R/parameter_descriptions.R

In lrstat: Power and Sample Size Calculation for Non-Proportional Hazards and Beyond

#' Parameter Description: accrualTime
#' @param accrualTime A vector that specifies the starting time of
#'   piecewise Poisson enrollment time intervals. Must start with 0, e.g.,
#'   \code{c(0, 3)} breaks the time axis into 2 accrual intervals:
#'   [0, 3) and [3, Inf).
#' @name param_accrualTime
#' @keywords internal
NULL

#' Parameter Description: accrualIntensity
#' @param accrualIntensity A vector of accrual intensities. One for
#'   each accrual time interval.
#' @name param_accrualIntensity
#' @keywords internal
NULL

#' Parameter Description: accrualDuration
#' @param accrualDuration Duration of the enrollment period.
#' @name param_accrualDuration
#' @keywords internal
NULL

#' Parameter Description: piecewiseSurvivalTime
#' @param piecewiseSurvivalTime A vector that specifies the starting time of
#'   piecewise exponential survival time intervals. Must start with 0, e.g.,
#'   \code{c(0, 6)} breaks the time axis into 2 event intervals:
#'   [0, 6) and [6, Inf).
#'   Defaults to 0 for exponential distribution.
#' @name param_piecewiseSurvivalTime
#' @keywords internal
NULL

#' Parameter Description: allocationRatioPlanned
#' @param allocationRatioPlanned Allocation ratio for the active treatment
#'   versus control. Defaults to 1 for equal randomization.
#' @name param_allocationRatioPlanned
#' @keywords internal
NULL

#' Parameter Description: hazardRatioH0
#' @param hazardRatioH0 Hazard ratio under the null hypothesis for the active
#'   treatment versus control. Defaults to 1 for superiority test.
#' @name param_hazardRatioH0
#' @keywords internal
NULL


#' Parameter Description: stratumFraction
#' @param stratumFraction A vector of stratum fractions that sum to 1.
#'   Defaults to 1 for no stratification.
#' @name param_stratumFraction
#' @keywords internal
NULL

#' Parameter Description: lambda
#' @param lambda A vector of hazard rates for the event. One for
#'   each analysis time interval.
#' @name param_lambda
#' @keywords internal
NULL

#' Parameter Description: lambda1
#' @param lambda1 A vector of hazard rates for the event for the
#'   active treatment group. One for each analysis time interval.
#' @name param_lambda1
#' @keywords internal
NULL

#' Parameter Description: lambda2
#' @param lambda2 A vector of hazard rates for the event for the
#'   control group. One for each analysis time interval.
#' @name param_lambda2
#' @keywords internal
NULL

#' Parameter Description: lambda1_stratified
#' @param lambda1 A vector of hazard rates for the event in each analysis
#'   time interval by stratum for the active treatment group.
#' @name param_lambda1_stratified
#' @keywords internal
NULL

#' Parameter Description: lambda2_stratified
#' @param lambda2 A vector of hazard rates for the event in each analysis
#'   time interval by stratum for the control group.
#' @name param_lambda2_stratified
#' @keywords internal
NULL

#' Parameter Description: gamma
#' @param gamma The hazard rate for exponential dropout, or a vector of
#'   hazard rates for piecewise exponential dropout.
#' @name param_gamma
#' @keywords internal
NULL

#' Parameter Description: gamma1
#' @param gamma1 The hazard rate for exponential dropout, or a vector of
#'   hazard rates for piecewise exponential dropout for the active
#'   treatment group.
#' @name param_gamma1
#' @keywords internal
NULL

#' Parameter Description: gamma2
#' @param gamma2 The hazard rate for exponential dropout, or a vector of
#'   hazard rates for piecewise exponential dropout for the control group.
#' @name param_gamma2
#' @keywords internal
NULL

#' Parameter Description: gamma1_stratified
#' @param gamma1 The hazard rate for exponential dropout, a vector of hazard
#'   rates for piecewise exponential dropout applicable for all strata, or a
#'   vector of hazard rates for dropout in each analysis time interval
#'   by stratum for the active treatment group.
#'
#' @name param_gamma1_stratified
#' @keywords internal
NULL

#' Parameter Description: gamma2_stratified
#' @param gamma2 The hazard rate for exponential dropout, a vector of hazard
#'   rates for piecewise exponential dropout applicable for all strata, or a
#'   vector of hazard rates for dropout in each analysis time interval
#'   by stratum for the control group.
#'
#' @name param_gamma2_stratified
#' @keywords internal
NULL


#' Parameter Description: followupTime
#' @param followupTime Follow-up time for the last enrolled subject.
#' @name param_followupTime
#' @keywords internal
NULL

#' Parameter Description: fixedFollowup
#' @param fixedFollowup Whether a fixed follow-up design is used.
#'   Defaults to 0 for variable follow-up.
#' @name param_fixedFollowup
#' @keywords internal
NULL

