From 16d17e1d238b54994b4d8be9135952520a3bff0a Mon Sep 17 00:00:00 2001
From: seonghobae <8172694+seonghobae@users.noreply.github.com>
Date: Sun, 5 Jul 2026 03:47:03 +0000
Subject: [PATCH 1/4] =?UTF-8?q?=E2=9A=A1=20Bolt:=20Cache=20inverted=20matr?=
 =?UTF-8?q?ices=20in=20vuongtest?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Extracted and cached the matrix inversion for AB1 and AB2 into local
variables before constructing the block matrix W in calcLambda to prevent
redundant O(n^3) computation.
---
 .jules/bolt.md |  3 +++
 R/vuongtest.R  | 11 +++++++----
 2 files changed, 10 insertions(+), 4 deletions(-)
 create mode 100644 .jules/bolt.md

diff --git a/.jules/bolt.md b/.jules/bolt.md
new file mode 100644
index 0000000..6e74844
--- /dev/null
+++ b/.jules/bolt.md
@@ -0,0 +1,3 @@
+## 2024-05-18 - Caching Matrix Inversions in vuongtest
+**Learning:** In statistical R packages involving likelihood calculations, matrix inversion is a common performance bottleneck. Repeating the exact same inversion inside matrix bindings multiplies this cost unnecessarily.
+**Action:** Always inspect matrix construction blocks for duplicated expensive operations and extract them into cached local variables before assembling the final block matrix.
diff --git a/R/vuongtest.R b/R/vuongtest.R
index 57c5f6b..3864774 100644
--- a/R/vuongtest.R
+++ b/R/vuongtest.R
@@ -271,10 +271,13 @@ calcLambda <- function(object1, object2, n, score1, score2, vc1, vc2) {
   AB2 <- calcAB(object2, n, score2, vc2)
   Bc <- calcBcross(AB1$sc, AB2$sc, n)
 
-  W <- cbind(rbind(-AB1$B %*% chol2inv(chol(AB1$A)),
-                   t(Bc) %*% chol2inv(chol(AB1$A))),
-             rbind(-Bc %*% chol2inv(chol(AB2$A)),
-                   AB2$B %*% chol2inv(chol(AB2$A))))
+  # Bolt: cache matrix inversions to avoid recalculating the O(n^3) inverse twice for each model
+  invA1 <- chol2inv(chol(AB1$A))
+  invA2 <- chol2inv(chol(AB2$A))
+  W <- cbind(rbind(-AB1$B %*% invA1,
+                   t(Bc) %*% invA1),
+             rbind(-Bc %*% invA2,
+                   AB2$B %*% invA2))
 
   lamstar <- eigen(W, only.values=TRUE)$values
   ## Discard imaginary part, as it only occurs for tiny eigenvalues?

From 7a6f5335e486f3a4f407275d2f48cc4c6018d11e Mon Sep 17 00:00:00 2001
From: seonghobae <8172694+seonghobae@users.noreply.github.com>
Date: Sun, 5 Jul 2026 04:04:23 +0000
Subject: [PATCH 2/4] =?UTF-8?q?=E2=9A=A1=20Bolt:=20Cache=20inverted=20matr?=
 =?UTF-8?q?ices=20in=20vuongtest?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Extracted and cached the matrix inversion for AB1 and AB2 into local
variables before constructing the block matrix W in calcLambda to prevent
redundant O(n^3) computation.

From a8429a2878201fc07cddff33e435d245ccd4f832 Mon Sep 17 00:00:00 2001
From: seonghobae <8172694+seonghobae@users.noreply.github.com>
Date: Sun, 5 Jul 2026 04:21:35 +0000
Subject: [PATCH 3/4] =?UTF-8?q?=E2=9A=A1=20Bolt:=20Cache=20inverted=20matr?=
 =?UTF-8?q?ices=20in=20vuongtest?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Extracted and cached the matrix inversion for AB1 and AB2 into local
variables before constructing the block matrix W in calcLambda to prevent
redundant O(n^3) computation.

From 30acd371aa5acf9b890c73128a1c0e5fa933557b Mon Sep 17 00:00:00 2001
From: seonghobae <8172694+seonghobae@users.noreply.github.com>
Date: Sun, 5 Jul 2026 04:38:35 +0000
Subject: [PATCH 4/4] =?UTF-8?q?=E2=9A=A1=20Bolt:=20Cache=20inverted=20matr?=
 =?UTF-8?q?ices=20in=20vuongtest?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Extracted and cached the matrix inversion for AB1 and AB2 into local
variables before constructing the block matrix W in calcLambda to prevent
redundant O(n^3) computation.