From 0ecf6f14dd4816a79ffb860f8f430cd6451efcbb Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 23 Apr 2026 12:14:04 -0500
Subject: [PATCH 01/31] Fix collinearity inflation for ordinal models

---
 R/check_collinearity.R | 24 ++++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index 86a28334a..d77cd7123 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -491,12 +491,24 @@ check_collinearity.zerocount <- function(
     }
   }
 
-  # check for missing intercept
-  if (insight::has_intercept(x)) {
-    v <- v[-1, -1]
-    term_assign <- term_assign[-1]
-  } else if (isTRUE(verbose)) {
-    insight::format_alert("Model has no intercept. VIFs may not be sensible.")
+  # Filter to true slope parameters (handles multiple intercepts in ordinal models)
+  if (inherits(x, c("clm", "clmm"))) {
+    slope_names <- names(x$beta)
+    keep_idx <- which(colnames(v) %in% slope_names)
+  } else if (insight::has_intercept(x)) {
+    # Standard behavior: drop the first column/row (the singular intercept)
+    keep_idx <- seq_len(ncol(v))[-1]
+  } else {
+    keep_idx <- seq_len(ncol(v))
+    if (isTRUE(verbose)) {
+      insight::format_alert("Model without intercept. VIFs may not be sensible.")
+    }
+  }
+  
+  # Safely subset both the matrix and the assignment vector
+  if (length(keep_idx) < ncol(v)) {
+    v <- v[keep_idx, keep_idx, drop = FALSE]
+    term_assign <- term_assign[keep_idx]
   }
 
   f <- insight::find_formula(x, verbose = FALSE)

From c645ff73b1fb24c6cb150407ded9fa3f364f9de0 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 23 Apr 2026 12:23:46 -0500
Subject: [PATCH 02/31] Address gemini-code-review feedback

---
 R/check_collinearity.R | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index d77cd7123..6fcb1ac0a 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -491,9 +491,10 @@ check_collinearity.zerocount <- function(
     }
   }
 
-  # Filter to true slope parameters (handles multiple intercepts in ordinal models)
+# Filter to true slope parameters (handles multiple intercepts in ordinal models)
   if (inherits(x, c("clm", "clmm"))) {
-    slope_names <- names(x$beta)
+    slope_names <- insight::find_parameters(x)$conditional
+    if (is.null(slope_names)) slope_names <- names(x$beta)
     keep_idx <- which(colnames(v) %in% slope_names)
   } else if (insight::has_intercept(x)) {
     # Standard behavior: drop the first column/row (the singular intercept)
@@ -504,11 +505,13 @@ check_collinearity.zerocount <- function(
       insight::format_alert("Model without intercept. VIFs may not be sensible.")
     }
   }
-  
-  # Safely subset both the matrix and the assignment vector
+
+  # Safely subset the matrix and the assignment vector
   if (length(keep_idx) < ncol(v)) {
+    if (!is.null(term_assign) && length(term_assign) == ncol(v)) {
+      term_assign <- term_assign[keep_idx]
+    }
     v <- v[keep_idx, keep_idx, drop = FALSE]
-    term_assign <- term_assign[keep_idx]
   }
 
   f <- insight::find_formula(x, verbose = FALSE)

From 75f16f08e056e45c8a17fdc8e9cde26e27d6ebcf Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 23 Apr 2026 12:25:15 -0500
Subject: [PATCH 03/31] Apply styling

---
 R/check_collinearity.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index 6fcb1ac0a..d4c4f0b9c 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -491,10 +491,12 @@ check_collinearity.zerocount <- function(
     }
   }
 
-# Filter to true slope parameters (handles multiple intercepts in ordinal models)
+  # Filter to true slope parameters (handles multiple intercepts in ordinal models)
   if (inherits(x, c("clm", "clmm"))) {
     slope_names <- insight::find_parameters(x)$conditional
-    if (is.null(slope_names)) slope_names <- names(x$beta)
+    if (is.null(slope_names)) {
+      slope_names <- names(x$beta)
+    }
     keep_idx <- which(colnames(v) %in% slope_names)
   } else if (insight::has_intercept(x)) {
     # Standard behavior: drop the first column/row (the singular intercept)

From 3a84e3e64cbef2d541c0da3a3bd2ef561c3c4e51 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 23 Apr 2026 12:49:09 -0500
Subject: [PATCH 04/31] Revert gemini suggestion and fix slope identification

---
 R/check_collinearity.R | 26 ++++++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index d4c4f0b9c..e70e42846 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -493,11 +493,29 @@ check_collinearity.zerocount <- function(
 
