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Gelman-Rubin-Brooks plot for beta parameters

Source: R/Mod_PlotGelman_Beta.R
PlotGelman_Beta.Rd

This function generates a Gelman-Rubin-Brooks plot for beta parameters from a Hmsc object. It is used to assess the convergence of MCMC simulations by plotting the evolution of the shrink factor over iterations. The plot helps in identifying whether the chains have converged to a common distribution. The plot includes lines for the median and the 97.5th percentile of the shrink factor, with a dashed line at 1.1 indicating the threshold for convergence. This function is not planned to be used in isolation but rather within PlotGelman.

Usage

PlotGelman_Beta(
  CodaObj,
  EnvFile = ".env",
  PlottingAlpha = 0.25,
  FromHPC = TRUE
)

Arguments

CodaObj

An object of class mcmc.list, representing the Hmsc samples.

EnvFile

String specifying the path to read the environment variables. Default value is .env.

PlottingAlpha

Double indicating the alpha (transparency) level for the plotting lines. Default value is 0.25.

FromHPC

Logical. Indicates whether the function is being run on an HPC environment, affecting file path handling. Default: TRUE.

Value

A ggplot object representing the Gelman-Rubin-Brooks plot for the beta parameters.

Author

Ahmed El-Gabbas