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Plot model convergence of multiple modelling alternatives

Source: R/mod_convergence_plot_all.R
Convergence_Plot_All.Rd

This function generates and saves a series of diagnostic plots to assess the convergence of Hmsc models across multiple modelling alternatives. It checks model convergence using trace plots and Gelman-Rubin diagnostics for key model parameters.

Usage

convergence_plot_all(
  model_dir = NULL,
  n_omega = 1000L,
  margin_type = "histogram",
  spatial_model = TRUE,
  n_cores = NULL,
  strategy = "multisession",
  n_rc_alpha = c(2L, 3L)
)

Arguments

model_dir

Character. Path to the root directory of the fitted model. The convergence outputs will be saved to the Model_Convergence_All subdirectory.

n_omega

Integer. Number of species interactions sampled for Omega parameter diagnostics. Default: 1000L

margin_type

Character. The type of marginal plot to add to the main plot. Valid options are "histogram" (default) or "density".

spatial_model

Logical. Whether the model is a spatial model. If TRUE (default), the function will generate additional plots for the model's Alpha parameter.

n_cores

Integer. Number of CPU cores to use for parallel processing.

strategy

Character. The parallel processing strategy to use. Valid options are "sequential", "multisession" (default), "multicore", and "cluster". See future::plan() and ecokit::set_parallel() for details.

n_rc_alpha

Numeric vector of length 2. Number of rows and columns for the convergence plots of the alpha parameter. Default: c(2L, 3L).

Value

The function returns invisible(NULL) and does not return any value, but saves a series of diagnostic plots in the specified path.

Author

Ahmed El-Gabbas