   # Filter to true slope parameters (handles multiple intercepts in ordinal models)
   if (inherits(x, c("clm", "clmm"))) {
-    slope_names <- insight::find_parameters(x)$conditional
-    if (is.null(slope_names)) {
-      slope_names <- names(x$beta)
-    }
+    slope_names <- names(x$beta)
     keep_idx <- which(colnames(v) %in% slope_names)
+
+    # Rebuild term_assign securely to prevent NA drops for categorical predictors
+    tryCatch(
+      {
+        f_cond <- insight::find_formula(x)$conditional
+        d <- insight::get_data(x, verbose = FALSE)
+        mm <- stats::model.matrix(f_cond, data = d)
+        assign_attr <- attr(mm, "assign")
+        
+        if (!is.null(assign_attr)) {
+          if (assign_attr[1] == 0) {
+            assign_attr <- assign_attr[-1] # Drop intercept
+          }
+          if (length(assign_attr) == length(keep_idx)) {
+            term_assign <- assign_attr
+          }
+        }
+      },
+      error = function(e) NULL
+    )
+
   } else if (insight::has_intercept(x)) {
     # Standard behavior: drop the first column/row (the singular intercept)
     keep_idx <- seq_len(ncol(v))[-1]

From b7f9fb580894545dd944682e649942bd25454482 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 23 Apr 2026 12:52:01 -0500
Subject: [PATCH 05/31] Remove extra whitespace for air

---
 R/check_collinearity.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index e70e42846..44fe4aafc 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -503,7 +503,6 @@ check_collinearity.zerocount <- function(
         d <- insight::get_data(x, verbose = FALSE)
         mm <- stats::model.matrix(f_cond, data = d)
         assign_attr <- attr(mm, "assign")
-        
         if (!is.null(assign_attr)) {
           if (assign_attr[1] == 0) {
             assign_attr <- assign_attr[-1] # Drop intercept
@@ -515,7 +514,6 @@ check_collinearity.zerocount <- function(
       },
       error = function(e) NULL
     )
-
   } else if (insight::has_intercept(x)) {
     # Standard behavior: drop the first column/row (the singular intercept)
     keep_idx <- seq_len(ncol(v))[-1]

From 091be3829ed6c1d9469a4f51f5480100177a45ae Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 23 Apr 2026 13:12:43 -0500
Subject: [PATCH 06/31] Move processing before rank deficiency checks

---
 R/check_collinearity.R | 40 +++++++++++++++++++---------------------
 1 file changed, 19 insertions(+), 21 deletions(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index 44fe4aafc..8d84cace6 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -481,34 +481,22 @@ check_collinearity.zerocount <- function(
     return(NULL)
   }
 
-  # we have rank-deficiency here. remove NA columns from assignment
-  if (isTRUE(attributes(v)$rank_deficient) && !is.null(attributes(v)$na_columns_index)) {
-    term_assign <- term_assign[-attributes(v)$na_columns_index]
-    if (isTRUE(verbose)) {
-      insight::format_alert(
-        "Model matrix is rank deficient. VIFs may not be sensible."
-      )
-    }
-  }
-
   # Filter to true slope parameters (handles multiple intercepts in ordinal models)
   if (inherits(x, c("clm", "clmm"))) {
+    # names(x$beta) returns only non-singular (surviving) slopes
     slope_names <- names(x$beta)
     keep_idx <- which(colnames(v) %in% slope_names)
 
-    # Rebuild term_assign securely to prevent NA drops for categorical predictors
+    # Rebuild term_assign to handle categorical predictors AND rank-deficiency
     tryCatch(
       {
-        f_cond <- insight::find_formula(x)$conditional
-        d <- insight::get_data(x, verbose = FALSE)
-        mm <- stats::model.matrix(f_cond, data = d)
+        mm <- insight::get_modelmatrix(x)
         assign_attr <- attr(mm, "assign")
         if (!is.null(assign_attr)) {
-          if (assign_attr[1] == 0) {
-            assign_attr <- assign_attr[-1] # Drop intercept
-          }
-          if (length(assign_attr) == length(keep_idx)) {
-            term_assign <- assign_attr
+          # Match surviving slopes in v to columns in the full model matrix
+          match_idx <- which(colnames(mm) %in% colnames(v)[keep_idx])
+          if (length(match_idx) > 0) {
+            term_assign <- assign_attr[match_idx]
           }
         }
       },
@@ -524,14 +512,24 @@ check_collinearity.zerocount <- function(
     }
   }
 
-  # Safely subset the matrix and the assignment vector
+  # Safely subset the matrix (term_assign is already synced for ordinal models)
   if (length(keep_idx) < ncol(v)) {
-    if (!is.null(term_assign) && length(term_assign) == ncol(v)) {
+    if (!inherits(x, c("clm", "clmm")) && !is.null(term_assign) && length(term_assign) == ncol(v)) {
       term_assign <- term_assign[keep_idx]
     }
     v <- v[keep_idx, keep_idx, drop = FALSE]
   }
 
