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plot.modelFits

Source: R/plot.R
plot.modelFits.Rd

Plot function based on the ggplot2 package. Providing visualizations for each model and a average Fit. Black lines show the fitted dose response models and an AIC based average model. Dots indicate the posterior median and vertical lines show corresponding credible intervals (i.e. the variability of the posterior distribution of the respective dose group). To assess the uncertainty of the model fit one can in addition visualize credible bands (default coloring as orange shaded areas). The calculation of these bands is performed via the getBootstrapQuantiles() function. The default setting is that these credible bands are not calculated.

Usage

# S3 method for class 'modelFits'
plot(
  x,
  probability_scale = attr(x, "probability_scale"),
  gAIC = TRUE,
  cr_intv = TRUE,
  alpha_CrI = 0.05,
  cr_bands = FALSE,
  alpha_CrB = c(0.05, 0.2),
  n_bs_smpl = 1000,
  acc_color = "orange",
  plot_res = 100,
  plot_diffs = FALSE,
  ...
)

Arguments

x

An object of type modelFits

probability_scale

A boolean to specify if the trial has a continuous or a binary outcome. Setting to TRUE will transform the output from the logit scale to the probability scale, which can be desirable for a binary outcome. Default attr(x, "probability_scale").

gAIC

Logical value indicating whether gAIC values are shown in the plot. Default TRUE

cr_intv

Logical value indicating whether credible intervals are included in the plot. Default TRUE

alpha_CrI

Numerical value of the width of the credible intervals. Default is set to 0.05 (i.e 95% CI are shown).

cr_bands

Logical value indicating whether bootstrapped based credible bands are shown in the plot. Default FALSE

alpha_CrB

Numerical vector of the width of the credible bands. Default is set to 0.05 and 0.5 (i.e 95% CB and 50% CB are shown).

n_bs_smpl

Number of bootstrap samples being used. Default 1000.

acc_color

Color of the credible bands. Default "orange".

plot_res

Number of plotted doses within the range of the dose levels, i.e., the resolution of the plot. Default 100.

plot_diffs

Logical flag. Plot differences to the control group. Default FALSE.

...

optional parameter to be passed to plot().

Value

A ggplot2 object

Examples

posterior_list <- list(Ctrl = RBesT::mixnorm(comp1 = c(w = 1, m = 0, s = 1), sigma = 2),
                       DG_1 = RBesT::mixnorm(comp1 = c(w = 1, m = 3, s = 1.2), sigma = 2),
                       DG_2 = RBesT::mixnorm(comp1 = c(w = 1, m = 4, s = 1.5), sigma = 2) ,
                       DG_3 = RBesT::mixnorm(comp1 = c(w = 1, m = 6, s = 1.2), sigma = 2) ,
                       DG_4 = RBesT::mixnorm(comp1 = c(w = 1, m = 6.5, s = 1.1), sigma = 2))
models <- c("exponential", "linear", "emax")
dose_levels <- c(0, 1, 2, 4, 8)
model_fits <- getModelFits(models      = models,
                           posterior   = posterior_list,
                           dose_levels = dose_levels,
                           simple       = TRUE)

plot(model_fits)


# plot with credible bands
plot(model_fits,
     cr_bands          = TRUE,
     plot_diffs        = FALSE,
     probability_scale = FALSE,
     n_bs_smpl         = 1e2) # speeding up example run-time