tests/testthat/helper-double-programming-gs_design_combo.R

In gsDesign2: Group Sequential Design with Non-Constant Effect

# Helper functions used by test-independent-gs_design_combo.R

test_gs_design_combo <- function() {
  load("fixtures/sim_gsd_pMaxCombo_exp1_H0_test.Rdata")
  load("fixtures/sim_gsd_pMaxCombo_exp1_H1_test.Rdata")

  ratio <- 1
  algorithm <- mvtnorm::GenzBretz(maxpts = 1e5, abseps = 1e-5)
  alpha <- 0.025
  beta <- 0.2
  enroll_rate <- define_enroll_rate(duration = 12, rate = 500 / 12)
  fail_rate <- define_fail_rate(
    duration = c(4, 100),
    fail_rate = log(2) / 15, # Median survival 15 month
    dropout_rate = 0.001,
    hr = c(1, .6)
  )

  fh_test <- rbind(
    data.frame(
      rho = 0,
      gamma = 0,
      tau = -1,
      test = 1,
      analysis = 1:3,
      analysis_time = c(12, 24, 36)
    ),
    data.frame(
      rho = c(0, 0.5),
      gamma = 0.5,
      tau = -1,
      test = 2:3,
      analysis = 3,
      analysis_time = 36
    )
  )

  x <- gsDesign::gsSurv(
    k = 3,
    test.type = 4,
    alpha = 0.025,
    beta = 0.2,
    astar = 0,
    timing = c(1),
    sfu = gsDesign::sfLDOF,
    sfupar = c(0),
    sfl = gsDesign::sfLDOF,
    sflpar = c(0),
    lambdaC = c(0.1),
    hr = 0.6,
    hr0 = 1,
    eta = 0.01,
    gamma = c(10),
    R = c(12),
    S = NULL,
    T = 36,
    minfup = 24,
    ratio = 1
  )

  # User-defined boundary
  gs_design_combo_test1 <- gs_design_combo(
    enroll_rate = enroll_rate,
    fail_rate = fail_rate,
    fh_test = fh_test,
    alpha = alpha,
    beta = beta,
    ratio = 1,
    binding = FALSE, # test.type = 4 non-binding futility bound
    upar = x$upper$bound,
    lpar = x$lower$bound
  )

  # Boundary derived by spending function testing
  gs_design_combo_test2 <- gs_design_combo(
    enroll_rate = enroll_rate,
    fail_rate = fail_rate,
    fh_test = fh_test,
    alpha = 0.025,
    beta = 0.2,
    ratio = 1,
    binding = FALSE, # test.type = 4 non-binding futility bound
    upper = gs_spending_combo,
    upar = list(sf = gsDesign::sfLDOF, total_spend = 0.025), # alpha spending
    lower = gs_spending_combo,
    lpar = list(sf = gsDesign::sfLDOF, total_spend = 0.2), # beta spending
  )

  list(
    "alpha" = alpha,
    "beta" = beta,
    "enroll_rate" = enroll_rate,
    "fail_rate" = fail_rate,
    "fh_test" = fh_test,
    "gs_design_combo_test2" = gs_design_combo_test2
  )
}