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

## ----temporal-----------------------------------------------------------------
# library(gdpar)
# 
# set.seed(1)
# n <- 150
# x <- rnorm(n)
# # AR(1) errors: serial dependence the working-independence fit ignores.
# y <- 1 + 0.5 * x + as.numeric(stats::arima.sim(list(ar = 0.6), n))
# df <- data.frame(x = x, y = y, t = seq_len(n))
# 
# fit <- gdpar_eb(y ~ x, amm = amm_spec(a = ~ x), data = df,
#                 chains = 2, iter_warmup = 300, iter_sampling = 300)
# 
# # Step 1 — diagnose. Lag-1 autocorrelation, Durbin-Watson, Ljung-Box.
# gdpar_dependence_diagnostic(fit, index = df$t)
# 
# # Step 2 — if flagged, re-estimate the uncertainty by a temporal block bootstrap.
# gdpar_dependence_robust(fit, data = df, index = df$t, B = 199, seed = 1)

## ----temporal-auto------------------------------------------------------------
# # Data-driven block length: the Politis-White (2004) automatic selector,
# # computed from the residuals (no extra refit), with the rate as fallback.
# gdpar_dependence_robust(fit, data = df, index = df$t,
#                         block_length = "auto", B = 199, seed = 1)

## ----spatial-diagnostic-------------------------------------------------------
# set.seed(2)
# n <- 200
# gx <- runif(n); gy <- runif(n)            # spatial coordinates
# x <- rnorm(n)
# # An omitted smooth spatial trend lands in the residuals.
# y <- 1 + 0.5 * x + 3 * (gx + gy) + rnorm(n, sd = 0.3)
# df <- data.frame(x = x, y = y)
# 
# fit_sp <- gdpar_eb(y ~ x, amm = amm_spec(a = ~ x), data = df,
#                    chains = 2, iter_warmup = 300, iter_sampling = 300)
# 
# gdpar_spatial_dependence_diagnostic(fit_sp, coords = cbind(gx, gy), seed = 1)

## ----spatial-robust-----------------------------------------------------------
# gdpar_spatial_dependence_robust(fit_sp, data = df, coords = cbind(gx, gy),
#                                 B = 199, seed = 1)

## ----spatial-auto-------------------------------------------------------------
# gdpar_spatial_dependence_robust(fit_sp, data = df, coords = cbind(gx, gy),
#                                 block_size = "auto", B = 199, seed = 1)