seqDesign (version 1.0.0)

rankTrial: Ranking and Selection, and Head-to-Head Comparison of Individual and Pooled Treatment Arms

Description

rankTrial assesses the probability of correctly selecting the winning most efficacious (individual and/or pooled) treatment arm, and assesses power to detect relative treatment efficacy in head-to-head comparisons of (individual and/or pooled) treatment arms.

Usage

rankTrial(censFile, idxHighestVE, headHead = NULL, poolHead = NULL, 
          stage1, stage2, alpha, saveDir = NULL)

Arguments

censFile

if saveDir = NULL, a list returned by censTrial; otherwise a name (character string) of an .RData file created by censTrial

idxHighestVE

an integer value identifying the treatment (vaccine) arm with the true highest VE(0--stage2)

headHead

a matrix (ncol = 2) of treatment arm indices for head-to-head comparisons, where the treatment with higher efficacy is listed first in each row

poolHead

a matrix (ncol equals 3 or 4) of treatment arm indices for pooled-arm comparisons, where the pooled treatment with higher efficacy pooled over the first two columns is compared with the (pooled) treatment defined by columns 3 and onward. Rank

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

alpha

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

saveDir

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

Value

• If saveDir is specified, the output list (named out) is saved as an .RData file in saveDir (the path to saveDir is printed); otherwise it is returned. The output object is a list with the following components:
• rankSelectPw
  the probability of correct selection of the winning most efficacious individual treatment
• headHeadPw
  if headHead is specified, a matrix of powers to detect relative VE(0--stage1) (column 1) and relative VE(0--stage2) (column 2) in head-to-head comparisons of individual treatment arms
• poolRankSelectPw
  if poolHead is specified, a numeric vector of the probabilities of correct selection of the winning most efficacious pooled treatment for each set of pooled treatments
• poolHeadPw
  if poolHead is specified, a matrix of powers to detect relative VE(0--stage1) (column 1) and relative VE(0--stage2) (column 2) in head-to-head comparisons of pooled treatment arms

Details

All time variables use week as the unit of time. Month is defined as 52/12 weeks. The probability of correct treatment selection is defined as the probability that the treatment arm with the highest estimated VE(0--stage2) is the one with the true highest VE(0--stage2) and for this treatment arm the null hypothesis H0: VE(0--stage1) $\le$ 0% is rejected. If poolHead is specified, the probability of correct pooled treatment selection is assessed for each set of two pooled treatment arms. VE(0--t) is estimated as one minus the ratio of Nelson-Aalen-based cumulative incidence functions. The null hypothesis H0 is evaluated using the one-sided Nelson-Aalen cumulative hazard-based Wald test at the alpha level of significance. For head-to-head individual and pooled treatment comparisons, powers to reject the null hypotheses that relative VE(0--stage1) $\le$ 0% and relative VE(0--stage2) $\le$ 0% are assessed using the aforementioned one-sided Wald test.

See Also

simTrial, monitorTrial, and censTrial

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=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)
                      
rankData <- rankTrial(censFile=censData, idxHighestVE=2, 
                      headHead=matrix(2:1, nrow=1, ncol=2), stage1=78, stage2=156, 
                      alpha=0.025)

### 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=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=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_combined.RData",
###  stage1=78, stage2=156, saveDir="./")
###
### rankTrial(censFile=
###  "trialDataCens_nPlac=1400_nVacc=1000_1000_aveVE=0.2_0.4_infRate=0.04_combined.RData",
###  idxHighestVE=2, headHead=matrix(2:1, nrow=1, ncol=2), stage1=78, stage2=156, 
###  alpha=0.025, saveDir="./")