+  # we have rank-deficiency here. remove NA columns from assignment
+  if (isTRUE(attributes(v)$rank_deficient) && !is.null(attributes(v)$na_columns_index)) {
+    term_assign <- term_assign[-attributes(v)$na_columns_index]
+    if (isTRUE(verbose)) {
+      insight::format_alert(
+        "Model matrix is rank deficient. VIFs may not be sensible."
+      )
+    }
+  }
+
   f <- insight::find_formula(x, verbose = FALSE)
 
   # hurdle or zeroinfl model can have no zero-inflation formula, in which case

From 035e33d83fae9ecc8eb2ee6b9a2cbbed4befdf81 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 23 Apr 2026 13:16:46 -0500
Subject: [PATCH 07/31] Break up condition for linter

---
 R/check_collinearity.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index 8d84cace6..249faee10 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -514,7 +514,11 @@ check_collinearity.zerocount <- function(
 
   # Safely subset the matrix (term_assign is already synced for ordinal models)
   if (length(keep_idx) < ncol(v)) {
-    if (!inherits(x, c("clm", "clmm")) && !is.null(term_assign) && length(term_assign) == ncol(v)) {
+    if (
+      !inherits(x, c("clm", "clmm")) && 
+        !is.null(term_assign) && 
+        length(term_assign) == ncol(v)
+    ) {
       term_assign <- term_assign[keep_idx]
     }
     v <- v[keep_idx, keep_idx, drop = FALSE]

From b3b266d38398465a8e1aa11b2c9fa78714317cf7 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 23 Apr 2026 13:18:19 -0500
Subject: [PATCH 08/31] Remove dangling spaces for linter

---
 R/check_collinearity.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index 249faee10..6f71f19fe 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -515,8 +515,8 @@ check_collinearity.zerocount <- function(
   # Safely subset the matrix (term_assign is already synced for ordinal models)
   if (length(keep_idx) < ncol(v)) {
     if (
-      !inherits(x, c("clm", "clmm")) && 
-        !is.null(term_assign) && 
+      !inherits(x, c("clm", "clmm")) &&
+        !is.null(term_assign) &&
         length(term_assign) == ncol(v)
     ) {
       term_assign <- term_assign[keep_idx]

From 577e59a9b785512bc32ab2f58cf3697229dcd06b Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 23 Apr 2026 13:36:08 -0500
Subject: [PATCH 09/31] Improve name-matching

---
 R/check_collinearity.R | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index 6f71f19fe..fd70fb00c 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -487,14 +487,14 @@ check_collinearity.zerocount <- function(
     slope_names <- names(x$beta)
     keep_idx <- which(colnames(v) %in% slope_names)
 
-    # Rebuild term_assign to handle categorical predictors AND rank-deficiency
+    # Rebuild term_assign by matching model matrix columns to surviving slopes
     tryCatch(
       {
         mm <- insight::get_modelmatrix(x)
         assign_attr <- attr(mm, "assign")
         if (!is.null(assign_attr)) {
-          # Match surviving slopes in v to columns in the full model matrix
-          match_idx <- which(colnames(mm) %in% colnames(v)[keep_idx])
+          # Use name-matching to isolate indices for estimated slopes
+          match_idx <- which(colnames(mm) %in% slope_names)
           if (length(match_idx) > 0) {
             term_assign <- assign_attr[match_idx]
           }
@@ -514,11 +514,7 @@ check_collinearity.zerocount <- function(
 
   # Safely subset the matrix (term_assign is already synced for ordinal models)
   if (length(keep_idx) < ncol(v)) {
-    if (
-      !inherits(x, c("clm", "clmm")) &&
-        !is.null(term_assign) &&
-        length(term_assign) == ncol(v)
-    ) {
+    if (!inherits(x, c("clm", "clmm")) && !is.null(term_assign) && length(term_assign) == ncol(v)) {
       term_assign <- term_assign[keep_idx]
     }
     v <- v[keep_idx, keep_idx, drop = FALSE]

From 6f8c986ce15ba5a1d867924ad6890837fe922286 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 23 Apr 2026 13:37:08 -0500
Subject: [PATCH 10/31] Fix line width again

---
 R/check_collinearity.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index fd70fb00c..3f945319f 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -514,7 +514,11 @@ check_collinearity.zerocount <- function(
 
   # Safely subset the matrix (term_assign is already synced for ordinal models)
   if (length(keep_idx) < ncol(v)) {
-    if (!inherits(x, c("clm", "clmm")) && !is.null(term_assign) && length(term_assign) == ncol(v)) {
+    if (
+      !inherits(x, c("clm", "clmm")) && 
+        !is.null(term_assign) && 
+        length(term_assign) == ncol(v)
+    ) {
       term_assign <- term_assign[keep_idx]
     }
     v <- v[keep_idx, keep_idx, drop = FALSE]

From adcf453ecaefe33b9bcb0cbe3e464b343fe96c53 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Thu, 23 Apr 2026 13:38:39 -0500
Subject: [PATCH 11/31] Fix dangling spaces again

