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Fix correlation crash on NA p-values #449

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Merged
jonathon-love merged 1 commit into from
Jun 17, 2026
Merged

Fix correlation crash on NA p-values #449

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6 changes: 3 additions & 3 deletions R/corrmatrix.b.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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$addSymbol(rowNo=i, paste0(colVarName, '[r]'), '***')
Expand All @@ -168,7 +168,7 @@ corrMatrixClass <- R6::R6Class(
else if (result$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$addSymbol(rowNo=i, paste0(colVarName, '[rho]'), '***')
Expand All @@ -177,7 +177,7 @@ corrMatrixClass <- R6::R6Class(
else if (result$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$addSymbol(rowNo=i, paste0(colVarName, '[tau]'), '***')
Expand Down
12 changes: 8 additions & 4 deletions R/corrpart.b.R
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Expand Up @@ -192,22 +192,26 @@ corrPartClass <- R6::R6Class(
matrix$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)
Expand Down
29 changes: 29 additions & 0 deletions tests/testthat/testcorrmatrix.R
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Expand Up @@ -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)))
})
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