## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(ReproStat)
set.seed(20260324)

## ----pattern1-----------------------------------------------------------------
diag_obj <- run_diagnostics(
  mpg ~ wt + hp + disp,
  data = mtcars,
  B = 200,
  method = "bootstrap"
)

reproducibility_index(diag_obj)
selection_stability(diag_obj)

## ----pattern2-----------------------------------------------------------------
diag_sub <- run_diagnostics(
  mpg ~ wt + hp + disp,
  data = mtcars,
  B = 200,
  method = "subsample",
  frac = 0.75
)

reproducibility_index(diag_sub)

## ----pattern3-----------------------------------------------------------------
diag_noise <- run_diagnostics(
  mpg ~ wt + hp + disp,
  data = mtcars,
  B = 150,
  method = "noise",
  noise_sd = 0.05
)

reproducibility_index(diag_noise)
prediction_stability(diag_noise)$mean_variance

## ----pattern4-----------------------------------------------------------------
diag_glm <- run_diagnostics(
  am ~ wt + hp + qsec,
  data = mtcars,
  B = 150,
  backend = "glm",
  family = stats::binomial()
)

reproducibility_index(diag_glm)

## ----pattern5, eval = requireNamespace("MASS", quietly = TRUE)----------------
if (requireNamespace("MASS", quietly = TRUE)) {
  diag_rlm <- run_diagnostics(
    mpg ~ wt + hp + disp,
    data = mtcars,
    B = 150,
    backend = "rlm"
  )

  reproducibility_index(diag_rlm)
}

## ----pattern6, eval = requireNamespace("glmnet", quietly = TRUE)--------------
if (requireNamespace("glmnet", quietly = TRUE)) {
  diag_lasso <- run_diagnostics(
    mpg ~ wt + hp + disp + qsec,
    data = mtcars,
    B = 150,
    backend = "glmnet",
    en_alpha = 1
  )

  reproducibility_index(diag_lasso)
  selection_stability(diag_lasso)
}

## ----pattern7-----------------------------------------------------------------
models <- list(
  compact  = mpg ~ wt + hp,
  standard = mpg ~ wt + hp + disp,
  expanded = mpg ~ wt + hp + disp + qsec
)

cv_obj <- cv_ranking_stability(models, mtcars, v = 5, R = 40)
cv_obj$summary

## ----pattern8-----------------------------------------------------------------
diag_obj <- run_diagnostics(
  mpg ~ wt + hp + disp,
  data = mtcars,
  B = 150,
  method = "bootstrap"
)

ri <- reproducibility_index(diag_obj)
ci <- ri_confidence_interval(diag_obj, R = 300, seed = 1)

ri
ci