---
 R/check_collinearity.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index 3f945319f..c3a449084 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -515,8 +515,8 @@ check_collinearity.zerocount <- function(
   # Safely subset the matrix (term_assign is already synced for ordinal models)
   if (length(keep_idx) < ncol(v)) {
     if (
-      !inherits(x, c("clm", "clmm")) && 
-        !is.null(term_assign) && 
+      !inherits(x, c("clm", "clmm")) &&
+        !is.null(term_assign) &&
         length(term_assign) == ncol(v)
     ) {
       term_assign <- term_assign[keep_idx]

From d5d8798a3136395bf96b66b5ba055e562262ad52 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 12:59:16 -0500
Subject: [PATCH 12/31] Add news and increment version

---
 .Rbuildignore     | 64 ++++++++++++++++++++++++-----------------------
 .gitignore        |  1 +
 DESCRIPTION       |  2 +-
 NEWS.md           |  7 ++++++
 performance.Rproj | 50 ++++++++++++++++++------------------
 5 files changed, 67 insertions(+), 57 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index d46eb037d..f6b27d8db 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,31 +1,33 @@
-^logo.png
-^README.Rmd
-^LICENSE
-
-^\.Rprofile$
-^.*\.Rproj$
-^\.Rproj\.user$
-
-^\.travis.yml
-^\_pkgdown.yml
-^\_pkgdown.yaml
-^paper.bib$
-^GEMINI\.md$
-
-^data/.
-^docs/.
-^vignettes/.
-^pkgdown/.
-^WIP/.
-^papers/.
-^.github/.
-^CODE_OF_CONDUCT\.md$
-^revdep$
-^tests/testthat/_snaps/.
-^cran-comments\.md$
-^\.github$
-\.code-workspace$
-\.lintr$
-^CRAN-SUBMISSION$
-^[.]?air[.]toml$
-^\.vscode$
+^logo.png
+^README.Rmd
+^LICENSE
+
+^\.Rprofile$
+^.*\.Rproj$
+^\.Rproj\.user$
+
+^\.travis.yml
+^\_pkgdown.yml
+^\_pkgdown.yaml
+^paper.bib$
+^GEMINI\.md$
+
+^data/.
+^docs/.
+^vignettes/.
+^pkgdown/.
+^WIP/.
+^papers/.
+^.github/.
+^CODE_OF_CONDUCT\.md$
+^revdep$
+^tests/testthat/_snaps/.
+^cran-comments\.md$
+^\.github$
+\.code-workspace$
+\.lintr$
+^CRAN-SUBMISSION$
+^[.]?air[.]toml$
+^\.vscode$
+^\.positai$
+^\.claude$
diff --git a/.gitignore b/.gitignore
index 1e3341f4a..ae0593944 100644
--- a/.gitignore
+++ b/.gitignore
@@ -50,3 +50,4 @@ Network Trash Folder
 Temporary Items
 .apdisk
 .Rprofile
+.positai
diff --git a/DESCRIPTION b/DESCRIPTION
index 0edd57763..1727096d1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: performance
 Title: Assessment of Regression Models Performance
-Version: 0.16.0.2
+Version: 0.16.0.3
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
diff --git a/NEWS.md b/NEWS.md
index 8653afe2b..efaec9d14 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+# performance 0.16.0.3
+
+## Bug fixes
+
+* Fixed issue in `check_collinearity()` that was causing inflated VIF values 
+  when applied to clm and clmm models from the ordinal package.
+
 # performance 0.16.0.2
 
 ## Changes
diff --git a/performance.Rproj b/performance.Rproj
index 2c52ed395..aacfcbeaa 100644
--- a/performance.Rproj
+++ b/performance.Rproj
@@ -1,25 +1,25 @@
-Version: 1.0
-ProjectId: af6facf3-033e-40d4-ac22-2830774814a9
-
-RestoreWorkspace: No
-SaveWorkspace: No
-AlwaysSaveHistory: No
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: knitr
-LaTeX: pdfLaTeX
-
-StripTrailingWhitespace: Yes
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
-PackageCheckArgs: --as-cran --run-donttest
-PackageRoxygenize: rd,collate,namespace
-
-QuitChildProcessesOnExit: Yes
-DisableExecuteRprofile: Yes
+Version: 1.0
+ProjectId: af6facf3-033e-40d4-ac22-2830774814a9
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran --run-donttest
+PackageRoxygenize: rd,collate,namespace
+
+QuitChildProcessesOnExit: Yes
+DisableExecuteRprofile: Yes

From 37cdbdce2883a07215f26c3d62f209408155f4bc Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 13:12:42 -0500
Subject: [PATCH 13/31] Add clmm test

