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Plot model convergence of a selected model

Source: R/Mod_Convergence_Plot.R, R/Mod_Convergence_Alpha.R, R/Mod_Convergence_Rho.R
Convergence_plots.Rd

The Convergence_Plot() function generates and saves convergence diagnostics plots for the rho, alpha, omega, and beta parameters in an Hmsc model. These plots help assess whether the MCMC chains have reached stationarity. It supports parallel processing and can work with models fitted on HPC environments.

Usage

Convergence_Plot(
  Path_Coda = NULL,
  Path_Model = NULL,
  EnvFile = ".env",
  Title = " ",
  NOmega = 1000L,
  NCores = 8L,
  NRC = c(2L, 2L),
  Beta_NRC = c(3L, 3L),
  SavePlotData = TRUE,
  PagePerFile = 20L,
  Cols = NULL,
  MarginType = "histogram"
)

Convergence_Alpha(
  Post = NULL,
  Model = NULL,
  Title = NULL,
  NRC = NULL,
  AddFooter = TRUE,
  AddTitle = TRUE,
  Cols = NULL,
  MarginType = "histogram"
)

Convergence_Rho(
  Post = NULL,
  Model = NULL,
  Title = NULL,
  Cols = NULL,
  MarginType = "histogram"
)

Arguments

Path_Coda

Character. Path to a saved coda object containing MCMC samples.

Path_Model

Character. Path to a saved Hmsc model object.

EnvFile

Character. Path to the environment file containing paths to data sources. Defaults to .env.

Title

Character. Title for rho and alpha convergence plots. Default: " "

NOmega

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

NCores

Integer. Number of CPU cores to use for parallel processing. Default: 8.

NRC

Numeric vector. Grid layout (rows×columns) for arranging alpha parameter plots. Default: c(2, 2). If NULL, the layout is automatically determined based on the number of alpha levels.

Beta_NRC

Numeric vector. The grid layout (rows×columns) for arranging beta parameter plots. Default: c(3, 3).

SavePlotData

Logical. If TRUE (default), saves the plot data as .RData files.

PagePerFile

Integer. Number of plots per page in the Omega parameter output. Default: 20L.

Cols

Character vector. MCMC chain colors (optional). Default: NULL.

MarginType

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

Post

mcmc.list or character. Either an MCMC object (mcmc.list) containing posterior samples, or a file path to a saved coda object.

Model

Hmsc object or character. Either a fitted Hmsc model object, or a file path to a saved Hmsc model.

AddFooter

Logical. If TRUE (default), adds a footer with page numbers to each plot.

AddTitle

Logical. If TRUE (default), adds the main title (Title) to the plot.

Details

Convergence_Alpha() and Convergence_Rho() are internal functions and should not be called directly.

Author

Ahmed El-Gabbas