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

## ----data---------------------------------------------------------------------
set.seed(2026)
n <- 120
p <- 6
X <- matrix(rnorm(n * p), nrow = n, ncol = p)
colnames(X) <- paste0("x", seq_len(p))
beta <- c(0.8, -0.6, 0.4, 0, 0, 0)
T <- rexp(n, rate = 0.06 * exp(drop(X %*% beta)))
C <- rexp(n, rate = 0.04)
time <- pmin(T, C)
status <- as.integer(T <= C)

## ----fit----------------------------------------------------------------------
library(selSurv)
fit <- coxlasso_fit(X, time, status, lambda_choice = "1se")
fit

## ----api-smoke, include=FALSE-------------------------------------------------
db_smoke <- coxlasso_debias(fit)
db_boot_smoke <- coxlasso_boot(
  fit, inference = "debiased", type = c("wild", "efron"),
  B = 3L, conf_level = 0.95, seed = 2026
)
fixed_smoke <- coxlasso_boot(
  fit, inference = "conditional",
  B = 3L, conf_level = 0.95, seed = 2026
)
split_smoke <- coxlasso_split(X, time, status, seed = 2026)
reselected_smoke <- coxlasso_boot_reselect(
  X, time, status, B = 3L, conf_level = 0.95,
  methods = c("fixed_support", "reselect_fixed_lambda", "reselect_cv_min"),
  seed = 2026, nfolds = 3L, standardize = TRUE
)

## ----routes, eval=FALSE-------------------------------------------------------
# # Full-model coefficient target: debiased Wald inference
# db <- coxlasso_debias(fit)
# 
# # Full-model coefficient target: wild bootstrap and Efron's bootstrap
# db_boot <- coxlasso_boot(
#   fit,
#   inference = "debiased",
#   type = c("wild", "efron"),
#   B = 500,
#   conf_level = 0.95,
#   seed = 2026
# )
# 
# # Selected-submodel target: observed support held fixed
# fixed <- coxlasso_boot(
#   fit,
#   inference = "conditional",
#   B = 500,
#   conf_level = 0.95,
#   seed = 2026
# )
# 
# # Selection and inference on disjoint samples
# split <- coxlasso_split(X, time, status, seed = 2026)
# 
# # Procedure-level re-selection
# reselected <- coxlasso_boot_reselect(
#   X, time, status,
#   B = 500,
#   conf_level = 0.95,
#   methods = c("fixed_support", "reselect_fixed_lambda", "reselect_cv_min"),
#   seed = 2026
# )

## ----summaries, eval=FALSE----------------------------------------------------
# summary(db)
# summary(db_boot)
# summary(fixed)
# summary(split)
# 
# rs <- summary(reselected)
# rs$diagnostics
# rs$intervals