This function generates and optionally saves a series of plots showing the evolution of Gelman and Rubin's shrink factor for various model parameters as the number of iterations increases. It is designed to help assess the convergence of Hmsc model by visualizing the shrink factor over iterations.
Usage
PlotGelman(
Path_Coda = NULL,
Alpha = TRUE,
Beta = TRUE,
Omega = TRUE,
Rho = TRUE,
NOmega = 1000,
FromHPC = TRUE,
PlottingAlpha = 0.25,
EnvFile = ".env",
ReturnPlots = FALSE
)Arguments
- Path_Coda
coda object or path to file containing the coda object.
- Alpha
Logical indicating whether to plot the Gelman-Rubin statistic for the Alpha parameter. If
TRUE(default), the function executes the PlotGelman_Alpha function.- Beta
Logical indicating whether to plot the Gelman-Rubin statistic for the Beta parameter. If
TRUE(default), the function executes the PlotGelman_Beta function.- Omega
Logical indicating whether to plot the Gelman-Rubin statistic for the Omega parameter. If
TRUE(default), the function executes the PlotGelman_Omega function.- Rho
Logical indicating whether to plot the Gelman-Rubin statistic for the Rho parameter. If
TRUE(default), the function executes the PlotGelman_Rho function.- NOmega
Integer specifying the number of species to be sampled for the Omega parameter.
- FromHPC
Logical. Indicates whether the function is being run on an HPC environment, affecting file path handling. Default:
TRUE.- PlottingAlpha
A numeric value between 0 and 1 indicating the transparency level of the plot lines. Defaults to 0.25.
- EnvFile
String specifying the path to the environment variables file. The default value is ".env".
- ReturnPlots
String specifying the folder path where output figures should be saved.