getSimulationCounts: Get Simulation Counts
In rpact: Confirmatory Adaptive Clinical Trial Design and Analysis

View source: R/f_simulation_base_count_data.R

getSimulationCounts

R Documentation

Get Simulation Counts

Description

Returns the simulated power, stopping probabilities, conditional power, and expected sample size for testing mean rates for negative binomial distributed event numbers in the two treatment groups testing situation.

Usage

getSimulationCounts(
  design = NULL,
  ...,
  plannedCalendarTime,
  maxNumberOfSubjects = NA_real_,
  lambda1 = NA_real_,
  lambda2 = NA_real_,
  lambda = NA_real_,
  theta = NA_real_,
  directionUpper = NA,
  thetaH0 = 1,
  overdispersion = 0,
  fixedExposureTime = NA_real_,
  accrualTime = NA_real_,
  accrualIntensity = NA_real_,
  followUpTime = NA_real_,
  allocationRatioPlanned = NA_real_,
  maxNumberOfIterations = 1000L,
  seed = NA_real_,
  showStatistics = FALSE
)

Arguments

`design`	The trial design. If no trial design is specified, a fixed sample size design is used. In this case, Type I error rate `alpha`, Type II error rate `beta`, `twoSidedPower`, and `sided` can be directly entered as argument where necessary.
`...`	Ensures that all arguments (starting from the "...") are to be named and that a warning will be displayed if unknown arguments are passed.
`plannedCalendarTime`	For simulating count data, the time points where an analysis is planned to be performed. Should be a vector of length `kMax`
`maxNumberOfSubjects`	`maxNumberOfSubjects > 0` needs to be specified for power calculations or calculation of necessary follow-up (count data). For two treatment arms, it is the maximum number of subjects for both treatment arms.
`lambda1`	A numeric value or vector that represents the assumed rate of a homogeneous Poisson process in the active treatment group, there is no default.
`lambda2`	A numeric value that represents the assumed rate of a homogeneous Poisson process in the control group, there is no default.
`lambda`	A numeric value or vector that represents the assumed rate of a homogeneous Poisson process in the pooled treatment groups, there is no default.
`theta`	A numeric value or vector that represents the assumed mean ratios lambda1/lambda2 of a homogeneous Poisson process, there is no default.
`directionUpper`	Logical. Specifies the direction of the alternative, only applicable for one-sided testing; default is `TRUE` which means that larger values of the test statistics yield smaller p-values.
`thetaH0`	The null hypothesis value, default is `0` for the normal and the binary case (testing means and rates, respectively), it is `1` for the survival case (testing the hazard ratio). For non-inferiority designs, `thetaH0` is the non-inferiority bound. That is, in case of (one-sided) testing of means: a value `!= 0` (or a value `!= 1` for testing the mean ratio) can be specified. rates: a value `!= 0` (or a value `!= 1` for testing the risk ratio `pi1 / pi2`) can be specified. survival data: a bound for testing H0: `hazard ratio = thetaH0 != 1` can be specified. count data: a bound for testing H0: `lambda1 / lambda2 = thetaH0 != 1` can be specified. For testing a rate in one sample, a value `thetaH0` in (0, 1) has to be specified for defining the null hypothesis H0: `pi = thetaH0`.
`overdispersion`	A numeric value that represents the assumed overdispersion of the negative binomial distribution, default is `0`.
`fixedExposureTime`	If specified, the fixed time of exposure per subject for count data, there is no default.
`accrualTime`	If specified, the assumed accrual time interval(s) for the study, there is no default.
`accrualIntensity`	If specified, the assumed accrual intensities for the study, there is no default.
`followUpTime`	If specified, the assumed (additional) follow-up time for the study, there is no default. The total study duration is `accrualTime + followUpTime`.
`allocationRatioPlanned`	The planned allocation ratio `n1 / n2` for a two treatment groups design, default is `1`. For multi-arm designs, it is the allocation ratio relating the active arm(s) to the control. For simulating means and rates for a two treatment groups design, it can be a vector of length `kMax`, the number of stages. It can be a vector of length kMax, too, for multi-arm and enrichment designs. In these cases, a change of allocating subjects to treatment groups over the stages can be assessed. Note that internally `allocationRatioPlanned` is treated as a vector of length `kMax`, not a scalar.
`maxNumberOfIterations`	The number of simulation iterations, default is `1000`. Must be a positive integer of length 1.
`seed`	The seed to reproduce the simulation, default is a random seed.
`showStatistics`	Logical. If `TRUE`, summary statistics of the simulated data are displayed for the `print` command, otherwise the output is suppressed, default is `FALSE`.

