Plots for dynamitefit Objects

Produces the traceplots and the density plots of the model parameters. Can also be used to plot the time-varying and time-invariant parameters of the model along with their posterior intervals. See the plot_type argument for details on available plots.

Usage

# S3 method for class 'dynamitefit'
plot(
  x,
  plot_type = c("default", "trace", "dag"),
  types = NULL,
  parameters = NULL,
  responses = NULL,
  groups = NULL,
  times = NULL,
  level = 0.05,
  alpha = 0.5,
  facet = TRUE,
  scales = c("fixed", "free"),
  n_params = NULL,
  ...
)

Arguments

x

[dynamitefit]
The model fit object.

plot_type

[character(1)]
What type of plot to draw? The default is "default" which draws posterior means and intervals of the parameters selected by types or parameters. If both "types" and parameters are NULL, all parameters are drawn up to the maximum specified by n_params. Option "trace" instead draws posterior densities and traceplots of the parameters. Option "dag" instead plots the directed acyclic graph of the model formula, see plot.dynamiteformula() for the arguments available for this option.

types

[character(1)]
Types of the parameter for which the plots should be drawn. Possible options can be found with the function get_parameter_types(). Ignored if the argument parameters is supplied.

parameters

[charecter()]
Parameter name(s) for which the plots should be drawn. Possible options can be found with the function get_parameter_names(). The default is all parameters, limited by n_params.

responses

[character()]
Response(s) for which the plots should be drawn. Possible options are unique(x$priors$response). Default is all responses. Ignored if the argument parameters is supplied.

groups

[character(1)]
Group name(s) for which the plots should be drawn for group-specific parameters.

times

[double()]
Time point(s) for which the plots should be drawn for time-varying parameters. By default, all time points are included, up to the maximum number of parameters specified by n_params starting from the first non-fixed time point.

level

[numeric(1)]
Level for posterior intervals. Default is 0.05, leading to 90% intervals.

alpha

[numeric(1)]
Opacity level for geom_ribbon. Default is 0.5.

facet

[logical(1)]
Should the time-invariant parameters be plotted separately (TRUE) or in a single plot (FALSE)?

scales

[character(1)]
Should y-axis of the panels be "fixed" (the default) or "free"? See ggplot2::facet_wrap().

n_params

[integer()]
A single value or a vector of length 2 specifying the maximum number of parameters to plot. If a single value is provided, the same limit is used for all parameters. If a vector is supplied, the first element defines the maximum number of time-invariant parameters to plot and the second the maximum number of time-varying parameters to plot. The defaults values are 20 for time-invariant parameters and 3 for time-varying parameters. The default value is 5 for plot_type == "trace".

...

Arguments passed to plot.dynamiteformula() when using plot_type = "dag".

Value

A ggplot object.

See also

Drawing plots plot.dynamiteformula()

Examples

data.table::setDTthreads(1) # For CRAN
plot(gaussian_example_fit, type = "beta")