makeESSPlots: Make ESS plots

In stcolema/mdiHelpR: Helper Functions for Analysis of Sampling-Based Clustering Methods

Make ESS plots

Description

Makes ESS plots for a list of MCMC chains (can be a list of 1). These are plots of the effective sample size calculated for different potential burn-in values and are an aid in choosing an appropriate burn-in value.

Usage

makeESSPlots(
  mcmc_lst,
  plot_titles = NULL,
  gen_ess_title = "Burn in diagnosis plot",
  save_plots = FALSE,
  save_dirs = ".",
  plot_type = ".png",
  common_burn_in = NULL
)

Arguments

mcmc_lst	A list of mcmc chains.
plot_titles	The vector of plot titles corresponding to each chain in mcmc_lst. If NULL defaults to the length of mcmc_lst of the format "chain_i"
gen_ess_title	The component of the title desired in each plot. Defaults to "Burn in diagnosis plot". Combined with plot_titles in the form “paste0(plot_titles[i], ": ", gen_ess_title)“
save_plots	Logical. Instruction to save the plots that are generated.
save_dirs	Characted vector. The locations to save the plots in.
plot_type	The plot type (one of ".png" or ".pdf"). Defaults to ".png".
common_burn_in	An integer. Represents the burn-in the user intends to apply to each chain. Added as a vertical line to each plot.

Value

A list of ggplot2 plots.

stcolema/mdiHelpR documentation built on July 28, 2024, 5:41 a.m.