Generate Posterior Density Plots by Species Complex

This function creates posterior density plots for the hierarchical Bayesian model parameters aggregated by species complex. It uses the stanfit object and associated data generated by `run_stan()`. The plot can optionally be saved to a specified directory.

plot_density(
  stan_results,
  unlabel = FALSE,
  plot_dir = NULL,
  complex_names = NULL
)

Arguments

stan_results

Named list output from `run_stan()` containing the fitted model and related data.

unlabel

Logical. If TRUE, removes labels from the plot. Default is FALSE.

plot_dir

Optional character. Directory path to save the plot image. If NULL, the plot is not saved.

complex_names

Optional character vector. Names of species complexes to include in the plot. If NULL, all are included.

genus

Logical. Adjusts vertical size of the plot. Default is TRUE.