censTrial: Generation of Pre-Unblinded Follow-Up Data-Sets by Applying...

In mjuraska/seqDesign: Simulation and Group-Sequential Monitoring of Randomized Treatment Efficacy Trials with Time-to-Event Endpoints

Generation of Pre-Unblinded Follow-Up Data-Sets by Applying the Monitoring Outcomes

Description

censTrial ‘correctly censors’ treatment arms in data-sets generated by simTrial by including pre-unblinded follow-up data only according to the monitoring conclusions as reported by monitorTrial.

Usage

censTrial(
  dataFile,
  monitorFile,
  stage1,
  stage2,
  saveFile = NULL,
  saveDir = NULL,
  verbose = TRUE
)

Arguments

dataFile	if saveDir = NULL, a list returned by simTrial; otherwise a name (character string) of an .RData file created by simTrial
monitorFile	if saveDir = NULL, a list returned by monitorTrial; otherwise a name (character string) of an .RData file created by monitorTrial
stage1	the final week of stage 1 in a two-stage trial
stage2	the final week of stage 2 in a two-stage trial, i.e., the maximum follow-up time
saveFile	a character string specifying the name of the output .RData file. If NULL (default), a default file name will be used.
saveDir	a character string specifying a path for both dataFile and monitorFile. If supplied, the output is also saved as an .RData file in this 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.

The following censoring rules are applied to each data-set generated by simTrial:

• If no vaccine arm registers efficacy or high efficacy in Stage 1, the placebo arm is censored on the date when the last vaccine arm hits the harm or non-efficacy boundary.

• If a vaccine arm hits the harm boundary, censor the arm immediately.

• If a vaccine arm hits the non-efficacy boundary, censor the arm on the earliest date of the two events: (1) the last vaccine arm hits the harm or non-efficacy boundary (if applicable); and (2) all subjects in the vaccine arm have completed the final stage1 visit.

Value

If saveDir is specified, the output list (named trialListCensor) is saved as an .RData file in saveDir (the path to saveDir is printed); otherwise it is returned. The output object is a list of length equal to the number of simulated trials, each of which is a data.frame with at least the variables trt, entry, exit, and event storing the treatment assignments, enrollment times, correctly censored study exit times, and event indicators, respectively. If available, indicators belonging to the per-protocol cohort (named pp1, pp2, etc.) are copied from the uncensored data-sets.

See Also

simTrial, monitorTrial, and rankTrial

Examples

simData <- simTrial(N=c(1000, rep(700, 2)), aveVE=seq(0, 0.4, by=0.2), 
                    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)

### alternatively, to save the .RData output file (no '<-' needed):
###
### simTrial(N=c(1400, rep(1000, 2)), aveVE=seq(0, 0.4, by=0.2), 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=1400_nVacc=1000_1000_aveVE=0.2_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=1400_nVacc=1000_1000_aveVE=0.2_0.4_infRate=0.04.RData",
###          monitorFile=
###          "monitorTrial_nPlac=1400_nVacc=1000_1000_aveVE=0.2_0.4_infRate=0.04_cuminc.RData",
###          stage1=78, stage2=156, saveDir="./")
 

mjuraska/seqDesign documentation built on Dec. 14, 2022, 4:26 p.m.