R: Unconditional Power to Detect Positive Treatment Efficacy in...

VEpowerPP {seqDesign}

R Documentation

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, lowerVEuncPower, alphaUncPower, VEcutoffWeek, stage1,
  outName = NULL, saveDir = NULL, verbose = TRUE)

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`
`lowerVEuncPower`	a numeric value specifying a one-sided null hypothesis H0: VE(`VEcutoffWeek`–`stage1`) `\le` `lowerVEuncPower` x 100%. Unconditional power (i.e., accounting for sequential monitoring) to reject H0 in the per-protocol cohort is calculated, where the rejection region is defined by the lower bound of the two-sided (1-`alphaUncPower`) x 100% confidence interval for VE(`VEcutoffWeek`–`stage1`) being above `lowerVEuncPower` (typically a number in the 0–0.5 range).
`alphaUncPower`	one minus the nominal confidence level of the two-sided confidence interval used to test the one-sided null hypothesis H0: VE(`VEcutoffWeek`–`stage1`) `\le` `lowerVEuncPower` x 100% against the alternative hypothesis H1: VE(`VEcutoffWeek`–`stage1`) `>` `lowerVEuncPower` x 100%.
`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
`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.
`verbose`	a logical value indicating whether information on the output directory and file name should be printed out (default is `TRUE`)

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(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) \le 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.

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:

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) \le lowerVEuncPower x 100% for each missing vaccination probability in missVaccProb of simTrial

Examples

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="./")

[Package seqDesign version 1.2 Index]