BayesERtools (version 0.2.0)

plot_er_gof: Default GOF plot for ER model

Description

This is a wrapper function for plot_er() with default options for goodness-of-fit (GOF) plots for ER models.

Usage

plot_er_gof(
  x,
  add_boxplot = !is.null(var_group),
  boxplot_height = 0.15,
  show_boxplot_y_title = FALSE,
  var_group = NULL,
  n_bins = 4,
  qi_width_obs = 0.95,
  show_coef_exp = FALSE,
  coef_pos_x = NULL,
  coef_pos_y = NULL,
  coef_size = 4,
  qi_width_coef = 0.95,
  qi_width_sim = 0.95,
  show_caption = TRUE
)

Value

A ggplot object

Arguments

x

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

add_boxplot

Logical, whether to add a boxplot of exposure values. Default is TRUE if var_group is specified, otherwise 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 FALSE.

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_obs

Confidence level for the observed probability summary. Default is 0.95.

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.

coef_pos_x

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

coef_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.

coef_size

Size of the text label. Default is 4.

qi_width_coef

Width of the credible interval for the exposure coefficient. Default is 0.95.

qi_width_sim

Width of the quantile interval to summarize simulated draws. Default is 0.95.

show_caption

Logical, whether to show the caption note for the plot. Default is TRUE.

Details

The following code will generate the same plot:

plot_er(
  x,
  show_orig_data = TRUE,
  show_coef_exp = show_coef_exp,
  show_caption = show_caption,
  options_orig_data = list(
    add_boxplot = add_boxplot, boxplot_height = boxplot_height,
    show_boxplot_y_title = show_boxplot_y_title,
    var_group = var_group,
    n_bins = n_bins, qi_width = qi_width_obs
  ),
  options_coef_exp = list(
    qi_width = qi_width_coef, pos_x = coef_pos_x, pos_y = coef_pos_y,
    size = coef_size
  ),
  options_caption = list(
    orig_data_summary = TRUE, coef_exp = show_coef_exp
  ),
  qi_width_sim = qi_width_sim
)

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"
)

plot_er_gof(ermod_bin, var_group = "Dose_mg", show_coef_exp = TRUE)