crmPack (version 2.0.0)

plot,Samples,GeneralModel-method: Plotting dose-toxicity model fits

Description

Plotting dose-toxicity model fits

Usage

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

Value

This returns the ggplot

object for the dose-toxicity model fit

Arguments

x

the Samples object

y

the GeneralModel object

data

the Data object

...

not used

xlab

the x axis label

ylab

the y axis label

showLegend

should the legend be shown? (default)

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