Plot the gain curve in addition with the dose-DLE and dose-efficacy curve using a given DLE pseudo model, a DLE sample, a given efficacy pseudo model and an efficacy sample

Plot the gain curve in addition with the dose-DLE and dose-efficacy curve using a given DLE pseudo model, a DLE sample, a given efficacy pseudo model and an efficacy sample

Plot the gain curve in addition with the dose-DLE and dose-efficacy curve using a given DLE pseudo model, and a given efficacy pseudo model

Usage

plotGain(DLEmodel, DLEsamples, Effmodel, Effsamples, data, ...)

# S4 method for class 'ModelTox,Samples,ModelEff,Samples'
plotGain(DLEmodel, DLEsamples, Effmodel, Effsamples, data, ...)

# S4 method for class 'ModelTox,missing,ModelEff,missing'
plotGain(DLEmodel, Effmodel, data, size = c(8L, 8L), shape = c(16L, 17L), ...)

Arguments

DLEmodel

the dose-DLE model of ModelTox class object

DLEsamples

the DLE sample of Samples class object

Effmodel

the dose-efficacy model of ModelEff class object

Effsamples

the efficacy sample of of Samples class object

data

the data input of DataDual class object

...

not used

size

(integer)
a vector of length two defining the sizes of the shapes used to identify the doses with, respectively, p(DLE = 0.3) and the maximum gain

shape

(integer)
a vector of length two defining the shapes used to identify the doses with, respectively, p(DLE = 0.3) and the maximum gain

Value

This returns the ggplot object for the plot

Functions

• plotGain( DLEmodel = ModelTox, DLEsamples = Samples, Effmodel = ModelEff, Effsamples = Samples ): Standard method

• plotGain( DLEmodel = ModelTox, DLEsamples = missing, Effmodel = ModelEff, Effsamples = missing ): Standard method

Examples

# nolint start

## we need a data object with doses >= 1:
data <- DataDual(
  x = c(25, 50, 25, 50, 75, 300, 250, 150),
  y = c(0, 0, 0, 0, 0, 1, 1, 0),
  w = c(0.31, 0.42, 0.59, 0.45, 0.6, 0.7, 0.6, 0.52),
  doseGrid = seq(25, 300, 25),
  placebo = FALSE
)
#> Used default patient IDs!
#> Used best guess cohort indices!
##plot the dose-DLE , dose-efficacy and gain curve in the same plot with DLE and efficacy samples
##define the DLE model which must be of 'ModelTox' class
##(e.g 'LogisticIndepBeta' class model)
DLEmodel <- LogisticIndepBeta(
  binDLE = c(1.05, 1.8),
  DLEweights = c(3, 3),
  DLEdose = c(25, 300),
  data = data
)
## define the efficacy model which must be of 'ModelEff' class
## (e.g 'Effloglog' class)
Effmodel <- Effloglog(
  eff = c(1.223, 2.513),
  eff_dose = c(25, 300),
  nu = c(a = 1, b = 0.025),
  data = data,
  const = 0
)
##define the DLE sample of 'Samples' class
##set up the same data set in class 'Data' for MCMC sampling for DLE
data1 <- Data(x = data@x, y = data@y, doseGrid = data@doseGrid)
#> Used default patient IDs!
#> Used best guess cohort indices!

##Define the options for MCMC
options <- McmcOptions(burnin = 100, step = 2, samples = 1000)


DLEsamples <- mcmc(data = data1, model = DLEmodel, options = options)
##define the efficacy sample of 'Samples' class
Effsamples <- mcmc(data = data, model = Effmodel, options = options)
##plot the three curves of mean values of the DLEsamples, Effsamples and
##gain value samples (obtained within this plotGain function) at all dose levels
plotGain(
  DLEmodel = DLEmodel,
  DLEsamples = DLEsamples,
  Effmodel = Effmodel,
  Effsamples = Effsamples,
  data = data
)

# nolint end
# nolint start
## we need a data object with doses >= 1:
data <- DataDual(
  x = c(25, 50, 25, 50, 75, 300, 250, 150),
  y = c(0, 0, 0, 0, 0, 1, 1, 0),
  w = c(0.31, 0.42, 0.59, 0.45, 0.6, 0.7, 0.6, 0.52),
  doseGrid = seq(25, 300, 25),
  placebo = FALSE
)
#> Used default patient IDs!
#> Used best guess cohort indices!
##plot the dose-DLE , dose-efficacy and gain curve in the same plot with DLE and efficacy samples
##define the DLE model which must be of 'ModelTox' class
##(e.g 'LogisticIndepBeta' class model)
DLEmodel <- LogisticIndepBeta(
  binDLE = c(1.05, 1.8),
  DLEweights = c(3, 3),
  DLEdose = c(25, 300),
  data = data
)
## define the efficacy model which must be of 'ModelEff' class
## (e.g 'Effloglog' class)
Effmodel <- Effloglog(
  eff = c(1.223, 2.513),
  eff_dose = c(25, 300),
  nu = c(a = 1, b = 0.025),
  data = data
)
##plot the three curves of using modal estimates of model parameters at all dose levels
plotGain(DLEmodel = DLEmodel, Effmodel = Effmodel, data = data)

# nolint end