Default GOF plot for ER model — plot_er

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,
  bin_breaks = NULL,
  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,
  return_components = FALSE
)

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.
bin_breaks: Manually specify bin breaks for binary models. If specified this overrides n_bins.
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.
return_components: Logical, whether to return plot components as a list instead of a combined plot. When TRUE, returns a list with $main (main plot), $boxplot (boxplot if applicable), $caption (caption text if applicable), and $metadata. This allows users to customize individual plot components before combining them. Default is FALSE.

Value

A ggplot object

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
)

To customize plot elements (titles, shapes, themes), use return_components = TRUE to get individual plot components, modify them, then recombine with combine_er_components().

Examples

# \donttest{
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) *
  # Use log10 scale for exposure, need to use `*` instead of `+`
  xgxr::xgx_scale_x_log10(guide = ggplot2::guide_axis(minor.ticks = TRUE))
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_point()`).


# Customize plot components
comps <- plot_er_gof(ermod_bin, var_group = "Dose_mg", return_components = TRUE)
comps$main <- comps$main +
  ggplot2::labs(title = "Exposure-Response Analysis", x = "AUC (ng*h/mL)") +
  ggplot2::theme_bw()
combine_er_components(comps)

# }