EMC2 (version 3.1.0)

plot_density: Plot Defective Densities

Description

Plots panels that contain a set of densities for each level of the specified defective factor in the data. These densities are defective; their areas are relative to the respective proportions of the defective factor levels. Across all levels, the area sums to 1. Optionally, posterior/prior predictive densities can be overlaid.

Usage

plot_density(
  input,
  post_predict = NULL,
  prior_predict = NULL,
  subject = NULL,
  quants = c(0.025, 0.975),
  functions = NULL,
  factors = NULL,
  defective_factor = "R",
  n_cores = 1,
  n_post = 50,
  layout = NA,
  to_plot = c("data", "posterior", "prior")[1:2],
  use_lim = c("data", "posterior", "prior")[1:2],
  legendpos = c("topright", "top"),
  posterior_args = list(),
  prior_args = list(),
  ...
)

Arguments

input

Either an emc object or a data frame, or a list of such objects.

post_predict

Optional posterior predictive data (matching columns) or list thereof.

prior_predict

Optional prior predictive data (matching columns) or list thereof.

subject

Subset the data to a single subject (by index or name).

quants

Numeric vector of credible interval bounds (e.g. c(0.025, 0.975)).

functions

A function (or list of functions) that create new columns in the datasets or predictives

factors

Character vector of factor names to aggregate over; defaults to plotting full data set ungrouped by factors if NULL.

defective_factor

Name of the factor used for the defective CDF (default "R").

n_cores

Number of CPU cores to use if generating predictives from an emc object.

n_post

Number of posterior draws to simulate if needed for predictives.

layout

Numeric vector used in par(mfrow=...); use NA for auto-layout.

to_plot

Character vector: any of "data", "posterior", "prior".

use_lim

Character vector controlling which source(s) define xlim.

legendpos

Character vector controlling the positions of the legends

posterior_args

Optional list of graphical parameters for posterior lines/ribbons.

prior_args

Optional list of graphical parameters for prior lines/ribbons.

...

Other graphical parameters for the real data lines.

Examples

# Plot defective densities for each subject and the factor combination in the design:
plot_density(forstmann)
# or for one subject:
plot_density(forstmann, subject = 1)
# Now collapsing across subjects and using a different defective factor:
plot_density(forstmann, factors = "S", defective_factor = "E")
# Or plot posterior predictives
plot_density(samples_LNR, n_post = 10)