plot-Samples-Model-method: Plotting dose-toxicity model fits

In 0liver0815/onc-crmpack-test: Object-Oriented Implementation of CRM Designs

Description

Plotting dose-toxicity model fits

Usage

## S4 method for signature 'Samples,Model'
plot(
  x,
  y,
  data,
  ...,
  xlab = "Dose level",
  ylab = "Probability of DLT [%]",
  showLegend = TRUE
)

Arguments

x	the Samples object
y	the Model object
data	the Data object
...	not used
xlab	the x axis label
ylab	the y axis label
showLegend	should the legend be shown? (default)

Value

This returns the ggplot object for the dose-toxicity model fit

Examples

# nolint start

# Create some data
data <- Data(x = c(0.1, 0.5, 1.5, 3, 6, 10, 10, 10),
             y = c(0, 0, 0, 0, 0, 0, 1, 0),
             cohort = c(0, 1, 2, 3, 4, 5, 5, 5),
             doseGrid = c(0.1, 0.5, 1.5, 3, 6,
                          seq(from = 10, to = 80, by=2)))

# Initialize a model 
model <- LogisticLogNormal(mean = c(-0.85, 1),
                           cov = matrix(c(1, -0.5, -0.5, 1), nrow = 2),
                           ref_dose = 56)

# Get posterior for all model parameters
options <- McmcOptions(burnin = 100,
                       step = 2,
                       samples = 2000)
set.seed(94)
samples <- mcmc(data, model, options)

# Plot the posterior mean  (and empirical 2.5 and 97.5 percentile)
# for the prob(DLT) by doses
plot(x = samples, y = model, data = data)
              
# nolint end

0liver0815/onc-crmpack-test documentation built on Feb. 19, 2022, 12:25 a.m.