seqDesign: Simulation and Group Sequential Monitoring of Randomized Two-Stage Treatment Efficacy Trials with Time-to-Event Endpoints
Version 1.1

A modification of the preventive vaccine efficacy trial design of Gilbert, Grove et al. (2011, Statistical Communications in Infectious Diseases) is implemented, with application generally to individual-randomized clinical trials with multiple active treatment groups and a shared control group, and a study endpoint that is a time-to-event endpoint subject to right-censoring. The design accounts for the issues that the efficacy of the treatment/vaccine groups may take time to accrue while the multiple treatment administrations/vaccinations are given; there is interest in assessing the durability of treatment efficacy over time; and group sequential monitoring of each treatment group for potential harm, non-efficacy/efficacy futility, and high efficacy is warranted. The design divides the trial into two stages of time periods, where each treatment is first evaluated for efficacy in the first stage of follow-up, and, if and only if it shows significant treatment efficacy in stage one, it is evaluated for longer-term durability of efficacy in stage two. The package produces plots and tables describing operating characteristics of a specified design including an unconditional power for intention-to-treat and per-protocol/as-treated analyses; trial duration; probabilities of the different possible trial monitoring outcomes (e.g., stopping early for non-efficacy); unconditional power for comparing treatment efficacies; and distributions of numbers of endpoint events occurring after the treatments/vaccinations are given, useful as input parameters for the design of studies of the association of biomarkers with a clinical outcome (surrogate endpoint problem). The code can be used for a single active treatment versus control design and for a single-stage design.

AuthorMichal Juraska and Doug Grove, with contributions from Xuesong Yu and Peter B. Gilbert
Date of publication2015-04-27 18:57:11
MaintainerMichal Juraska <mjuraska@fhcrc.org>
LicenseGPL-2
Version1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("seqDesign")

Popular man pages

censTrial: Generation of Pre-Unblinded Follow-Up Data-Sets by Applying...
getBlockSize: Determine block size for use in blocked randomization
monitorTrial: Group Sequential Monitoring of Simulated Efficacy Trials for...
rankTrial: Ranking and Selection, and Head-to-Head Comparison of...
simTrial: Simulation of Multi-Arm Randomized Phase IIb/III Efficacy...
VEpowerPP: Unconditional Power to Detect Positive Treatment Efficacy in...
See all...

All man pages Function index File listing

Man pages

censTrial: Generation of Pre-Unblinded Follow-Up Data-Sets by Applying...
getBlockSize: Determine block size for use in blocked randomization
monitorTrial: Group Sequential Monitoring of Simulated Efficacy Trials for...
rankTrial: Ranking and Selection, and Head-to-Head Comparison of...
simTrial: Simulation of Multi-Arm Randomized Phase IIb/III Efficacy...
VEpowerPP: Unconditional Power to Detect Positive Treatment Efficacy in...

Functions

Constant Source code
GammaDist Source code
VEpowerPP Man page Source code
applyStopRules Source code
buildBounds Source code
censTrial Man page Source code
constructPartialPosteriorObject Source code
constructPosteriorObject Source code
do_harm_monitoring Source code
do_harm_monitoring2 Source code
dropoutEstimationFunction Source code
enrollmentEstimationFunction Source code
extractSummaryMeasures Source code
fileNameFunc Source code
finalLogRankTest Source code
gammaInput Source code
gcd Source code
generateDropout Source code
generateEnrollment Source code
generateInfection Source code
getAlphaPerTest Source code
getBlockSize Man page Source code
getDropout Source code
getEnrollment Source code
getHarmBound Source code
getInfecCntFirstNonEff Source code
getInfection Source code
getTreatmentAssignment Source code
getVisitWeek Source code
get_firstTest_infecCnt Source code
headHeadTest Source code
headTestVE Source code
infectionUpdateFunction Source code
is.TRUE Source code
monitorTrial Man page Source code
pNS Source code
rankTrial Man page Source code
sampleRates Source code
semiConstSpending Source code
simFullEDIdata Source code
simTrial Man page Source code
simulateObservedEDIdata Source code
sumTrialOneTrtArm Source code
summInterimData Source code
testVE Source code
visitScheduleTruncated Source code

Files

inst
inst/extdata
inst/extdata/seqDesignReportSample.Rnw
inst/extdata/seqDesignReportSample.pdf
inst/doc
inst/doc/seqDesignInstructions.pdf
inst/doc/seqDesignInstructions.Rnw
inst/doc/seqDesignInstructions.R
NAMESPACE
R
R/seqDesign.R
vignettes
vignettes/seqDesignInstructions.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/simTrial.Rd
man/getBlockSize.Rd
man/VEpowerPP.Rd
man/monitorTrial.Rd
man/rankTrial.Rd
man/censTrial.Rd
seqDesign documentation built on May 19, 2017, 8:24 p.m.

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