---
 .vscode/settings.json                    |  5 ++++
 tests/testthat/test-check_collinearity.R | 34 ++++++++++++++++++++++++
 2 files changed, 39 insertions(+)
 create mode 100644 .vscode/settings.json

diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 000000000..9eb545797
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,5 @@
+{
+    "python.autoComplete.extraPaths": [
+        "c:\\Users\\jeffg\\.positron\\extensions\\continue.continue-0.0.412-win32-x64"
+    ]
+}
\ No newline at end of file
diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index c6b192643..7d31d0b7c 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -300,3 +300,37 @@ test_that("check_collinearity, validate adjusted vif against car", {
   expect_equal(out1[, 1], out2$VIF, tolerance = 1e-3, ignore_attr = TRUE)
   expect_equal(out1[, 3], out2$SE_factor, tolerance = 1e-3, ignore_attr = TRUE)
 })
+
+test_that("check_collinearity, ordinal clmm models", {
+  skip_if_not_installed("ordinal")
+  
+  set.seed(999)
+  n <- 500
+  
+  x_continuous <- rnorm(n, mean = 0, sd = 1)
+  x_binary <- sample(c(-0.5, 0.5), size = n, replace = TRUE, prob = c(0.85, 0.15))
+  subject_id <- factor(rep(1:50, each = 10))
+  random_intercepts <- rnorm(50, 0, 1)
+  
+  latent_y <- 2 * x_continuous + 
+    3 * x_binary + 
+    random_intercepts[as.numeric(subject_id)] + 
+    rlogis(n)
+    
+  y_ordinal <- cut(
+    latent_y,
+    breaks = 15,
+    ordered_result = TRUE
+  )
+  
+  dat <- data.frame(y_ordinal, x_continuous, x_binary, subject_id)
+  mod_clmm <- ordinal::clmm(
+    y_ordinal ~ x_continuous + x_binary + (1 | subject_id), 
+    data = dat
+  )
+  out <- check_collinearity(mod_clmm)
+  
+  expect_s3_class(out, "check_collinearity")
+  expect_identical(out$Term, c("x_continuous", "x_binary"))
+  expect_equal(out$VIF, c(1.12, 1.12), tolerance = 0.05)
+})
\ No newline at end of file

From 0f2e0a5adb0a7382e01dd41a142fc7079739e54f Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 13:14:00 -0500
Subject: [PATCH 14/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index 7d31d0b7c..7cb6e2530 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -303,7 +303,6 @@ test_that("check_collinearity, validate adjusted vif against car", {
 
 test_that("check_collinearity, ordinal clmm models", {
   skip_if_not_installed("ordinal")
-  
   set.seed(999)
   n <- 500
   

From 1df8633b7ff875a7671005e8c0b35770862a7daa Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 13:14:16 -0500
Subject: [PATCH 15/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index 7cb6e2530..fdaa7fbb3 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -305,7 +305,6 @@ test_that("check_collinearity, ordinal clmm models", {
   skip_if_not_installed("ordinal")
   set.seed(999)
   n <- 500
-  
   x_continuous <- rnorm(n, mean = 0, sd = 1)
   x_binary <- sample(c(-0.5, 0.5), size = n, replace = TRUE, prob = c(0.85, 0.15))
   subject_id <- factor(rep(1:50, each = 10))

From 93cde3780f83f72883837418894e858d1a7fbbbf Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 13:14:54 -0500
Subject: [PATCH 16/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index fdaa7fbb3..c2044af6b 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -309,10 +309,11 @@ test_that("check_collinearity, ordinal clmm models", {
   x_binary <- sample(c(-0.5, 0.5), size = n, replace = TRUE, prob = c(0.85, 0.15))
   subject_id <- factor(rep(1:50, each = 10))
   random_intercepts <- rnorm(50, 0, 1)
-  
-  latent_y <- 2 * x_continuous + 
-    3 * x_binary + 
-    random_intercepts[as.numeric(subject_id)] + 
+
+  latent_y <- 2 *
+    x_continuous +
+    3 * x_binary +
+    random_intercepts[as.numeric(subject_id)] +
     rlogis(n)
     
   y_ordinal <- cut(

From f51ef91dac88fe8bf5a932ee61933751a141ca21 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 13:15:06 -0500
Subject: [PATCH 17/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index c2044af6b..970e94581 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -315,7 +315,6 @@ test_that("check_collinearity, ordinal clmm models", {
     3 * x_binary +
     random_intercepts[as.numeric(subject_id)] +
     rlogis(n)
-    
   y_ordinal <- cut(
     latent_y,
     breaks = 15,

From ab7d8aff797e8e090884d07035b1d3106123e13e Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 13:23:21 -0500
Subject: [PATCH 18/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index 970e94581..fb8312ade 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -320,7 +320,6 @@ test_that("check_collinearity, ordinal clmm models", {
     breaks = 15,
     ordered_result = TRUE
   )
-  
   dat <- data.frame(y_ordinal, x_continuous, x_binary, subject_id)
   mod_clmm <- ordinal::clmm(
     y_ordinal ~ x_continuous + x_binary + (1 | subject_id), 

