⚡ Bolt: Optimize DataFrame Column Vector Subsetting

.Rbuildignore

@@ -22,3 +22,4 @@
 ^\.jules(/.*)?$
 ^\.trivyignore\.yaml$
 ^trivy\.yaml$
+^\.semgrepignore$

.jules/bolt.md

@@ -16,3 +16,6 @@
 ## 2025-02-12 - R 언어에서 반복적인 mirt 모델 생성 시 불필요한 데이터프레임 부분집합 추출 최적화
 **Learning:** R에서 데이터프레임의 특정 열을 추출하는 작업(`df[cols]`)은 O(N)의 메모리 복사를 수반합니다. `autoFIPC`에서 `mirt` 모델의 파라미터를 설정하거나 호출하는 과정 중에 `newformXDataK[colnames(newFormModel@Data$data)]` 코드가 반복해서 사용되었고, 심지어 `ncol()`을 위해 단순히 개수를 구할 때도 사용되어 불필요한 메모리 할당과 오버헤드를 초래했습니다.
 **Action:** 조건문이나 반복문 내부에서 불필요하게 데이터프레임 부분집합 연산이 반복되지 않도록 외부에서 한 번만 `linkedFormData <- newformXDataK[colnames(newFormModel@Data$data)]`로 캐싱(caching)한 뒤, `ncol(linkedFormData)`와 `data = linkedFormData` 형태로 재사용하여 메모리 복사와 O(N) 오버헤드를 방지해야 합니다.
+## 2024-11-20 - [Optimizing DataFrame Column Vector Subsetting]
+**Learning:** In the `aFIPC` codebase, the parameter updating logic frequently used two-dimensional subsetting with conditional matching (e.g., `NewScaleParms[NewScaleParms$item == 'GROUP', "est"] <- FALSE`). This pattern in R is much slower than direct column vector subsetting because it incurs row/column matching overhead and matrix/dataframe intermediate object creation.
+**Action:** When updating a specific column based on a conditional match, use direct vector subsetting (e.g., `NewScaleParms$est[NewScaleParms$item == 'GROUP'] <- FALSE`) which is significantly faster and avoids O(N) subset overhead.

R/aFIPC.R

@@ -598,15 +598,16 @@ autoFIPC <-
     # Preserve mirt's structural estimability flags. Forcing every row TRUE
     # frees boundary parameters such as 2PL g/u and makes the Hessian unstable.
 
-    NewScaleParms[NewScaleParms$item == 'GROUP', "est"] <- FALSE
-    OldScaleParms[OldScaleParms$item == 'GROUP', "est"] <- FALSE
+    # ⚡ Bolt: Direct vector assignment is faster and avoids full row/column subsetting overhead
+    NewScaleParms$est[NewScaleParms$item == 'GROUP'] <- FALSE
+    OldScaleParms$est[OldScaleParms$item == 'GROUP'] <- FALSE
 
-    NewScaleParms[NewScaleParms$name == "COV_11", "est"] <- TRUE
-    OldScaleParms[OldScaleParms$name == "COV_11", "est"] <- TRUE
+    NewScaleParms$est[NewScaleParms$name == "COV_11"] <- TRUE
+    OldScaleParms$est[OldScaleParms$name == "COV_11"] <- TRUE
 
     if (itemtype == 'Rasch') {
-      NewScaleParms[NewScaleParms$name == "a1", "est"] <- FALSE
-      OldScaleParms[OldScaleParms$name == "a1", "est"] <- FALSE
+      NewScaleParms$est[NewScaleParms$name == "a1"] <- FALSE
+      OldScaleParms$est[OldScaleParms$name == "a1"] <- FALSE
     }
 
     #IPD
@@ -789,11 +790,11 @@ autoFIPC <-
         message('   Newform Parms: ', paste(NewScaleParms[newIdx, "value"], collapse = ' '))
         message('   Oldform Parms: ', paste(OldScaleParms[oldIdx, "value"], collapse = ' '))
 
-        NewScaleParms[newIdx, "value"] <-
-          OldScaleParms[oldIdx, "value"]
-        message('   Linkedform Parms: ', paste(NewScaleParms[newIdx, "value"], collapse = ' '), '\n')
+        NewScaleParms$value[newIdx] <-
+          OldScaleParms$value[oldIdx]
+        message('   Linkedform Parms: ', paste(NewScaleParms$value[newIdx], collapse = ' '), '\n')
 
-        NewScaleParms[newIdx, "est"] <-
+        NewScaleParms$est[newIdx] <-
           FALSE
       } else {
         message(
@@ -813,17 +814,17 @@ autoFIPC <-
       newBetaIdx <- NewScaleParms$item == 'BETA'
       oldBetaIdx <- OldScaleParms$item == 'BETA'
 
-      NewScaleParms[newBetaIdx, "value"] <-
-        OldScaleParms[oldBetaIdx, "value"]
-      NewScaleParms[newBetaIdx, "est"] <-
+      NewScaleParms$value[newBetaIdx] <-
+        OldScaleParms$value[oldBetaIdx]
+      NewScaleParms$est[newBetaIdx] <-
         FALSE
 
       message('applying BETA parameter as linking')
 
       message(
         '   Linkedform Parms: ',
         paste0(
-          NewScaleParms[newBetaIdx, "value"],
+          NewScaleParms$value[newBetaIdx],
           ' '
         ),
         '\n'
@@ -858,13 +859,13 @@ autoFIPC <-
       new_mean11_idx <- NewScaleParms$name == "MEAN_11"
       old_mean11_idx <- OldScaleParms$name == "MEAN_11"
 
-      NewScaleParms[new_cov11_idx, "est"] <- FALSE
-      OldScaleParms[old_cov11_idx, "est"] <- FALSE
-      NewScaleParms[new_mean11_idx, "est"] <- FALSE
-      OldScaleParms[old_mean11_idx, "est"] <- FALSE
+      NewScaleParms$est[new_cov11_idx] <- FALSE
+      OldScaleParms$est[old_cov11_idx] <- FALSE
+      NewScaleParms$est[new_mean11_idx] <- FALSE
+      OldScaleParms$est[old_mean11_idx] <- FALSE
 
-      NewScaleParms[new_cov11_idx, "value"] <- 1
-      OldScaleParms[old_mean11_idx, "value"] <- 0
+      NewScaleParms$value[new_cov11_idx] <- 1
+      OldScaleParms$value[old_mean11_idx] <- 0
     }
     if (freeMEAN == T) {
       LinkedModelSyntax <-
@@ -875,8 +876,8 @@ autoFIPC <-
           'MEAN = F1'
         ))
 
-      NewScaleParms[NewScaleParms$name == "MEAN_1", "est"] <- TRUE
-      OldScaleParms[OldScaleParms$name == "MEAN_1", "est"] <- TRUE
+      NewScaleParms$est[NewScaleParms$name == "MEAN_1"] <- TRUE
+      OldScaleParms$est[OldScaleParms$name == "MEAN_1"] <- TRUE
     } else {
       LinkedModelSyntax <-
         mirt::mirt.model(paste0(