From a2d7c6449d18764dcb6c6b62e1dd7df74047287c Mon Sep 17 00:00:00 2001
From: Jonathan Sulc <jonsulc@gmail.com>
Date: Wed, 3 Jun 2026 16:22:30 +0200
Subject: [PATCH] Fix yeojohnson lambda estimate ignoring missing values

estimate_yeojohnson_lambda computed n with length(x) before dropping
NAs, so the count of "observations" included missing values. That
inflated n in the log-likelihood, shifting the optimized lambda.
Appending NAs to a vector therefore changed the estimated lambda.

Compute n after removing missing values so the log-likelihood uses the
number of nonmissing observations. Add a regression test asserting the
estimated lambda is unchanged when NAs are appended.
---
 DESCRIPTION                      | 2 +-
 R/yeojohnson.R                   | 2 +-
 tests/testthat/test_yeojohnson.R | 7 +++++++
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8326fdb..ce3476e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: bestNormalize
 Type: Package
 Title: Normalizing Transformation Functions
-Version: 1.9.2
+Version: 1.9.3
 Date: 2025-11-29
 Authors@R: person("Ryan A", "Peterson", 
                   email = "ryan-peterson@uiowa.edu", 
diff --git a/R/yeojohnson.R b/R/yeojohnson.R
index e70f1d2..c24756c 100644
--- a/R/yeojohnson.R
+++ b/R/yeojohnson.R
@@ -126,9 +126,9 @@ print.yeojohnson <- function(x, ...) {
 # Helper functions that estimates yj lambda parameter
 #' @importFrom stats var optimize
 estimate_yeojohnson_lambda <- function(x, lower = -5, upper = 5, eps = .001, ...) {
-  n <- length(x)
   ccID <- !is.na(x)
   x <- x[ccID]
+  n <- length(x)
   pos_idx = which(x >= 0)
   neg_idx = which(x < 0)
   
diff --git a/tests/testthat/test_yeojohnson.R b/tests/testthat/test_yeojohnson.R
index e50cb4f..b1c2302 100644
--- a/tests/testthat/test_yeojohnson.R
+++ b/tests/testthat/test_yeojohnson.R
@@ -33,6 +33,13 @@ test_that('yeojohnson correctly handles missing new data', {
   expect_equal(as.numeric(NA), predict(b, newdata = c(1, NA), inverse = TRUE)[2])
 })
 
+test_that('yeojohnson lambda is unaffected by appended missing values', {
+  expect_equal(
+    yeojohnson(train)$lambda,
+    yeojohnson(c(train, NA, NA, NA))$lambda
+  )
+})
+
 # without standardization
 
 yeojohnson_obj <- yeojohnson(train, standardize = FALSE)