Creates a Gelman-Rubin-Brooks plot for omega parameters.

This function generates a Gelman-Rubin-Brooks plot specifically for omega parameters using the provided Hmsc model object. It is designed to help assess the convergence of MCMC simulations by plotting the shrink factor over iterations for a subset of species' omega parameters. This function is not planned to be used in isolation but rather within PlotGelman.

Usage

PlotGelman_Omega(CodaObj, NOmega = 1000, PlottingAlpha = 0.25)

Arguments

CodaObj

n object of class mcmc.list representing the MCMC chains.

NOmega

An optional integer indicating the number of species' omega parameters to sample and plot. Defaults to 1000.

PlottingAlpha

A numeric value between 0 and 1 indicating the transparency level of the plot lines. Defaults to 0.25.

Value

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

Author

Ahmed El-Gabbas