nbsamplesize1s: Sample Size for One-Sample Negative Binomial Rate

Description

Obtains the needed accrual duration given power and follow-up time, the needed follow-up time given power and accrual duration, or the needed absolute accrual rates given power, accrual duration, follow-up duration, and relative accrual rates in a one-group negative binomial design.

Usage

nbsamplesize1s(
  beta = 0.2,
  kMax = 1L,
  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_,
  userBetaSpending = NA_real_,
  lambdaH0 = NA_real_,
  accrualTime = 0L,
  accrualIntensity = NA_real_,
  piecewiseSurvivalTime = 0L,
  stratumFraction = 1L,
  kappa = NA_real_,
  lambda = NA_real_,
  gamma = 0L,
  accrualDuration = NA_real_,
  followupTime = NA_real_,
  fixedFollowup = 0L,
  interval = as.numeric(c(0.001, 240)),
  spendingTime = NA_real_,
  rounding = 1L
)

Value

A list of two components:

resultsUnderH1: An S3 class nbpower1s object under the alternative hypothesis.
resultsUnderH0: An S3 class nbpower1s object under the null hypothesis.

Arguments

beta: Type II error. Defaults to 0.2.
kMax: The maximum number of stages.
informationRates: The information rates. Defaults to (1:kMax) / kMax if left unspecified.
efficacyStopping: Indicators of whether efficacy stopping is allowed at each stage. Defaults to true if left unspecified.
futilityStopping: Indicators of whether futility stopping is allowed at each stage. Defaults to true if left unspecified.
criticalValues: Upper boundaries on the z-test statistic scale for stopping for efficacy.
alpha: The significance level. Defaults to 0.025.
typeAlphaSpending: The type of alpha spending. 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 for the alpha spending. Corresponds to Delta for "WT", rho for "sfKD", and gamma for "sfHSD".
userAlphaSpending: The user defined alpha spending. Cumulative alpha spent up to each stage.
futilityBounds: Lower boundaries on the z-test statistic scale for stopping for futility at stages 1, ..., kMax-1. Defaults to rep(-6, kMax-1) if left unspecified. The futility bounds are non-binding for the calculation of critical values.
typeBetaSpending: The type of beta spending. 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".
parameterBetaSpending: The parameter value for the beta spending. Corresponds to rho for "sfKD", and gamma for "sfHSD".
userBetaSpending: The user defined beta spending. Cumulative beta spent up to each stage.
lambdaH0: The rate parameter of the negative binomial distribution under the null hypothesis.
accrualTime: A vector that specifies the starting time of piecewise Poisson enrollment time intervals. Must start with 0, e.g., c(0, 3) breaks the time axis into 2 accrual intervals: [0, 3) and [3, Inf).
accrualIntensity: A vector of accrual intensities. One for each accrual time interval.
piecewiseSurvivalTime: A vector that specifies the starting time of piecewise exponential survival time intervals. Must start with 0, e.g., c(0, 6) breaks the time axis into 2 event intervals: [0, 6) and [6, Inf). Defaults to 0 for exponential distribution.
stratumFraction: A vector of stratum fractions that sum to 1. Defaults to 1 for no stratification.
kappa: The dispersion parameter (reciprocal of the shape parameter of the gamma mixing distribution) of the negative binomial distribution by stratum.
lambda: The rate parameter of the negative binomial distribution under the alternative hypothesis by stratum.
gamma: The hazard rate for exponential dropout or a vector of hazard rates for piecewise exponential dropout by stratum. Defaults to 0 for no dropout.
accrualDuration: Duration of the enrollment period.
followupTime: Follow-up time for the last enrolled subject.
fixedFollowup: Whether a fixed follow-up design is used. Defaults to 0 for variable follow-up.
interval: The interval to search for the solution of accrualDuration, followupDuration, or the proportionality constant of accrualIntensity. Defaults to c(0.001, 240).
spendingTime: A vector of length kMax for the error spending time at each analysis. Defaults to missing, in which case, it is the same as informationRates.
rounding: Whether to round up sample size. Defaults to 1 for sample size rounding.

Author

Kaifeng Lu, kaifenglu@gmail.com

Examples

Run this code

# Example 1: Obtains follow-up duration given power, accrual intensity,
# and accrual duration for variable follow-up

nbsamplesize1s(beta = 0.2, kMax = 2,
               informationRates = c(0.5, 1),
               alpha = 0.025, typeAlphaSpending = "sfOF",
               lambdaH0 = 0.125, accrualIntensity = 500,
               stratumFraction = c(0.2, 0.8),
               kappa = c(3, 5), lambda = c(0.0875, 0.085),
               gamma = 0, accrualDuration = 1.25,
               followupTime = NA, fixedFollowup = FALSE)

# Example 2: Obtains accrual intensity given power, accrual duration, and
# follow-up duration for variable follow-up

nbsamplesize1s(beta = 0.2, kMax = 2,
               informationRates = c(0.5, 1),
               alpha = 0.025, typeAlphaSpending = "sfOF",
               lambdaH0 = 0.125, accrualIntensity = 100,
               kappa = 5, lambda = 0.0875,
               gamma = 0, accrualDuration = 1.25,
               followupTime = 2.25, fixedFollowup = FALSE)


# Example 3: Obtains accrual duration given power, accrual intensity, and
# follow-up duration for fixed follow-up

nbsamplesize1s(beta = 0.2, kMax = 2,
               informationRates = c(0.5, 1),
               alpha = 0.025, typeAlphaSpending = "sfOF",
               lambdaH0 = 8.4, accrualIntensity = 40,
               kappa = 3, lambda = 4.2,
               gamma = 0, accrualDuration = NA,
               followupTime = 0.5, fixedFollowup = TRUE)