From c3e85d46f41c2a1b6625916fe9d2deb00b677361 Mon Sep 17 00:00:00 2001
From: Ravi Selker <selker.ravi@gmail.com>
Date: Wed, 10 Jun 2026 17:15:08 +0200
Subject: [PATCH] Fix correlation crash on NA p-values

Constant or degenerate inputs make cor.test return an NA
p-value, which broke the significance-flag comparisons and
aborted the whole table. Skip flagging when the p-value is
missing.
---
 R/corrmatrix.b.R                |  6 +++---
 R/corrpart.b.R                  | 12 ++++++++----
 tests/testthat/testcorrmatrix.R | 29 +++++++++++++++++++++++++++++
 3 files changed, 40 insertions(+), 7 deletions(-)

diff --git a/R/corrmatrix.b.R b/R/corrmatrix.b.R
index 964c2cd3..6363a1b4 100644
--- a/R/corrmatrix.b.R
+++ b/R/corrmatrix.b.R
@@ -159,7 +159,7 @@ corrMatrixClass <- R6::R6Class(
                         matrix$addFootnote(rowNo=i, paste0(colVarName, '[r]'), .('Pearson correlation cannot be calculated for non-numeric values'))
 
                     if (flag) {
-                        if ( ! self$options$pearson || mtord)
+                        if ( ! self$options$pearson || mtord || is.na(result$rp))
                             {}  # do nothing
                         else if (result$rp < .001)
                             matrix$addSymbol(rowNo=i, paste0(colVarName, '[r]'), '***')
@@ -168,7 +168,7 @@ corrMatrixClass <- R6::R6Class(
                         else if (result$rp < .05)
                             matrix$addSymbol(rowNo=i, paste0(colVarName, '[r]'), '*')
 
-                        if ( ! self$options$spearman)
+                        if ( ! self$options$spearman || is.na(result$rhop))
                             {}  # do nothing
                         else if (result$rhop < .001)
                             matrix$addSymbol(rowNo=i, paste0(colVarName, '[rho]'), '***')
@@ -177,7 +177,7 @@ corrMatrixClass <- R6::R6Class(
                         else if (result$rhop < .05)
                             matrix$addSymbol(rowNo=i, paste0(colVarName, '[rho]'), '*')
 
-                        if ( ! self$options$kendall)
+                        if ( ! self$options$kendall || is.na(result$taup))
                             {}  # do nothing
                         else if (result$taup < .001)
                             matrix$addSymbol(rowNo=i, paste0(colVarName, '[tau]'), '***')
diff --git a/R/corrpart.b.R b/R/corrpart.b.R
index 889e6e37..d2cd2ffb 100644
--- a/R/corrpart.b.R
+++ b/R/corrpart.b.R
@@ -192,22 +192,26 @@ corrPartClass <- R6::R6Class(
                         matrix$setRow(rowNo=i, values)
 
                         if (flag) {
-                            if (result$rp < .001)
+                            if (is.na(result$rp))
+                                {}  # do nothing
+                            else if (result$rp < .001)
                                 matrix$addSymbol(rowNo=i, paste0(colVarName, '[r]'), '***')
                             else if (result$rp < .01)
                                 matrix$addSymbol(rowNo=i, paste0(colVarName, '[r]'), '**')
                             else if (result$rp < .05)
                                 matrix$addSymbol(rowNo=i, paste0(colVarName, '[r]'), '*')
 
-                            if (result$rhop < .001)
+                            if (is.na(result$rhop))
+                                {}  # do nothing
+                            else if (result$rhop < .001)
                                 matrix$addSymbol(rowNo=i, paste0(colVarName, '[rho]'), '***')
                             else if (result$rhop < .01)
                                 matrix$addSymbol(rowNo=i, paste0(colVarName, '[rho]'), '**')
                             else if (result$rhop < .05)
                                 matrix$addSymbol(rowNo=i, paste0(colVarName, '[rho]'), '*')
 
-                            if ( ! self$options$kendall)
-                            {}  # do nothing
+                            if ( ! self$options$kendall || is.na(result$taup))
+                                {}  # do nothing
                             else if (result$taup < .001)
                                 matrix$addSymbol(rowNo=i, paste0(colVarName, '[tau]'), '***')
                             else if (result$taup < .01)
diff --git a/tests/testthat/testcorrmatrix.R b/tests/testthat/testcorrmatrix.R
index dc09462d..69067c8d 100644
--- a/tests/testthat/testcorrmatrix.R
+++ b/tests/testthat/testcorrmatrix.R
@@ -123,3 +123,32 @@ testthat::test_that('All options in the corrMatrix work (sunny)', {
     testthat::expect_equal(13, as.numeric(corTable$getCell(rowKey="var 3", "var 1[n]")$value))
     testthat::expect_equal(11, as.numeric(corTable$getCell(rowKey="var 3", "var 2[n]")$value))
 })
+
+testthat::test_that('corrMatrix does not error on NaN p-values with flagging enabled', {
+    # GIVEN a variable paired with a constant column (zero variance), which
+    # makes cor.test return an NA p-value
+    df <- data.frame(
+        `var 1` = c(8, 51, 2, 74, 1, 91, 5, 25, 1, 59, 5, 32, 7),
+        `constant` = rep(3, 13),
+        check.names = FALSE
+    )
+
+    # WHEN we run a correlation with significance flagging enabled
+    # THEN the analysis should not error (the flag logic used to do
+    # `if (p < .001)` on NA and crash with "missing value where TRUE/FALSE needed")
+    testthat::expect_error(
+        r <- jmv::corrMatrix(
+            data = df,
+            vars = c("var 1", "constant"),
+            pearson = TRUE,
+            spearman = TRUE,
+            kendall = TRUE,
+            flag = TRUE
+        ),
+        regexp = NA
+    )
+
+    # AND the degenerate correlation should be reported as a missing value
+    corTable <- r$matrix
+    testthat::expect_true(is.na(as.numeric(corTable$getCell(rowKey="constant", "var 1[rho]")$value)))
+})