create_diagnostic_plots: Create Diagnostic Plots for Multiple Sampling Chains

In topolow: Force-Directed Euclidean Embedding of Dissimilarity Data

Create Diagnostic Plots for Multiple Sampling Chains

Description

Creates trace and density plots for multiple sampling or optimization chains to help assess convergence and mixing. It displays parameter trajectories and their distributions across all chains.

Usage

create_diagnostic_plots(
  chain_files,
  mutual_size = 2000,
  output_file = "diagnostic_plots.png",
  output_dir,
  save_plot = FALSE,
  width = 3000,
  height = 3000,
  res = 300
)

Arguments

chain_files	A character vector of paths to CSV files, where each file contains data for one chain.
mutual_size	Integer. The number of samples to use from the end of each chain for plotting.
output_file	Character. The path for saving the plot. Required if save_plot is TRUE.
output_dir	Character. The directory for saving output files. Required if save_plot is TRUE.
save_plot	Logical. If TRUE, saves the plot to a file. Default: FALSE.
width, height, res	Numeric. The dimensions and resolution for the saved plot.

Value

A ggplot object of the combined plots.

Examples

# This example uses sample data files that would be included with the package.
chain_files <- c(
  system.file("extdata", "diag_chain1.csv", package = "topolow"),
  system.file("extdata", "diag_chain2.csv", package = "topolow"),
  system.file("extdata", "diag_chain3.csv", package = "topolow")
)

# Only run the example if the files are found
if (all(nzchar(chain_files))) {
  # Create diagnostic plot without saving to a file
  create_diagnostic_plots(chain_files, mutual_size = 50, save_plot = FALSE)
}

topolow documentation built on Aug. 31, 2025, 1:07 a.m.