plotESS: Plot barplot of ESS values

In laduplessis/beastio: Functions for pre- and post-processing of BEAST and BEAST2 files.

Description

Plot barplot of ESS values

Usage

plotESS(
  data,
  ess = NULL,
  cutoff = 200,
  title = "",
  col1 = "gray",
  col2 = "red2",
  border1 = "black",
  border2 = "darkred",
  labels = TRUE,
  ...
)

Arguments

data	The object containing the MCMC sample - usually of class "mcmc" or "mcmc.list"
ess	Output of running coda::effectiveSize(data) - this is optional and can be supplied to save time
cutoff	The cutoff ESS value for a parameter to be considered stationary (default = 200)
title	Title of the plot (x-label)
col1	Fill colour used for stationary parameters (ess >= cutoff)
col2	Fill colour used for non-stationary parameters (ess < cutoff)
border1	Border colour used for stationary parameters (ess >= cutoff)
border2	Border colour used for non-stationary parameters and labels (ess < cutoff)
labels	Label non-stationary parameters (ess < cutoff)
...	Extra parameters passed to the barplot2' function

laduplessis/beastio documentation built on Dec. 14, 2021, 7:04 p.m.