From dfb6c7befefb4dc05d45750dd4c56c85a5c0e023 Mon Sep 17 00:00:00 2001
From: Adam <adam@klebus.com>
Date: Fri, 6 Jun 2025 12:35:07 +0200
Subject: [PATCH 1/2] thinning after stan

---
 R/mcmc.R | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/R/mcmc.R b/R/mcmc.R
index c0c7554b6..ac78454c4 100644
--- a/R/mcmc.R
+++ b/R/mcmc.R
@@ -89,14 +89,19 @@ fit_mcmc <- function(
         mmrm_initial$sigma
     )
 
+    # We perform thinning after the rstan::sampling call,
+    # so that we keep the whole chain in the stan fit object.
+    thin <- method$control$thin
+    method$control$thin <- 1
+
     control <- complete_control_bayes(
         control = method$control,
-        n_samples = method$n_samples,
+        n_samples = method$n_samples * thin,
         quiet = quiet,
         stan_data = stan_data,
         mmrm_initial = mmrm_initial
     )
-    
+
     sampling_args <- c(
         list(
             object = get_stan_model(),
@@ -128,7 +133,10 @@ fit_mcmc <- function(
     fit <- stan_fit$results
     check_mcmc(fit, method$n_samples)
 
-    draws <- extract_draws(fit, method$n_samples)
+    draws <- extract_draws(fit, method$n_samples * thin)
+    # Perform thinning on parameter draws
+    draws$beta <- draws$beta[seq(1, method$n_samples * thin, by = thin)]
+    draws$sigma <- draws$sigma[seq(1, method$n_samples * thin, by = thin)]
 
     ret_obj <- list(
         "samples" = draws,

From ba7cb11c0364d07e8be349f02cb72ffbbef34f41 Mon Sep 17 00:00:00 2001
From: Adam <adam@klebus.com>
Date: Wed, 18 Jun 2025 14:29:19 +0200
Subject: [PATCH 2/2] basic test

---
 tests/testthat/test-mcmc.R | 42 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/tests/testthat/test-mcmc.R b/tests/testthat/test-mcmc.R
index d9a41fa23..8cf19ab4d 100644
--- a/tests/testthat/test-mcmc.R
+++ b/tests/testthat/test-mcmc.R
@@ -683,3 +683,45 @@ test_that("fit_mcmc works with multiple chains", {
         n_visits = 3
     )
 })
+
+test_that("full chain (before thinning) is retained in the stan fit object", {
+
+    skip_if_not(is_full_test())
+
+    set.seed(7251)
+
+    mcoefs <- list(
+        "int" = 10,
+        "age" = 3,
+        "sex" = 6,
+        "trtslope" = 7
+    )
+    sigma <- as_vcov(c(3, 5, 7), c(0.1, 0.4, 0.7))
+
+    dat <- get_mcmc_sim_dat(1000, mcoefs, sigma)
+    mat <- model.matrix(data = dat, ~ 1 + sex + age + group + visit + group * visit)
+
+    method <- method_bayes(
+        n_samples = 150,
+        same_cov = TRUE,
+        control = control_bayes(
+            warmup = 200,
+            thin = 3,
+        )
+    )
+
+    fit <- fit_mcmc(
+        designmat = mat,
+        outcome = dat$outcome,
+        group = dat$group,
+        subjid = dat$id,
+        visit = dat$visit,
+        method = method,
+        quiet = TRUE
+    )
+    # Samples are thinned
+    expect_true(length(fit$samples$beta) == method$n_samples)
+    expect_true(length(fit$samples$sigma) == method$n_samples)
+    # Stan fit object retains unthinned samples
+    expect_true(nrow(as.matrix(fit$fit)) == method$n_samples * method$control$thin)
+})
\ No newline at end of file