DEFUSE3Design: The DEFUSE3 design

Description Usage Format Methods References See Also Examples

Description

DEFUSE3Design is a slight variant of the the adaptive clinical trial design of Lai, Lavori and Liao. Simulation is used to compute the expected maximum sample size and the boundary for early futility is adjusted to account as well.

Usage

1
# design <- DEFUSE3Design$new(designParameters, trialParameters)

Format

An R6Class generator object

Methods

DEFUSE3Design$new(designParameters, trialParameters, discreteData = FALSE, numberOfSimulations = 5000, rngSeed = 54321, showProgress = TRUE, boundaries)

Create a new DEFUSE3Design instance object using the parameters specified. If discreteData is TRUE use a discrete distribution for the Rankin scores and designParameters must contain the appropriate distributions to sample from. If boundaries is specified, it is used.

getDesignParameters,getTrialParameters, getBoundaries

Accessor methods for (obvious) object slots

setBoundaries

Modifier method for boundaries a named vector of double values with names btilde, b, and c, in that order

print()

Print the object in a human readable form

adjustCriticalValues(numberOfSimulations, rngSeed, showProgress)

Adjust the critical values by performing simulations using the parameters provided

computeCriticalValues()

Compute the critical boundary value c_α

explore(numberOfSimulations = 5000, rngSeed = 12345, trueParameters = self$getDesignParameters(), recordStats = TRUE, showProgress = TRUE, saveRawData = FALSE)

Explore the design using the specified number of simulations and random number seed. trueParameters is by default the same as designParameters as would be the case for a Type I error calculation. If changed, would yield power. Record statistics, save raw data and show progress if so desired. Returns a list of results

analyze(trialHistory)

Analyze the design given the trialHistory which is the result of a call to explore to simulate the design. Return a list of summary quantities

summary(analysis)

Print the operating characteristics of the design, using the analysis result from the analyze call

References

Adaptive design of confirmatory trials: Advances and challenges, 2015 45(Pt A):93-102, by Tze Leung Lai and Philip W. Lavori and Ka Wai Tsang. doi:10.1016/j.cct.2015.06.007

See Also

ASSISTDesign which is a superclass of this object

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
trialParameters <- list(N = c(200, 340, 476), type1Error = 0.025,
                        eps = 1/2, type2Error = 0.1)
designParameters <- list(
   nul0 = list(prevalence = rep(1/6, 6), mean = matrix(0, 2, 6),
               sd = matrix(1, 2, 6)),
   alt1 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
               c(0.5, 0.4, 0.3, 0, 0, 0)),
               sd = matrix(1, 2, 6)),
   alt2 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
               c(0.5, 0.5, 0, 0, 0, 0)),
               sd = matrix(1,2, 6)),
   alt3 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6), rep(0.36, 6)),
               sd = matrix(1,2, 6)),
   alt4 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6), rep(0.30, 6)),
               sd = matrix(1,2, 6)),
   alt5 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
               c(0.4, 0.3, 0.2, 0, 0, 0)),
               sd = matrix(1,2, 6)),
   alt6 = list(prevalence = rep(1/6, 6), mean = rbind(rep(0, 6),
               c(0.5, 0.5, 0.3, 0.3, 0.1, 0.1)),
               sd = matrix(1,2, 6)))

## Not run: 
## A realistic design uses 5000 simulations or more!
defuse3 <- DEFUSE3Design$new(trialParameters = trialParameters,
                             numberOfSimulations = 25,
                             designParameters = designParameters$nul0,
                             showProgress = FALSE)
print(defuse3)
result <- defuse3$explore(showProgress = interactive())
analysis <- defuse3$analyze(result)
print(defuse3$summary(analysis))

## End(Not run)
## For full examples, try:
## browseURL(system.file("full_doc/defuse3.html", package="ASSISTant"))

ASSISTant documentation built on May 6, 2019, 1:02 a.m.