From a46a0b36a798d1ac66ab8f4981dfa162f8087ff5 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 13:23:35 -0500
Subject: [PATCH 19/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index fb8312ade..903e2fe55 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -322,7 +322,7 @@ test_that("check_collinearity, ordinal clmm models", {
   )
   dat <- data.frame(y_ordinal, x_continuous, x_binary, subject_id)
   mod_clmm <- ordinal::clmm(
-    y_ordinal ~ x_continuous + x_binary + (1 | subject_id), 
+    y_ordinal ~ x_continuous + x_binary + (1 | subject_id),
     data = dat
   )
   out <- check_collinearity(mod_clmm)

From c2a6b5c8ca558a68115a436469ff4f2a88b4c893 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 13:24:06 -0500
Subject: [PATCH 20/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index 903e2fe55..f3d850ecf 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -326,7 +326,6 @@ test_that("check_collinearity, ordinal clmm models", {
     data = dat
   )
   out <- check_collinearity(mod_clmm)
-  
   expect_s3_class(out, "check_collinearity")
   expect_identical(out$Term, c("x_continuous", "x_binary"))
   expect_equal(out$VIF, c(1.12, 1.12), tolerance = 0.05)

From e52bb0886a8f533d19dffc2981949ee497c77564 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 13:24:21 -0500
Subject: [PATCH 21/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index f3d850ecf..6311578e2 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -329,4 +329,4 @@ test_that("check_collinearity, ordinal clmm models", {
   expect_s3_class(out, "check_collinearity")
   expect_identical(out$Term, c("x_continuous", "x_binary"))
   expect_equal(out$VIF, c(1.12, 1.12), tolerance = 0.05)
-})
\ No newline at end of file
+})

From 16cbe71e5d333437f8acda95090d40d2cff5a8a0 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 13:51:20 -0500
Subject: [PATCH 22/31] Add clm test and fix bug

---
 R/check_collinearity.R                   |  7 +++----
 tests/testthat/test-check_collinearity.R | 24 +++++++++++++++++++++++-
 2 files changed, 26 insertions(+), 5 deletions(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index c3a449084..ef26f2a60 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -512,12 +512,11 @@ check_collinearity.zerocount <- function(
     }
   }
 
-  # Safely subset the matrix (term_assign is already synced for ordinal models)
+  # Safely subset the matrix
   if (length(keep_idx) < ncol(v)) {
     if (
-      !inherits(x, c("clm", "clmm")) &&
-        !is.null(term_assign) &&
-        length(term_assign) == ncol(v)
+      !is.null(term_assign) &&
+      length(term_assign) == ncol(v)
     ) {
       term_assign <- term_assign[keep_idx]
     }
diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index 6311578e2..fb6aaa91c 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -309,7 +309,6 @@ test_that("check_collinearity, ordinal clmm models", {
   x_binary <- sample(c(-0.5, 0.5), size = n, replace = TRUE, prob = c(0.85, 0.15))
   subject_id <- factor(rep(1:50, each = 10))
   random_intercepts <- rnorm(50, 0, 1)
-
   latent_y <- 2 *
     x_continuous +
     3 * x_binary +
@@ -330,3 +329,26 @@ test_that("check_collinearity, ordinal clmm models", {
   expect_identical(out$Term, c("x_continuous", "x_binary"))
   expect_equal(out$VIF, c(1.12, 1.12), tolerance = 0.05)
 })
+
+test_that("check_collinearity, ordinal clm models", {
+  skip_if_not_installed("ordinal")
+  set.seed(999)
+  n <- 500
+  x_continuous <- rnorm(n, mean = 0, sd = 1)
+  x_binary <- sample(c(-0.5, 0.5), size = n, replace = TRUE, prob = c(0.85, 0.15))
+  latent_y <- 2 * x_continuous + 3 * x_binary + rlogis(n)
+  y_ordinal <- cut(
+    latent_y,
+    breaks = 15,
+    ordered_result = TRUE
+  )
+  dat <- data.frame(y_ordinal, x_continuous, x_binary)
+  mod_clm <- ordinal::clm(
+    y_ordinal ~ x_continuous + x_binary, 
+    data = dat
+  )
+  out <- check_collinearity(mod_clm)
+  expect_s3_class(out, "check_collinearity")
+  expect_identical(out$Term, c("x_continuous", "x_binary"))
+  expect_equal(out$VIF, c(1.11, 1.11), tolerance = 0.05)
+})
\ No newline at end of file

From fe9f4249d73a41d23f343b13c7b0fb99b15e2d9a Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sun, 26 Apr 2026 13:52:54 -0500
Subject: [PATCH 23/31] Style for air

---
 R/check_collinearity.R                   | 5 +----
 tests/testthat/test-check_collinearity.R | 4 ++--
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index ef26f2a60..2ae38ca14 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -514,10 +514,7 @@ check_collinearity.zerocount <- function(
 
