## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

## ----setup--------------------------------------------------------------------
library(EDI)
set.seed(20260916)

n = 100
X = data.frame(
  age   = round(rnorm(n, 60, 10)),
  stage = sample(1:3, n, replace = TRUE)
)
true_log_hr = -0.5   # treatment lowers the hazard

## ----fixed--------------------------------------------------------------------
des = DesignFixedBernoulli$new(n = n, response_type = "survival", verbose = FALSE)
des$add_all_subjects_to_experiment(X)
des$assign_w_to_all_subjects()
w = des$get_w()

rate       = exp(-2 + true_log_hr * w + 0.02 * (X$age - 60) + 0.3 * (X$stage - 2))
event_time = rexp(n, rate)
censored   = rbinom(n, 1, 0.3) == 1
follow_up  = pmin(event_time, runif(n, 0, 2 * median(event_time)))  # observed time

for (i in seq_len(n)) {
  if (censored[i]) {
    des$add_one_subject_response(i, y_L = follow_up[i], y_R = Inf)   # right-censored at follow_up
  } else {
    des$add_one_subject_response(i, y = event_time[i])               # exact event
  }
}
table(censored = censored)

## ----cox----------------------------------------------------------------------
inf = InferenceSurvivalCoxPHRegr$new(des, verbose = FALSE)
inf$num_cores = 1L
inf$compute_estimate()                         # log hazard ratio for treatment
inf$compute_asymp_confidence_interval(alpha = 0.05)
inf$compute_asymp_two_sided_pval()

## ----cox-resampling-----------------------------------------------------------
inf$set_seed(1)
inf$compute_rand_two_sided_pval(r = 200, show_progress = FALSE)
inf$set_seed(1)
inf$compute_bootstrap_confidence_interval(alpha = 0.05, B = 200, show_progress = FALSE)

## ----suite--------------------------------------------------------------------
suite = InferenceSuite$new(des)
res = suite$run_all_inference(screen = TRUE, plots = FALSE, num_cores = 1L,
                              methods = c("wald", "score", "lik_ratio"), max_secs_per_class = 15)

## ----seq----------------------------------------------------------------------
des_seq = DesignSeqOneByOneKK14$new(n = n, response_type = "survival", verbose = FALSE)
for (i in seq_len(n)) {
  w_i  = des_seq$add_one_subject_to_experiment_and_assign(X[i, , drop = FALSE])
  t_i  = rexp(1, exp(-2 + true_log_hr * w_i + 0.02 * (X$age[i] - 60) + 0.3 * (X$stage[i] - 2)))
  if (rbinom(1, 1, 0.3) == 1) {
    des_seq$add_one_subject_response(i, y_L = min(t_i, 3), y_R = Inf)
  } else {
    des_seq$add_one_subject_response(i, y = t_i)
  }
}

inf_seq = InferenceSurvivalCoxPHRegr$new(des_seq, verbose = FALSE)
inf_seq$num_cores = 1L
inf_seq$compute_estimate()
inf_seq$set_seed(1)
inf_seq$compute_rand_two_sided_pval(r = 200, show_progress = FALSE)