plot_pairs_mcmc: Plot MCMC pairs for iSCAM models

In pbs-assess/gfiscamutils: Provide functions for iSCAM models

Plot MCMC pairs for iSCAM models

Description

Pairs plots for parameters in an MCMC run

Usage

plot_pairs_mcmc(
  model,
  plot_sel = NULL,
  param_rm = c("rho", "vartheta", "so", "beta", "phie"),
  list_param_names = FALSE,
  text_title_size = 12,
  point_size = 1,
  tick_label_size = 5,
  tick_label_angle = 45
)

Arguments

model	An iscam model object (class mdl_cls)
plot_sel	Logical. If TRUE, plot only the selectivity parameters. If FALSE, plot only non-selectivity parameters. If NULL, plot all parameters except those in param_rm
param_rm	A vector of parameter names to remove. If any are not found in the output, a warning will be issued. If NULL, nothing is removed
list_param_names	Logical. If TRUE, list the parameter names that will be plot by this function, but do not actually plot it. This is to help you to use the param_rm argument, so you know what the names to be removed can be
text_title_size	Add the model description as a title with this font size. The text comes from the model_desc attribute of model. If this is NULL, don't show a title
point_size	Size of the points on each pairs panel in the lower triangle
tick_label_size	Size of the tick labels on both axes
tick_label_angle	Angle of tick labels on both axes

Details

Show correlations between parameters as scatterplots in the lower triangular area, density of each parameter in the diagonals, and the correlation value with text size scaled to be larger for higher correlations in the upper triangular area

Value

A ggplot2::ggplot() object made from the GGally::ggpairs() function

See Also

Other MCMC diagnostics plots: plot_autocorr_mcmc(), plot_priors_posts_mcmc(), plot_traces_mcmc()

pbs-assess/gfiscamutils documentation built on Oct. 24, 2024, 1:37 p.m.