   # Safely subset the matrix
   if (length(keep_idx) < ncol(v)) {
-    if (
-      !is.null(term_assign) &&
-      length(term_assign) == ncol(v)
-    ) {
+    if (!is.null(term_assign) && length(term_assign) == ncol(v)) {
       term_assign <- term_assign[keep_idx]
     }
     v <- v[keep_idx, keep_idx, drop = FALSE]
diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index fb6aaa91c..1cbd1624e 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -344,11 +344,11 @@ test_that("check_collinearity, ordinal clm models", {
   )
   dat <- data.frame(y_ordinal, x_continuous, x_binary)
   mod_clm <- ordinal::clm(
-    y_ordinal ~ x_continuous + x_binary, 
+    y_ordinal ~ x_continuous + x_binary,
     data = dat
   )
   out <- check_collinearity(mod_clm)
   expect_s3_class(out, "check_collinearity")
   expect_identical(out$Term, c("x_continuous", "x_binary"))
   expect_equal(out$VIF, c(1.11, 1.11), tolerance = 0.05)
-})
\ No newline at end of file
+})

From 4639d89b08ff411ff3c7510e0d3ad5e142b54e2e Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Fri, 1 May 2026 15:58:17 -0500
Subject: [PATCH 24/31] Delete .vscode/settings.json

---
 .vscode/settings.json | 5 -----
 1 file changed, 5 deletions(-)
 delete mode 100644 .vscode/settings.json

diff --git a/.vscode/settings.json b/.vscode/settings.json
deleted file mode 100644
index 9eb545797..000000000
--- a/.vscode/settings.json
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-    "python.autoComplete.extraPaths": [
-        "c:\\Users\\jeffg\\.positron\\extensions\\continue.continue-0.0.412-win32-x64"
-    ]
-}
\ No newline at end of file

From 8e5caa3f5612840e336ecbaa2d3b61e0e101066a Mon Sep 17 00:00:00 2001
From: jmgirard <me@jmgirard.com>
Date: Sat, 2 May 2026 10:53:42 -0500
Subject: [PATCH 25/31] add offset test

---
 tests/testthat/test-check_collinearity.R | 56 ++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index 1cbd1624e..e38f90756 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -352,3 +352,59 @@ test_that("check_collinearity, ordinal clm models", {
   expect_identical(out$Term, c("x_continuous", "x_binary"))
   expect_equal(out$VIF, c(1.11, 1.11), tolerance = 0.05)
 })
+
+test_that("check_collinearity, ordinal clmm models with offset", {
+  skip_if_not_installed("ordinal")
+  set.seed(999)
+  n <- 500
+  x_continuous <- rnorm(n, mean = 0, sd = 1)
+  x_binary <- sample(c(-0.5, 0.5), size = n, replace = TRUE, prob = c(0.85, 0.15))
+  x_offset <- rnorm(n, mean = 0, sd = 0.5)
+  subject_id <- factor(rep(1:50, each = 10))
+  random_intercepts <- rnorm(50, 0, 1)
+  
+  latent_y <- 2 * x_continuous + 3 * x_binary + random_intercepts[as.numeric(subject_id)] + x_offset + rlogis(n)
+  y_ordinal <- cut(latent_y, breaks = 15, ordered_result = TRUE)
+  
+  dat <- data.frame(y_ordinal, x_continuous, x_binary, x_offset, subject_id)
+  
+  mod_clmm_offset <- ordinal::clmm(
+    y_ordinal ~ x_continuous + x_binary + offset(x_offset) + (1 | subject_id),
+    data = dat
+  )
+  
+  out <- check_collinearity(mod_clmm_offset)
+  expect_s3_class(out, "check_collinearity")
+  expect_identical(out$Term, c("x_continuous", "x_binary"))
+  expect_equal(out$VIF, c(1.12, 1.12), tolerance = 0.05)
+})
+
+test_that("check_collinearity, ordinal clm models with offset", {
+  skip_if_not_installed("ordinal")
+  set.seed(999)
+  n <- 500
+  x_continuous <- rnorm(n, mean = 0, sd = 1)
+  x_binary <- sample(c(-0.5, 0.5), size = n, replace = TRUE, prob = c(0.85, 0.15))
+  x_offset <- rnorm(n, mean = 0, sd = 0.5)
+  latent_y <- 2 * x_continuous + 3 * x_binary + x_offset + rlogis(n)
+  y_ordinal <- cut(latent_y, breaks = 15, ordered_result = TRUE)
+  dat <- data.frame(y_ordinal, x_continuous, x_binary, x_offset)
+  mod_clm_offset <- ordinal::clm(
+    y_ordinal ~ x_continuous + x_binary + offset(x_offset),
+    data = dat
+  )
+  out <- check_collinearity(mod_clm_offset)
+  expect_s3_class(out, "check_collinearity")
+  expect_identical(out$Term, c("x_continuous", "x_binary"))
+  expect_equal(out$VIF, c(1.11, 1.11), tolerance = 0.05)
+})
+
+test_that("check_collinearity, standard lm models with offset", {
+  # Standard linear model with an offset
+  m_lm_offset <- lm(mpg ~ wt + cyl + offset(disp), data = mtcars)
+  out <- check_collinearity(m_lm_offset)
+  expect_s3_class(out, "check_collinearity")
+  # The offset should not be evaluated for collinearity
+  expect_identical(out$Term, c("wt", "cyl"))
+  expect_false("disp" %in% out$Term)
+})

