R: Adaptive design at an interim look

adaptDesign {lrstat}

R Documentation

Adaptive design at an interim look

Description

Obtains the conditional power for specified incremental information given the interim results, parameter value, and data-dependent changes in the error spending function, and the number and spacing of interim looks. Conversely, obtains the incremental information needed to attain a specified conditional power given the interim results, parameter value, and data-dependent changes in the error spending function, and the number and spacing of interim looks.

Usage

adaptDesign(
  betaNew = NA_real_,
  INew = NA_real_,
  L = NA_integer_,
  zL = NA_real_,
  theta = NA_real_,
  IMax = NA_real_,
  kMax = NA_integer_,
  informationRates = NA_real_,
  efficacyStopping = NA_integer_,
  futilityStopping = NA_integer_,
  criticalValues = NA_real_,
  alpha = 0.025,
  typeAlphaSpending = "sfOF",
  parameterAlphaSpending = NA_real_,
  userAlphaSpending = NA_real_,
  futilityBounds = NA_real_,
  typeBetaSpending = "none",
  parameterBetaSpending = NA_real_,
  spendingTime = NA_real_,
  MullerSchafer = 0L,
  kNew = NA_integer_,
  informationRatesNew = NA_real_,
  efficacyStoppingNew = NA_integer_,
  futilityStoppingNew = NA_integer_,
  typeAlphaSpendingNew = "sfOF",
  parameterAlphaSpendingNew = NA_real_,
  typeBetaSpendingNew = "none",
  parameterBetaSpendingNew = NA_real_,
  userBetaSpendingNew = NA_real_,
  spendingTimeNew = NA_real_,
  varianceRatio = 1
)

Arguments

`betaNew`	The type II error for the secondary trial.
`INew`	The maximum information of the secondary trial. Either `betaNew` or `INew` should be provided while the other one should be missing.
`L`	The interim adaptation look of the primary trial.
`zL`	The z-test statistic at the interim adaptation look of the primary trial.
`theta`	The parameter value.
`IMax`	The maximum information of the primary trial. Must be provided if `futilityBounds` is missing and `typeBetaSpending` is not equal to "none", or if conditional power calculation is desired.
`kMax`	The maximum number of stages of the primary trial.
`informationRates`	The information rates of the primary trial.
`efficacyStopping`	Indicators of whether efficacy stopping is allowed at each stage of the primary trial. Defaults to true if left unspecified.
`futilityStopping`	Indicators of whether futility stopping is allowed at each stage of the primary trial. Defaults to true if left unspecified.
`criticalValues`	The upper boundaries on the z-test statistic scale for efficacy stopping for the primary trial.
`alpha`	The significance level of the primary trial. Defaults to 0.025.
`typeAlphaSpending`	The type of alpha spending for the primary trial. One of the following: "OF" for O'Brien-Fleming boundaries, "P" for Pocock boundaries, "WT" for Wang & Tsiatis boundaries, "sfOF" for O'Brien-Fleming type spending function, "sfP" for Pocock type spending function, "sfKD" for Kim & DeMets spending function, "sfHSD" for Hwang, Shi & DeCani spending function, "user" for user defined spending, and "none" for no early efficacy stopping. Defaults to "sfOF".
`parameterAlphaSpending`	The parameter value of alpha spending for the primary trial. Corresponds to Delta for "WT", rho for "sfKD", and gamma for "sfHSD".
`userAlphaSpending`	The user defined alpha spending for the primary trial. Cumulative alpha spent up to each stage.
`futilityBounds`	The lower boundaries on the z-test statistic scale for futility stopping for the primary trial. Defaults to `rep(-6, kMax-1)` if left unspecified.
`typeBetaSpending`	The type of beta spending for the primary trial. One of the following: "sfOF" for O'Brien-Fleming type spending function, "sfP" for Pocock type spending function, "sfKD" for Kim & DeMets spending function, "sfHSD" for Hwang, Shi & DeCani spending function, and "none" for no early futility stopping. Defaults to "none".
`parameterBetaSpending`	The parameter value of beta spending for the primary trial. Corresponds to rho for "sfKD", and gamma for "sfHSD".
`spendingTime`	The error spending time of the primary trial. Defaults to missing, in which case, it is the same as `informationRates`.
`MullerSchafer`	Whether to use the Muller and Schafer (2001) method for trial adaptation.
`kNew`	The number of looks of the secondary trial.
`informationRatesNew`	The spacing of looks of the secondary trial.
`efficacyStoppingNew`	The indicators of whether efficacy stopping is allowed at each look of the secondary trial. Defaults to true if left unspecified.
`futilityStoppingNew`	The indicators of whether futility stopping is allowed at each look of the secondary trial. Defaults to true if left unspecified.
`typeAlphaSpendingNew`	The type of alpha spending for the secondary trial. One of the following: "OF" for O'Brien-Fleming boundaries, "P" for Pocock boundaries, "WT" for Wang & Tsiatis boundaries, "sfOF" for O'Brien-Fleming type spending function, "sfP" for Pocock type spending function, "sfKD" for Kim & DeMets spending function, "sfHSD" for Hwang, Shi & DeCani spending function, and "none" for no early efficacy stopping. Defaults to "sfOF".
`parameterAlphaSpendingNew`	The parameter value of alpha spending for the secondary trial. Corresponds to Delta for "WT", rho for "sfKD", and gamma for "sfHSD".
`typeBetaSpendingNew`	The type of beta spending for the secondary trial. One of the following: "sfOF" for O'Brien-Fleming type spending function, "sfP" for Pocock type spending function, "sfKD" for Kim & DeMets spending function, "sfHSD" for Hwang, Shi & DeCani spending function, "user" for user defined spending, and "none" for no early futility stopping. Defaults to "none".
`parameterBetaSpendingNew`	The parameter value of beta spending for the secondary trial. Corresponds to rho for "sfKD", and gamma for "sfHSD".
`userBetaSpendingNew`	The user defined cumulative beta spending. Cumulative beta spent up to each stage of the secondary trial.
`spendingTimeNew`	The error spending time of the secondary trial. Defaults to missing, in which case, it is the same as `informationRatesNew`.
`varianceRatio`	The ratio of the variance under H0 to the variance under H1.

