R/lrstat-package.R

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

#' @name lrstat-package
#' @aliases lrstat-package
#' @keywords internal
#' "_PACKAGE"
#'
#' @title Power and Sample Size Calculation for Non-Proportional Hazards
#' and Beyond
#'
#' @description Performs power and sample size calculation for
#' non-proportional hazards model using the Fleming-Harrington family
#' of weighted log-rank tests.
#'
#' @details For proportional hazards, the power is determined by the
#' total number of events and the constant hazard ratio along with
#' information rates and spending functions. For
#' non-proportional hazards, the hazard ratio varies over time and
#' the calendar time plays a key role in determining the mean and
#' variance of the log-rank test score statistic. It requires an
#' iterative algorithm to find the calendar time at which the
#' targeted number of events will be reached for each interim
#' analysis. The lrstat package uses the analytic method
#' in Lu (2021) to find the mean and variance of the weighted
#' log-rank test score statistic at each interim analysis. In
#' addition, the package approximates the variance and covariance
#' matrix of the sequentially calculated log-rank test statistics
#' under the alternative hypothesis with that under the null hypothesis
#' to take advantage of the independent increments structure in
#' Tsiatis (1982) applicable for the Fleming-Harrington family
#' of weighted log-rank tests.
#'
#' The most useful functions in the package are \code{lrstat},
#' \code{lrpower}, \code{lrsamplesize}, and \code{lrsim}, which calculate
#' the mean and variance of log-rank test score statistic at a sequence
#' of given calendar times, the power of the log-rank test, the sample
#' size in terms of accrual duration and follow-up duration, and the
#' log-rank test simulation, respectively. The \code{accrual} function
#' calculates the number of patients accrued at given calendar times. The
#' \code{caltime} function finds the calendar times to reach the targeted
#' number of events. The \code{exitprob} function calculates the stagewise
#' exit probabilities for specified boundaries with a varying mean
#' parameter over time based on an adaptation of the recursive
#' integration algorithm described in Chapter 19 of Jennison and
#' Turnbull (2000).
#'
#' The development of the lrstat package is heavily influenced by
#' the rpact package. We find their function arguments to be
#' self-explanatory. We have used the same names whenever appropriate
#' so that users familiar with the rpact package can learn the
#' lrstat package quickly. However, there are notable differences:
#' \itemize{
#'   \item lrstat uses direct approximation, while rpact uses the Schoenfeld
#'     method for log-rank test power and sample size calculation.
#'   \item lrstat uses \code{accrualDuration} to explicitly set the end of
#'     accrual period, while rpact incorporates the end of accrual period
#'     in \code{accrualTime}.
#'   \item lrstat considers the trial a failure at the last stage if
#'     the log-rank test cannot reject the null hypothesis up to this
#'     stage and cannot stop for futility at an earlier stage.
#'   \item the \code{lrsim} function uses the variance of the log-rank
#'     test score statistic as the information.
#' }
#'
#' In addition to the log-rank test power and sample size calculations,
#' the lrstat package can also be used for the following tasks:
#' \itemize{
#'   \item design generic group sequential trials.
#'   \item design generic group sequential equivalence trials.
#'   \item design adaptive group sequential trials for changes in sample
#'     size, error spending function, number and spacing or future looks.
#'   \item calculate the terminating and repeated confidence intervals for
#'     standard and adaptive group sequential trials.
#'   \item calculate the conditional power for non-proportional hazards
#'     with or without design changes.
#'   \item perform multiplicity adjustment based on graphical approaches
#'     using weighted Bonferroni tests, Bonferroni mixture of weighted
#'     Simes test, and Bonferroni mixture of Dunnett test as well as
#'     group sequential trials with multiple hypotheses.
#'   \item perform multiplicity adjustment using stepwise gatekeeping
#'     procedures for two sequences of hypotheses and the standard or
#'     modified mixture gatekeeping procedures in the general case.
#'   \item design parallel-group trials with the primary endpoint
#'     analyzed using mixed-model for repeated measures (MMRM).
#'   \item design crossover trials to estimate direct treatment
#'     effects while accounting for carryover effects.
#'   \item design one-way repeated measures ANOVA trials.
#'   \item design two-way ANOVA trials.
#'   \item design Simon's 2-stage trials.
#'   \item design modified toxicity probability-2 (mTPI-2) trials.
#'   \item design Bayesian optimal interval (BOIN) trials.
#'   \item design group sequential trials for negative binomial
#'     endpoints with censoring.
#'   \item design trials using Wilcoxon, Fisher's exact, and McNemar's test.
#'   \item calculate Clopper-Pearson confidence interval for single
#'     proportions.
#'   \item calculate Brookmeyer-Crowley confidence interval for quantiles
#'     of censored survival data.
#'   \item calculate Miettinen & Nurminen confidence interval for stratified
#'     risk difference, risk ratio, odds ratio, rate difference, and
#'     rate ratio.
#'   \item perform power and sample size calculation for logistic regression.
#'   \item perform power and sample size calculation for Cohen's kappa.
#'   \item calculate Hedges' g effect size.
#'   \item generate random numbers from truncated piecewise exponential
#'     distribution.
#'   \item perform power and sample size calculations for negative binomial
#'     data.
#' }
#'
#' @author Kaifeng Lu, \email{kaifenglu@@gmail.com}
#'
#' @references
#' Anastasios A. Tsiatis. Repeated significance testing for a general class
#' of statistics used in censored survival analysis. J Am Stat Assoc.
#' 1982;77:855-861.
#'
#' Christopher Jennison, Bruce W. Turnbull. Group Sequential Methods with
#' Applications to Clinical Trials. Chapman & Hall/CRC: Boca Raton, 2000,
#' ISBN:0849303168
#'
#' Kaifeng Lu. Sample size calculation for logrank test and prediction of
#' number of events over time. Pharm Stat. 2021;20:229-244.
#'
#'
#' @seealso rpact, gsDesign
#'
#' @examples
#' lrpower(kMax = 2, informationRates = c(0.8, 1),
#'         criticalValues = c(2.250, 2.025), accrualIntensity = 20,
#'         piecewiseSurvivalTime = c(0, 6),
#'         lambda1 = c(0.0533, 0.0309), lambda2 = c(0.0533, 0.0533),
#'         gamma1 = 0.00427, gamma2 = 0.00427,
#'         accrualDuration = 22, followupTime = 18)
#'
#' @useDynLib lrstat, .registration = TRUE
#' @importFrom Rcpp evalCpp
#' @importFrom mvtnorm pmvnorm
#' @importFrom stats dgamma dlogis dnorm integrate optimize pbeta pchisq pf
#' plogis pnorm pt qbeta qchisq qf qlogis qnorm qt uniroot var
#' @importFrom lpSolve lp
#' @importFrom shiny shinyAppDir
#'
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