rstatix package anova_test function gives partial eta squared despite setting effect.size = 'ges'

Question

I am not able to obtain eta squared, only partial eta squared, when I use rstatix::anova_test.

Example from the iris dataset:

First using aov:

aov <- aov(Sepal.Length ~ Sepal.Width + Species, data = iris)
summary(aov)
             Df Sum Sq Mean Sq F value  Pr(>F)    
Sepal.Width   1   1.41    1.41   7.363 0.00746 ** 
Species       2  72.75   36.38 189.651 < 2e-16 ***
Residuals   146  28.00    0.19      

Then using sjstats::eta_sq, if I choose partial = TRUE or FALSE I get a different effect size, as I would expect.

eta_sq(aov, partial = FALSE) 
         term etasq
1 Sepal.Width 0.014
2     Species 0.712

eta_sq(aov, partial = TRUE)
         term partial.etasq
1 Sepal.Width         0.048
2     Species         0.722

However, when I do the same in anova_test, I get the partial eta squared both times regardless of whether the effect size is pes or ges, both times it's the partial eta squared:

aov_pes <- iris %>% anova_test(Sepal.Length ~ Sepal.Width + Species,
                               detailed = T,
                               effect.size = "pes")
get_anova_table(aov_pes)

       Effect    SSn    SSd DFn DFd       F        p p<.05
1 Sepal.Width 10.953 28.004   1 146  57.102 4.19e-12     *
2     Species 72.752 28.004   2 146 189.651 2.56e-41     *
    pes
1 0.281
2 0.722

aov_ges <- iris %>% anova_test(Sepal.Length ~ Sepal.Width + Species,
                               detailed = T,
                               effect.size = "ges")
get_anova_table(aov_ges)

       Effect    SSn    SSd DFn DFd       F        p p<.05
1 Sepal.Width 10.953 28.004   1 146  57.102 4.19e-12     *
2     Species 72.752 28.004   2 146 189.651 2.56e-41     *
    ges
1 0.281
2 0.722

Does anyone know why this is? Thanks!

Answer 1

Answer

rstatix::anova_test seems to contain a mistake in the calculation! I would be very, very careful with this function.

Note that eta_sq is deprecated, and effectsize::eta_squared should be used.

---

Proper calculation

We have three SS values: 1.412238, 72.752431, and 28.003665. We can calculate the pes and ges:

• pes: 1.412238 / (1.412238 + 28.003665)
• ges: 1.412238 / (1.412238 + 72.752431 + 28.003665)

---

anova_test

Under the hood, anova_test calls two functions for pes and ges calculation:

• pes: rstatix:::add_partial_eta_squared
• ges: rstatix:::add_generalized_eta_squared

---

The pes calculation by anova_test

res.anova.summary$ANOVA %>% mutate(pes = .data$SSn/(.data$SSn + .data$SSd))

This indeed calculates the pes as we expect it to.

---

The ges calculation by anova_test

aov.table <- res.anova.summary$ANOVA
aov.table %>% mutate(ges = .data$SSn/(.data$SSn + sum(unique(.data$SSd)) + obs.SSn1 - obs.SSn2))

Here, we run into a problem. This code seems blatantly incorrect. It just divides each sum of square value by itself + the residual sum of squares (28.004). That is the pes, not the ges.

You could contact the maintainer of the package (maintainer("rstatix")) or create a new issue for the rstatix package here.