View source: R/postMonitoring.R
VEpowerPP | R Documentation |
VEpowerPP
computes unconditional power to detect positive treatment (vaccine) efficacy in per-protocol cohorts identified in simTrial
-generated data-sets.
VEpowerPP( dataList, lowerVEuncPower, alphaUncPower, VEcutoffWeek, stage1, outName = NULL, saveDir = NULL, verbose = TRUE )
dataList |
if |
lowerVEuncPower |
a numeric value specifying a one-sided null hypothesis H0: VE( |
alphaUncPower |
one minus the nominal confidence level of the two-sided confidence interval used to test the one-sided null hypothesis H0: VE( |
VEcutoffWeek |
a cut-off time (in weeks). Only subjects with the follow-up time exceeding |
stage1 |
the final week of stage 1 in a two-stage trial |
outName |
a character string specifying the output |
saveDir |
a character string specifying a path for the output directory. If supplied, the output is saved as an |
verbose |
a logical value indicating whether information on the output directory and file name should be printed out (default is |
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(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(VEcutoffWeek
–stage1
) ≤ lowerVEuncPower
x 100%. H0 is rejected if the lower bound of the two-sided (1-alphaUncPower
) x 100% confidence interval for VE(VEcutoffWeek
–stage1
) lies above lowerVEuncPower
.
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:
VE
: a numeric vector of VE(VEcutoffWeek
–stage1
) estimates for each missing vaccination probability in missVaccProb
of simTrial
VEpwPP
: a numeric vector of powers to reject the null hypothesis H0: VE(VEcutoffWeek
–stage1
) ≤ lowerVEuncPower
x 100% for each missing vaccination probability in missVaccProb
of simTrial
simTrial
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=NULL, nonEffStartMethod="FKG", nonEffInterval=20, lowerVEnoneff=0, upperVEnoneff=0.4, highVE=0.7, stage1VE=0, lowerVEuncPower=0, alphaNoneff=0.05, alphaHigh=0.05, alphaStage1=0.05, alphaUncPower=0.05, estimand="cuminc", lagTime=26) censData <- censTrial(dataFile=simData, monitorFile=monitorData, stage1=78, stage2=156) VEpwPP <- VEpowerPP(dataList=list(censData), lowerVEuncPower=0, alphaUncPower=0.05, VEcutoffWeek=26, stage1=78) ### 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=5, ### 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=NULL, ### nonEffStartMethod="FKG", nonEffInterval=20, ### lowerVEnoneff=0, upperVEnoneff=0.4, highVE=0.7, stage1VE=0, ### lowerVEuncPower=0, alphaNoneff=0.05, alphaHigh=0.05, alphaStage1=0.05, ### alphaUncPower=0.05, estimand="cuminc", lagTime=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_cuminc.RData", ### stage1=78, stage2=156, saveDir="./") ### ### VEpowerPP(dataList= ### list("trialDataCens_nPlac=1000_nVacc=1000_aveVE=0.4_infRate=0.04_cuminc.RData"), ### lowerVEuncPower=0, alphaUncPower=0.05, VEcutoffWeek=26, stage1=78, saveDir="./")
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