Use getFromNamespace instead of ::: to fix S3 dispatch for as_gt()

[jdblischak]

Removes the NOTE from R CMD check (#490)

xref: Merck/simtrial#284, #467, Merck/simtrial#287

Demonstration that it still works:

library("simtrial")
packageVersion("simtrial")
## [1] ‘0.4.2’
library("gsDesign2")
##
## Attaching package: ‘gsDesign2’
##
## The following object is masked from ‘package:simtrial’:
##
##   as_gt
##
packageVersion("gsDesign2")
## [1] ‘1.1.3’

# Parameters for enrollment
enroll_rampup_duration <- 4 # Duration for enrollment ramp up
enroll_duration <- 16 # Total enrollment duration
enroll_rate <- define_enroll_rate(
  duration = c(
    enroll_rampup_duration, enroll_duration - enroll_rampup_duration),
  rate = c(10, 30))

# Parameters for treatment effect
delay_effect_duration <- 3 # Delay treatment effect in months
median_ctrl <- 9 # Survival median of the control arm
median_exp <- c(9, 14) # Survival median of the experimental arm
dropout_rate <- 0.001
fail_rate <- define_fail_rate(
  duration = c(delay_effect_duration, 100),
  fail_rate = log(2) / median_ctrl,
  hr = median_ctrl / median_exp,
  dropout_rate = dropout_rate)

# Other related parameters
alpha <- 0.025 # Type I error
beta <- 0.1 # Type II error
ratio <- 1 # Randomization ratio (experimental:control)

# Build a one-sided group sequential design
design <- gs_design_ahr(
  enroll_rate = enroll_rate, fail_rate = fail_rate,
  ratio = ratio, alpha = alpha, beta = beta,
  analysis_time = c(12, 24, 36),
  upper = gs_spending_bound,
  upar = list(sf = gsDesign::sfLDOF, total_spend = alpha),
  lower = gs_b,
  lpar = rep(-Inf, 3))

# Define cuttings of 2 IAs and 1 FA
ia1_cut <- create_cut(target_event_overall = ceiling(design$analysis$event[1]))
ia2_cut <- create_cut(target_event_overall = ceiling(design$analysis$event[2]))
fa_cut <- create_cut(target_event_overall = ceiling(design$analysis$event[3]))

# Run simulations
simulation <- sim_gs_n(
  n_sim = 3,
  sample_size = ceiling(design$analysis$n[3]),
  enroll_rate = design$enroll_rate,
  fail_rate = design$fail_rate,
  test = wlr,
  cut = list(ia1 = ia1_cut, ia2 = ia2_cut, fa = fa_cut),
  weight = fh(rho = 0, gamma = 0.5))

# Summarize simulation and compare with the planned design
class(simulation)
## [1] "simtrial_gs_wlr" "data.frame"
simulation |> summary(design = design) |> as_gt()

[jdblischak]

@LittleBeannie R CMD check returned Status: OK for all 5 builds

[LittleBeannie]

Thank you, @jdblischak !

[yihui]

The CRAN incoming queue is empty at the moment: https://cran.r-project.org/incoming/pretest/ I guess it shouldn't take more than 10 minutes for the new submission of pass the auto check if you submit this afternoon.