From 4a2acab8183254fc72e220243990f4ab1e38a59d Mon Sep 17 00:00:00 2001
From: jmgirard <me@jmgirard.com>
Date: Sat, 2 May 2026 10:54:32 -0500
Subject: [PATCH 26/31] remove sanity check comment

---
 R/check_collinearity.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/check_collinearity.R b/R/check_collinearity.R
index 2ae38ca14..fdb684c2d 100644
--- a/R/check_collinearity.R
+++ b/R/check_collinearity.R
@@ -572,7 +572,6 @@ check_collinearity.zerocount <- function(
   result <- vector("numeric")
   na_terms <- vector("numeric")
 
-  # sanity check - models with offset(?) may contain too many term assignments
   if (length(term_assign) > ncol(v)) {
     term_assign <- term_assign[seq_len(ncol(v))]
   }

From 9f622e94f0fd7f424b729c2a8033db45cbf84dd3 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sat, 2 May 2026 10:55:55 -0500
Subject: [PATCH 27/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index e38f90756..cc9d67425 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -362,8 +362,13 @@ test_that("check_collinearity, ordinal clmm models with offset", {
   x_offset <- rnorm(n, mean = 0, sd = 0.5)
   subject_id <- factor(rep(1:50, each = 10))
   random_intercepts <- rnorm(50, 0, 1)
-  
-  latent_y <- 2 * x_continuous + 3 * x_binary + random_intercepts[as.numeric(subject_id)] + x_offset + rlogis(n)
+
+  latent_y <- 2 *
+    x_continuous +
+    3 * x_binary +
+    random_intercepts[as.numeric(subject_id)] +
+    x_offset +
+    rlogis(n)
   y_ordinal <- cut(latent_y, breaks = 15, ordered_result = TRUE)
   
   dat <- data.frame(y_ordinal, x_continuous, x_binary, x_offset, subject_id)

From d84bf41c2b2f3c06947a25fdf65c98dd03471f9c Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sat, 2 May 2026 10:56:45 -0500
Subject: [PATCH 28/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index cc9d67425..103b39c6c 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -370,7 +370,6 @@ test_that("check_collinearity, ordinal clmm models with offset", {
     x_offset +
     rlogis(n)
   y_ordinal <- cut(latent_y, breaks = 15, ordered_result = TRUE)
-  
   dat <- data.frame(y_ordinal, x_continuous, x_binary, x_offset, subject_id)
   
   mod_clmm_offset <- ordinal::clmm(

From 7311745378e701e2c8852923df4e1408fe76ecd6 Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sat, 2 May 2026 10:57:33 -0500
Subject: [PATCH 29/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index 103b39c6c..57ec9c1f1 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -371,7 +371,6 @@ test_that("check_collinearity, ordinal clmm models with offset", {
     rlogis(n)
   y_ordinal <- cut(latent_y, breaks = 15, ordered_result = TRUE)
   dat <- data.frame(y_ordinal, x_continuous, x_binary, x_offset, subject_id)
-  
   mod_clmm_offset <- ordinal::clmm(
     y_ordinal ~ x_continuous + x_binary + offset(x_offset) + (1 | subject_id),
     data = dat

From 4a1f33e094c67309aa1776b8c66985b7a081eceb Mon Sep 17 00:00:00 2001
From: Jeffrey Girard <me@jmgirard.com>
Date: Sat, 2 May 2026 10:58:23 -0500
Subject: [PATCH 30/31] Style for air

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
---
 tests/testthat/test-check_collinearity.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index 57ec9c1f1..fadd683a6 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -375,7 +375,6 @@ test_that("check_collinearity, ordinal clmm models with offset", {
     y_ordinal ~ x_continuous + x_binary + offset(x_offset) + (1 | subject_id),
     data = dat
   )
-  
   out <- check_collinearity(mod_clmm_offset)
   expect_s3_class(out, "check_collinearity")
   expect_identical(out$Term, c("x_continuous", "x_binary"))

From 56d95564b0873889b8098e27373f702b7f19edf0 Mon Sep 17 00:00:00 2001
From: jmgirard <me@jmgirard.com>
Date: Sat, 2 May 2026 11:02:52 -0500
Subject: [PATCH 31/31] ignore .vscode

---
 .gitignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index ae0593944..270c13cf8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -50,4 +50,5 @@ Network Trash Folder
 Temporary Items
 .apdisk
 .Rprofile
-.positai
+.positai
+.vscode