BayesERtools (version 0.2.0)

plot_er: Plot ER model simulations

Description

Plot ER model simulations

Usage

plot_er(x, ...)
# S3 method for ersim_med_qi
plot_er(
  x,
  show_orig_data = FALSE,
  show_coef_exp = FALSE,
  show_caption = FALSE,
  options_orig_data = list(),
  options_coef_exp = list(),
  options_caption = list(),
  ...
)
# S3 method for ersim
plot_er(
  x,
  show_orig_data = FALSE,
  show_coef_exp = FALSE,
  show_caption = FALSE,
  options_orig_data = list(),
  options_coef_exp = list(),
  options_caption = list(),
  qi_width_sim = 0.95,
  ...
)
# S3 method for ermod
plot_er(
  x,
  show_orig_data = FALSE,
  show_coef_exp = FALSE,
  show_caption = FALSE,
  options_orig_data = list(),
  options_coef_exp = list(),
  options_caption = list(),
  n_draws_sim = if (marginal) 200 else NULL,
  seed_sample_draws = NULL,
  marginal = FALSE,
  exposure_range = NULL,
  num_exposures = 51,
  qi_width_sim = 0.95,
  ...
)

Value

A ggplot object

Arguments

x

an object of class ermod, ersim,ersim_med_qi, or their subclasses

...

currently not used

show_orig_data

logical, whether to show the data points in the model development dataset. Default is FALSE. Only support plotting with data that was used in the model development. If you want to use other data, consider adding geom_point() to the plot manually.

show_coef_exp

logical, whether to show the credible interval of the exposure coefficient. Default is FALSE. This is only available for linear and linear logistic regression models.

show_caption

logical, whether to show the caption note for the plot. Default is FALSE.

options_orig_data

List of options for configuring how original data is displayed. Possible options include:

• add_boxplot: Logical, whether to add a boxplot of exposure values. Default is FALSE.

• boxplot_height: Height of the boxplot relative to the main plot. Default is 0.15.

• show_boxplot_y_title: Logical, whether to show the y-axis title for the boxplot. Default is TRUE.

• var_group: The column to use for grouping data for plotting. If specified, observed data points and boxplot will be grouped and colored by this column. Default is NULL.

• n_bins: Number of bins to use for observed probability summary. Only relevant for binary models. Default is 4.

• qi_width: Width of the quantile interval (confidence interval) for the observed probability summary. Only relevant for binary models. Default is 0.95.

options_coef_exp

List of options for configuring how the exposure coefficient credible interval is displayed. Possible options include:

• qi_width: Width of the quantile interval (credible interval) for the exposure coefficient. Default is 0.95.

• n_sigfig: Number of significant figures to display. Default is 3.

• pos_x: x-coordinate of the text label. If NULL (default), it is set to the minimum value for the exposure variable.

• pos_y: y-coordinate of the text label. If NULL (default), it is set to 0.9 for logistic regression models and the maximum value of the response variable in the original data for linear regression models.

• size: Size of the text label. Default is 4.

options_caption

List of options for configuring the caption note. Possible options include:

• orig_data: Logical, whether to show the caption note for the observed data. Default is FALSE.

• orig_data_summary: Logical, whether to show the caption note for the observed data summary. Default is FALSE. Only relevant for binary models.

• coef_exp: Logical, whether to show the caption note for the exposure coefficient credible interval. Default is FALSE.

qi_width_sim

Width of the quantile interval to summarize simulated draws.

n_draws_sim

Number of draws to simulate response for each exposure value. Set to NULL to use all draws in the model object. Default is NULL unless marginal is set to TRUE (in that case 200 by default to reduce computation time).

seed_sample_draws

Seed for sampling draws. Default is NULL.

marginal

logical, whether to use marginal ER simulation. Default to FALSE. Need to set to TRUE if the model has covariates for the plot to work.

exposure_range

Only relevant when the input x is an ermod object. Range of exposure values to simulate. If NULL (default), it is set to the range of the exposure variable in the original data for model development.

num_exposures

Only relevant as with exposure_range. Number of exposure values to simulate.

Details

Plotting with ermod is done with some default values. If they are not suitable, you can always perform the simulation manually and use plot_er() on the simulated data.

Examples

data(d_sim_binom_cov_hgly2)

ermod_bin <- dev_ermod_bin(
  data = d_sim_binom_cov_hgly2,
  var_resp = "AEFLAG",
  var_exposure = "AUCss_1000"
)

ersim_med_qi <- sim_er_curve(
  ermod_bin,
  output_type = "median_qi"
)

plot_er(ersim_med_qi, show_orig_data = TRUE) +
  xgxr::xgx_scale_x_log10()