VEpowerPP: Unconditional Power to Detect Positive Treatment Efficacy in a Per-Protocol Cohort

Description

VEpowerPP computes unconditional power to detect positive treatment (vaccine) efficacy in per-protocol cohorts identified in simTrial-generated data-sets.

Usage

VEpowerPP(dataList, VEcutoffWeek, stage1, alpha, outName = NULL, 
          saveDir = NULL)

Arguments

dataList

if saveDir = NULL, a list of objects (lists) returned by censTrial; otherwise a list of .RData file names (character strings) generated by censTrial

VEcutoffWeek

a cut-off time (in weeks). Only subjects with the follow-up time exceeding VEcutoffWeek are included in the per-protocol cohort.

stage1

the final week of stage 1 in a two-stage trial. The VE(post-VEcutoffWeek--stage1) estimand is considered in the power calculation.

alpha

the nominal significance level of the one-sided test of the null hypothesis that VE(post-VEcutoffWeek--stage1) $\le$ 0%

outName

a character string specifying the output .RData file name. If outName = NULL but saveDir is specified, the output file is named VEpwPP.RData.

saveDir

a character string specifying a path for the output directory. If supplied, the output is saved as an .RData file named outName in the directory; otherwise the output is returned as a list.

Value

If saveDir is specified, the output list (named pwList) is saved as an .RData file named outName (or VEpwPP.RData if left unspecified); otherwise the output list is returned. The output object is a list (of equal length as dataList) of lists with the following components:
VEa numeric vector of VE(post-VEcutoffWeek--stage1) estimates for each missing vaccination probability in missVaccProb of simTrial
VEpwPPa numeric vector of powers to reject the null hypothesis H0: VE(post-VEcutoffWeek--stage1) $\le$ 0% for each missing vaccination probability in missVaccProb of simTrial

Details

All time variables use week as the unit of time. Month is defined as 52/12 weeks. A per-protocol cohort indicator is assumed to be included in the simTrial-generated data-sets, which is ensured by specifying the missVaccProb argument in simTrial. VE(post-VEcutoffWeek--stage1) is estimated as one minus the ratio of Nelson-Aalen-based cumulative incidence functions. VEpowerPP computes power to reject the null hypothesis H0: VE(post-VEcutoffWeek--stage1) $\le$ 0% using the one-sided Nelson-Aalen cumulative hazard-based Wald test at the alpha level of significance.

Examples

Run this code

simData <- simTrial(N=rep(1000, 2), aveVE=c(0, 0.4), VEmodel="half", 
                    vePeriods=c(1, 27, 79), enrollPeriod=78, 
                    enrollPartial=13, enrollPartialRelRate=0.5, dropoutRate=0.05, 
                    infecRate=0.04, fuTime=156, 
                    visitSchedule=c(0, (13/3)*(1:4), seq(13*6/3, 156, by=13*2/3)),
                    missVaccProb=c(0,0.05,0.1,0.15), VEcutoffWeek=26, nTrials=5, 
                    stage1=78, randomSeed=300)
                    
monitorData <- monitorTrial(dataFile=simData, stage1=78, stage2=156, 
                            harmMonitorRange=c(10,100), alphaPerTest=0.0106, 
                            minCnt=50, minPct=0.33, week1=26, minCnt2=2, week2=52, 
                            nonEffInterval=20, nullVE=0, altVE=0.4, highVE=0.6, 
                            alpha=0.025, estimand="combined", VEcutoffWeek=26)
                            
censData <- censTrial(dataFile=simData, monitorFile=monitorData, stage1=78, 
                      stage2=156)
                    
VEpwPP <- VEpowerPP(dataList=list(censData), VEcutoffWeek=26, stage1=78, 
                    alpha=0.025)

### alternatively, to save the .RData output file (no '<-' needed):
###
### simTrial(N=rep(1000, 2), aveVE=c(0, 0.4), VEmodel="half", 
###          vePeriods=c(1, 27, 79), enrollPeriod=78, enrollPartial=13, 
###          enrollPartialRelRate=0.5, dropoutRate=0.05, infecRate=0.04, fuTime=156, 
###          visitSchedule=c(0, (13/3)*(1:4), seq(13*6/3, 156, by=13*2/3)), 
###          missVaccProb=c(0,0.05,0.1,0.15), VEcutoffWeek=26, nTrials=30, 
###          stage1=78, saveDir="./", randomSeed=300)
###
### monitorTrial(dataFile=
###          "simTrial_nPlac=1000_nVacc=1000_aveVE=0.4_infRate=0.04.RData", 
###          stage1=78, stage2=156, harmMonitorRange=c(10,100), alphaPerTest=0.0106, 
###          minCnt=50, minPct=0.33, week1=26, minCnt2=2, week2=52, nonEffInterval=20, 
###          nullVE=0, altVE=0.4, highVE=0.6, alpha=0.025, estimand="combined", 
###          VEcutoffWeek=26, saveDir="./")
###
### censTrial(dataFile=
###  "simTrial_nPlac=1000_nVacc=1000_aveVE=0.4_infRate=0.04.RData",
###  monitorFile=
###  "monitorTrial_nPlac=1000_nVacc=1000_aveVE=0.4_infRate=0.04_combined.RData",
###  stage1=78, stage2=156, saveDir="./")
###
### VEpowerPP(dataList=
###  list("trialDataCens_nPlac=1000_nVacc=1000_aveVE=0.4_infRate=0.04_combined.RData"),
###  VEcutoffWeek=26, stage1=78, alpha=0.025, saveDir="./")