Value

An adaptDesign object with two list components:

primaryTrial: A list of selected information for the primary trial, including L, zL, theta, kMax, informationRates, efficacyBounds, futilityBounds, and MullerSchafer.
secondaryTrial: A design object for the secondary trial.

Author(s)

Kaifeng Lu, kaifenglu@gmail.com

References

Lu Chi, H. M. James Hung, and Sue-Jane Wang. Modification of sample size in group sequential clinical trials. Biometrics 1999;55:853-857.

Hans-Helge Muller and Helmut Schafer. Adaptive group sequential designs for clinical trials: Combining the advantages of adaptive and of classical group sequential approaches. Biometrics 2001;57:886-891.

Examples


# original group sequential design with 90% power to detect delta = 6
delta = 6
sigma = 17
n = 282
(des1 = getDesign(IMax = n/(4*sigma^2), theta = delta, kMax = 3,
                  alpha = 0.05, typeAlphaSpending = "sfHSD",
                  parameterAlphaSpending = -4))

# interim look results
L = 1
n1 = n/3
delta1 = 4.5
sigma1 = 20
zL = delta1/sqrt(4/n1*sigma1^2)

t = des1$byStageResults$informationRates

# conditional power with sample size increase
(des2 = adaptDesign(
  betaNew = NA, INew = 420/(4*sigma1^2),
  L, zL, theta = delta1,
  IMax = n/(4*sigma1^2), kMax = 3, informationRates = t,
  alpha = 0.05, typeAlphaSpending = "sfHSD",
  parameterAlphaSpending = -4))

# Muller & Schafer (2001) method to design the secondary trial:
# 3-look gamma(-2) spending with 84% power at delta = 4.5 and sigma = 20
(des2 = adaptDesign(
  betaNew = 0.16, INew = NA,
  L, zL, theta = delta1,
  IMax = n/(4*sigma1^2), kMax = 3, informationRates = t,
  alpha = 0.05, typeAlphaSpending = "sfHSD",
  parameterAlphaSpending = -4,
  MullerSchafer = TRUE,
  kNew = 3, typeAlphaSpendingNew = "sfHSD",
  parameterAlphaSpendingNew = -2))

# incremental sample size for sigma = 20
(nNew = 4*sigma1^2*des2$secondaryTrial$overallResults$information)

[Package lrstat version 0.2.6 Index]