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Fix eta_squared() when factors have reprex-mathing names #699

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Merged
mattansb merged 2 commits into from
Mar 29, 2026
Merged

Fix eta_squared() when factors have reprex-mathing names #699

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7c0c40b
fix #697
mattansb Mar 27, 2026
1bbeeeb
fix typo
mattansb Mar 29, 2026
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,7 +1,7 @@
Type: Package
Package: effectsize
Title: Indices of Effect Size
Version: 1.0.2
Version: 1.0.2.0000001
Authors@R:
c(person(given = "Mattan S.",
family = "Ben-Shachar",
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6 changes: 6 additions & 0 deletions NEWS.md
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# effectsize 1.0.x

## Bug fixes

- `eta_squared(<afex> / <Anova.mlm>)` with partially overlapping factor names now return correct effect sizes ( #697 )

# effectsize 1.0.2

## New features
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2 changes: 1 addition & 1 deletion R/eta_squared-methods.R
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Expand Up @@ -152,10 +152,10 @@
within_subj <- sapply(within_subj, paste, collapse = ":")
within_subj <- within_subj[order(ns)]
within_subj <- Filter(function(x) nzchar(x, keepNA = TRUE), within_subj)
l <- sapply(within_subj, grepl, x = aov_tab$Parameter, simplify = TRUE)
l <- sapply(paste0("\\b", within_subj, "\\b"), grepl, x = aov_tab$Parameter, simplify = TRUE)
l <- apply(l, 1, function(x) if (any(x)) max(which(x)) else 0)
l <- c(NA, within_subj)[l + 1]
l <- sapply(l, function(x) paste0(stats::na.omit(c(id, x)), collapse = ":"))

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file=R/eta_squared-methods.R,line=158,col=32,[paste_linter] Use paste(), not paste0(), to collapse a character vector when sep= is not used.
aov_tab$Group <- l

aov_tab <- split(aov_tab, aov_tab$Group)
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47 changes: 47 additions & 0 deletions tests/testthat/test-eta_squared.R
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test_that("alternative = NULL", {
m <- aov(mpg ~ factor(cyl) + hp, mtcars)
expect_equal(

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file=tests/testthat/test-eta_squared.R,line=3,col=3,[expect_identical_linter] Use expect_identical(x, y) by default; resort to expect_equal() only when needed, e.g. when setting ignore_attr= or tolerance=.
eta_squared(m),
eta_squared(m, alternative = NULL)
)
Expand Down Expand Up @@ -93,8 +93,8 @@
c(1.360, 0.373, 0.036),
tolerance = 0.001
)
expect_equal(cohens_f(fit, squared = TRUE), cohens_f_squared(fit))

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file=tests/testthat/test-eta_squared.R,line=96,col=3,[expect_identical_linter] Use expect_identical(x, y) by default; resort to expect_equal() only when needed, e.g. when setting ignore_attr= or tolerance=.
expect_equal(cohens_f_squared(fit, squared = FALSE), cohens_f(fit))

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file=tests/testthat/test-eta_squared.R,line=97,col=3,[expect_identical_linter] Use expect_identical(x, y) by default; resort to expect_equal() only when needed, e.g. when setting ignore_attr= or tolerance=.

#### One way-between
expect_message(eta_squared(aov(mpg ~ factor(gear), mtcars)))
Expand All @@ -104,10 +104,10 @@
m <<- aov(mpg ~ factor(gear) + am, mtcars)
et1 <- eta_squared(m)
et2 <- eta_squared(m, ci = 0.9, alternative = "two.sided")
expect_equal(et1$CI_low, et2$CI_low)

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file=tests/testthat/test-eta_squared.R,line=107,col=3,[expect_identical_linter] Use expect_identical(x, y) by default; resort to expect_equal() only when needed, e.g. when setting ignore_attr= or tolerance=.

### parameters:
expect_equal(

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file=tests/testthat/test-eta_squared.R,line=110,col=3,[expect_identical_linter] Use expect_identical(x, y) by default; resort to expect_equal() only when needed, e.g. when setting ignore_attr= or tolerance=.
eta_squared(parameters::model_parameters(m)),
eta_squared(m)
)
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tolerance = 0.001
)

expect_equal(

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file=tests/testthat/test-eta_squared.R,line=152,col=3,[expect_identical_linter] Use expect_identical(x, y) by default; resort to expect_equal() only when needed, e.g. when setting ignore_attr= or tolerance=.
eta_squared(parameters::model_parameters(model)),
eta_squared(model)
)
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rownames(a1) <- a1$Parameter
rownames(a2) <- a2$Parameter

expect_equal(

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file=tests/testthat/test-eta_squared.R,line=186,col=3,[expect_identical_linter] Use expect_identical(x, y) by default; resort to expect_equal() only when needed, e.g. when setting ignore_attr= or tolerance=.
a1[a1$Parameter, "Eta2"],
a2[a1$Parameter, "Eta2"]
)
Expand All @@ -199,12 +199,12 @@
m1 <- lm(mpg ~ am_f * cyl_f, data = mtcars)
m2 <- lm(qsec ~ am_f * cyl_f, data = mtcars)

expect_equal(

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file=tests/testthat/test-eta_squared.R,line=202,col=3,[expect_identical_linter] Use expect_identical(x, y) by default; resort to expect_equal() only when needed, e.g. when setting ignore_attr= or tolerance=.
eta_squared(mod)$Eta2_partial[1:3],
eta_squared(m1)$Eta2_partial
)

expect_equal(

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file=tests/testthat/test-eta_squared.R,line=207,col=3,[expect_identical_linter] Use expect_identical(x, y) by default; resort to expect_equal() only when needed, e.g. when setting ignore_attr= or tolerance=.
eta_squared(mod)$Eta2_partial[4:6],
eta_squared(m2)$Eta2_partial
)
Expand Down Expand Up @@ -779,6 +779,53 @@
expect_equal(A1[c(2:4, 6:7), ], A2[c(2:4, 6:7), -1], ignore_attr = TRUE)
})

test_that("Anova.mlm / afex | overlapping factor names", {
skip_if_not_installed("car")
skip_if_not_installed("afex")

data <- data.frame(
subject = c(1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 9L, 10L, 9L, 10L, 9L, 10L, 9L, 10L),
XBlock = factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), labels = c("a1", "a2")),
Block = factor(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L), labels = c("aa1", "aa2")),
C = factor(c(1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L), labels = c("C_c1", "C_c2")),
y = c(-0.09, -0.29, 0.13, 0.06, 0.17, -0.01, 0.07, 0.27, 0.05, -0.01, -0.07, -0.05, 0.15, 0.12, 0.09, 0.26)
)
contrasts(data$XBlock) <- contr.sum
data$X <- data$XBlock


# list partial eta_squared:
aov_overlap <- afex::aov_ez(
"subject", "y", data,
between = "XBlock",
within = c("Block", "C"),
anova_table = list(es = "pes")
)

aov_nooverlap <- afex::aov_ez(
"subject", "y", data,
between = "X",
within = c("Block", "C"),
anova_table = list(es = "pes")
)

expect_equal(
aov_overlap$anova_table$pes,
eta_squared(aov_overlap)$Eta2_partial
)

expect_equal(
eta_squared(aov_overlap)$Eta2_partial,
eta_squared(aov_nooverlap)$Eta2_partial
)

expect_equal(
eta_squared(aov_overlap)$Eta2_partial,
eta_squared(aov_overlap$Anova)$Eta2_partial
)
})


## merMod --------------------

test_that("merMod and lmerModLmerTest", {
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