plot_mcmc_diagnostics_all_params: Creates the plot showing the 4 MCMC diagnostics for all...

In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

Creates the plot showing the 4 MCMC diagnostics for all parameters combined

Description

Creates the plot showing the 4 MCMC diagnostics for all parameters combined

Usage

plot_mcmc_diagnostics_all_params(
  model,
  diag_fill = "royalblue",
  diag_alpha = 0.3,
  diag_outline_color = "black",
  ro_arrow_lengths = rep(20, 4),
  ro_text_nudges = rep(0, 4),
  y_lim_geweke = c(0, 30),
  ...
)

Arguments

model	A model object as output by create_rds_file().
diag_fill	The fill color for the bars in the plots
diag_alpha	The transparency for the bars in the plots
diag_outline_color	The bar outline color for the bars in the plots
ro_arrow_lengths	A vector of 4 values to use for the arrow lengths in the 4 plots. Note the plot orders in this vector is: top left, top right bottom left bottom right
ro_text_nudges	A vector of 4 for the R0 text left/right nudges. See plot_mcmc_histogram()
y_lim_geweke	A y limit vector of two values for the Geweke plot only
...	Arguments passed to calc_mcmc_param_stats() and plot_mcmc_histogram()

Value

A ggplot2::ggplot() object

pacific-hake/hake-assessment documentation built on Jan. 14, 2025, 9:12 p.m.