#' Parameter Description: minFollowupTime
#' @param minFollowupTime Follow-up time for the last enrolled subject.
#' @name param_minFollowupTime
#' @keywords internal
NULL

#' Parameter Description: maxFollowupTime
#' @param maxFollowupTime Follow-up time for the first enrolled subject.
#'   For fixed followup, \code{maxFollowupTime = minFollowupTime}.
#'   For variable followup,
#'   \code{maxFollowupTime = accrualDuration + minFollowupTime}.
#' @name param_maxFollowupTime
#' @keywords internal
NULL

#' Parameter Description: rho1
#' @param rho1 The first parameter of the Fleming-Harrington family of
#'   weighted log-rank test. Defaults to 0 for conventional log-rank test.
#' @name param_rho1
#' @keywords internal
NULL

#' Parameter Description: rho2
#' @param rho2 The second parameter of the Fleming-Harrington family of
#'   weighted log-rank test. Defaults to 0 for conventional log-rank test.
#' @name param_rho2
#' @keywords internal
NULL

#' Parameter Description: numSubintervals
#' @param numSubintervals Number of sub-intervals to approximate the mean
#'   and variance of the weighted log-rank test score statistic.
#'   Defaults to 300. Specify a larger number for better approximation.
#' @name param_numSubintervals
#' @keywords internal
NULL

#' Parameter Description: kMax
#' @param kMax The maximum number of stages.
#' @name param_kMax
#' @keywords internal
NULL

#' Parameter Description: informationRates
#' @param informationRates The information rates in terms of number of
#'   events. Fixed prior to the trial. Defaults to \code{(1:kMax) / kMax}
#'   if left unspecified.
#' @name param_informationRates
#' @keywords internal
NULL

#' Parameter Description: efficacyStopping
#' @param efficacyStopping Indicators of whether efficacy stopping is allowed
#'   at each stage. Defaults to true if left unspecified.
#' @name param_efficacyStopping
#' @keywords internal
NULL

#' Parameter Description: futilityStopping
#' @param futilityStopping Indicators of whether futility stopping is allowed
#'   at each stage. Defaults to true if left unspecified.
#' @name param_futilityStopping
#' @keywords internal
NULL


#' Parameter Description: criticalValues
#' @param criticalValues Upper boundaries on the z-test statistic scale
#'   for stopping for efficacy.
#' @name param_criticalValues
#' @keywords internal
NULL

#' Parameter Description: alpha
#' @param alpha The significance level. Defaults to 0.025.
#' @name param_alpha
#' @keywords internal
NULL


#' Parameter Description: typeAlphaSpending
#' @param 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".
#' @name param_typeAlphaSpending
#' @keywords internal
NULL

#' Parameter Description: parameterAlphaSpending
#' @param parameterAlphaSpending The parameter value for the alpha spending.
#'   Corresponds to Delta for "WT", rho for "sfKD", and gamma for "sfHSD".
#' @name param_parameterAlphaSpending
#' @keywords internal
NULL

#' Parameter Description: userAlphaSpending
#' @param userAlphaSpending The user defined alpha spending. Cumulative alpha
#'   spent up to each stage.
#' @name param_userAlphaSpending
#' @keywords internal
NULL


#' Parameter Description: futilityBounds
#' @param futilityBounds Lower boundaries on the z-test statistic scale
#'   for stopping for futility at stages 1, ..., \code{kMax-1}. Defaults to
#'   \code{rep(-6, kMax-1)} if left unspecified. The futility bounds are
#'   non-binding for the calculation of critical values.
#' @name param_futilityBounds
#' @keywords internal
NULL

#' Parameter Description: typeBetaSpending
#' @param 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".
#' @name param_typeBetaSpending
#' @keywords internal
NULL

#' Parameter Description: parameterBetaSpending
#' @param parameterBetaSpending The parameter value for the beta spending.
#'   Corresponds to rho for "sfKD", and gamma for "sfHSD".
#' @name param_parameterBetaSpending
#' @keywords internal
NULL

#' Parameter Description: userBetaSpending
#' @param userBetaSpending The user defined beta spending. Cumulative beta
#'   spent up to each stage.
#' @name param_userBetaSpending
#' @keywords internal
NULL

#' Parameter Description: estimateHazardRatio
#' @param estimateHazardRatio Whether to estimate the hazard ratio from
#'   weighted Cox regression model and report the stopping boundaries on
#'   the hazard ratio scale.
#' @name param_estimateHazardRatio
#' @keywords internal
NULL

#' Parameter Description: typeOfComputation
#' @param typeOfComputation The type of computation,
#'   either "direct" for the direct approximation method,
#'   or "schoenfeld" for the Schoenfeld method.
#'   Defaults to "direct". Can use "Schoenfeld"
#'   under proportional hazards and conventional log-rank test.
#' @name param_typeOfComputation
#' @keywords internal
NULL