Plot diagnostics of a 'JAGS' model

Source: R/JAGS-diagnostics.R

Creates density plots, trace plots, and autocorrelation plots for a given parameter of a JAGS model.

JAGS_diagnostics(
  fit,
  parameter,
  type,
  plot_type = "base",
  xlim = NULL,
  ylim = NULL,
  lags = 30,
  n_points = 1000,
  transformations = NULL,
  transform_factors = FALSE,
  transform_orthonormal = FALSE,
  short_name = FALSE,
  parameter_names = FALSE,
  formula_prefix = TRUE,
  ...
)

JAGS_diagnostics_density(
  fit,
  parameter,
  plot_type = "base",
  xlim = NULL,
  n_points = 1000,
  transformations = NULL,
  transform_factors = FALSE,
  transform_orthonormal = FALSE,
  short_name = FALSE,
  parameter_names = FALSE,
  formula_prefix = TRUE,
  ...
)

JAGS_diagnostics_trace(
  fit,
  parameter,
  plot_type = "base",
  ylim = NULL,
  transformations = NULL,
  transform_factors = FALSE,
  transform_orthonormal = FALSE,
  short_name = FALSE,
  parameter_names = FALSE,
  formula_prefix = TRUE,
  ...
)

JAGS_diagnostics_autocorrelation(
  fit,
  parameter,
  plot_type = "base",
  lags = 30,
  transformations = NULL,
  transform_factors = FALSE,
  transform_orthonormal = FALSE,
  short_name = FALSE,
  parameter_names = FALSE,
  formula_prefix = TRUE,
  ...
)

Arguments

fit

a JAGS model fitted via JAGS_fit()

parameter

parameter to be plotted

type

what type of model diagnostic should be plotted. The available options are "density", "trace", and "autocorrelation"

plot_type

whether to use a base plot "base" or ggplot2 "ggplot" for plotting.

xlim

x plotting range

ylim

y plotting range

lags

number of lags to be shown for the autocorrelation plot. Defaults to 30.

n_points

number of equally spaced points in the x_range if x_seq is unspecified

transformations

named list of transformations to be applied to specific parameters

transform_factors

whether factors with orthonormal/meandif prior distribution should be transformed to differences from the grand mean

transform_orthonormal

(to be depreciated) whether factors with orthonormal prior distributions should be transformed to differences from the grand mean

short_name

whether prior distribution names should be shorted

parameter_names

whether parameter names should be printed

formula_prefix

whether the parameter prefix from formula should be printed. Defaults to TRUE.

...

additional arguments

Value

diagnostics returns either NULL if plot_type = "base"

or an object/list of objects (depending on the number of parameters to be plotted) of class 'ggplot2' if plot_type = "ggplot2".