Details

At given design the function simulates the power, stopping probabilities, conditional power, and expected sample size at given number of subjects and parameter configuration. Additionally, an allocation ratio = n1/n2 and a null hypothesis value thetaH0 can be specified.

Value

Returns a SimulationResults object. The following generics (R generic functions) are available for this object:

names() to obtain the field names,
print() to print the object,
summary() to display a summary of the object,
plot() to plot the object,
as.data.frame() to coerce the object to a data.frame,
as.matrix() to coerce the object to a matrix.

Simulation Data

The summary statistics "Simulated data" contains the following parameters: median range; mean +/-sd

$show(showStatistics = FALSE) or $setShowStatistics(FALSE) can be used to disable the output of the aggregated simulated data.

getData() can be used to get the aggregated simulated data from the object as data.frame. The data frame contains the following columns:

iterationNumber: The number of the simulation iteration.
stageNumber: The stage.
lambda1: The assumed or derived event rate in the treatment group.
lambda2: The assumed or derived event rate in the control group.
accrualTime: The assumed accrualTime.
followUpTime: The assumed followUpTime.
overdispersion: The assumed overdispersion.
fixedFollowUp: The assumed fixedFollowUp.
numberOfSubjects: The number of subjects under consideration when the (interim) analysis takes place.
rejectPerStage: 1 if null hypothesis can be rejected, 0 otherwise.
futilityPerStage: 1 if study should be stopped for futility, 0 otherwise.
testStatistic: The test statistic that is used for the test decision
estimatedLambda1: The estimated rate in treatment group 1.
estimatedLambda2: The estimated rate in treatment group 2.
estimatedOverdispersion: The estimated overdispersion.
infoAnalysis: The Fisher information at interim stage.
trialStop: TRUE if study should be stopped for efficacy or futility or final stage, FALSE otherwise.
conditionalPowerAchieved: Not yet available

How to get help for generic functions

Click on the link of a generic in the list above to go directly to the help documentation of the rpact specific implementation of the generic. Note that you can use the R function methods to get all the methods of a generic and to identify the object specific name of it, e.g., use methods("plot") to get all the methods for the plot generic. There you can find, e.g., plot.AnalysisResults and obtain the specific help documentation linked above by typing ?plot.AnalysisResults.

Examples

## Not run: 
# Fixed sample size design with two groups, fixed exposure time
getSimulationCounts(
    theta = 1.8,
    lambda2 = 0.2,
    maxNumberOfSubjects = 200,
    plannedCalendarTime = 8,
    maxNumberOfIterations = 1000,
    fixedExposureTime = 6,
    accrualTime = 3,
    overdispersion = 2)

# Group sequential design alpha spending function design with O'Brien and 
# Fleming type boundaries: Power and test characteristics for N = 264, 
# under variable exposure time with uniform recruitment over 1.25 months,
# study time (accrual + followup) = 4, interim analysis take place after
# equidistant time points (lambda1, lambda2, and overdispersion as specified,
# no futility stopping):
dOF <- getDesignGroupSequential(
    kMax = 3,
    alpha = 0.025,
    beta = 0.2,
    typeOfDesign = "asOF")

getSimulationCounts(design = dOF,
    lambda1 = seq(0.04, 0.12, 0.02),
    lambda2 = 0.12,
    directionUpper = FALSE,
    overdispersion = 5,
    plannedCalendarTime = (1:3)/3*4,
    maxNumberOfSubjects = 264,
    followUpTime = 2.75,
    accrualTime = 1.25,
    maxNumberOfIterations = 1000)

## End(Not run)

rpact documentation built on Sept. 27, 2024, 5:08 p.m.