Plot convergence traceplots for the alpha parameter

This function generates and plots convergence traceplots for the alpha parameter from an Hmsc model, using various diagnostics and visualizations to assess convergence. It supports customization of plot aesthetics and layout.

Usage

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

Arguments

Post

A coda object or a string path to a saved coda object containing the posterior samples for the alpha parameter.

Model

A fitted model object or a string path to a saved model object containing the samples and metadata necessary for plotting.

Title

A string specifying the main title of the plot.

NRC

numeric vector of length 2 specifying the number of rows and columns per page of plots. If NULL, it is automatically determined based on the number of levels of the alpha parameter.

AddFooter

A logical value indicating whether to add a footer with page numbers to each plot page. Defaults to TRUE.

AddTitle

A logical value indicating whether to add the main title (specified by Title) to the plot. Defaults to TRUE.

Cols

Character vector for chain colours (optional). Default: NULL.

FromHPC

Logical. Indicates whether the function is being run on an HPC environment, affecting file path handling. Default: TRUE.

MarginType

A string specifying the type of marginal plot to add to the main plot. Must be either "histogram" or "density". Default: "histogram".

Value

A grid of ggplot2 objects representing the traceplots for the alpha parameter, arranged according to the specified number of rows and columns per page. If AddTitle or AddFooter is TRUE, additional text elements are included as specified.

Author

Ahmed El-Gabbas