parameter values over the length of the MCMC chain

Usage

makeplot.param(
  chains,
  burnin = 0,
  parameter = "LnL",
  facet = TRUE,
  free_y = FALSE
)

Arguments

chains	A set of rwty.chain objects.
burnin	The number of trees to omit as burnin.
parameter	The column name of the parameter to plot.
facet	Boolean denoting whether to make a facet plot.
free_y	TRUE/FALSE to turn free y scales on the facetted plots on or off (default FALSE). Only works if facet = TRUE.

Value

param.plot Returns a ggplot object.

Examples

## Not run: 
data(fungus)
makeplot.param(fungus, burnin=20, parameter="pi.A.")

## End(Not run)

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