Incorrect eta^2 for afex objects when factor names overlap #697

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1. mattansb

   added a commit that references this issue on Mar 27, 2026

   fix #697

   This issue will close once commit 7c0c40b is merged into the 'main' branch.

   7c0c40b
2. mattansb commented on Mar 27, 2026

   

   mattansb

   on Mar 27, 2026

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   Well that was a fun puzzle!

   library(Superpower)
   #> Warning: package 'Superpower' was built under R version 4.5.3
   #> Registered S3 method overwritten by 'lme4':
   #>   method           from
   #>   na.action.merMod car
   library(afex)
   #> Loading required package: lme4
   #> Loading required package: Matrix
   #> ************
   #> Welcome to afex. For support visit: http://afex.singmann.science/
   #> - Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
   #> - Methods for calculating p-values with mixed(): 'S', 'KR', 'LRT', and 'PB'
   #> - 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests
   #> - Get and set global package options with: afex_options()
   #> - Set sum-to-zero contrasts globally: set_sum_contrasts()
   #> - For example analyses see: browseVignettes("afex")
   #> ************
   #> 
   #> Attaching package: 'afex'
   #> The following object is masked from 'package:lme4':
   #> 
   #>     lmer
   library(effectsize)
   set.seed(2123)
   # create data set:
   aov.3way.design <- ANOVA_design(design = "2b*2w*2w",
                                   n=20,
                                   mu=0.025*c(-1,-1,-1,-1,1,1,1,1) + 0.05*c(-1,-1,1,1,-1,-1,1,1) + 0.05*c(-1,1,-1,1,-1,1,-1,1) + 0.05*c(-1,1,1,-1,-1,1,1,-1) + 0.05*c(-1,1,1,-1,1,-1,-1,1) + 0.05*c(-1,1,-1,1,1,-1,1,-1) + 0.05*c(-1,-1,1,1,1,-1,-1,1),
                                   sd=0.15,
                                   r=0.6,
                                   plot=FALSE,
                                   labelnames=c("XBlock","a1","a2","Block","aa1","aa2","C","c1","c2"))
   #> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
   #> ℹ Please use tidy evaluation idioms with `aes()`.
   #> ℹ See also `vignette("ggplot2-in-packages")` for more information.
   #> ℹ The deprecated feature was likely used in the Superpower package.
   #>   Please report the issue at
   #>   <https://github.com/arcaldwell49/Superpower/issues>.
   #> This warning is displayed once per session.
   #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
   #> generated.
   #> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
   #> ℹ Please use `linewidth` instead.
   #> ℹ The deprecated feature was likely used in the Superpower package.
   #>   Please report the issue at
   #>   <https://github.com/arcaldwell49/Superpower/issues>.
   #> This warning is displayed once per session.
   #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
   #> generated.
   aov.exact.01b <- ANOVA_exact(aov.3way.design,verbose=F)
   dat1b <- aov.exact.01b$dataframe
   dat1b$y <- dat1b$y+rnorm(n=dim(dat1b)[1],0,0.01)
   
   # list partial eta_squared:
   aov.01b <- aov_ez(id = "subject", dv = "y", between = "XBlock", within = c("Block", "C"), data = dat1b, anova_table = list(es = "pes"))
   #> Contrasts set to contr.sum for the following variables: XBlock
   
   tibble::tibble(
     term = afex::nice(aov.01b)$Effect
     , afex = aov.01b$anova_table$pes
     , effectsize_anova_table = effectsize::eta_squared(aov.01b$anova_table, partial = TRUE)$Eta2_partial
     , effectsize_Anova = effectsize::eta_squared(aov.01b, partial = TRUE)$Eta2_partial
     # , effectsize_Anova = effectsize::eta_squared(aov.01b$Anova, partial = TRUE)$Eta2_partial
     , diff = afex - effectsize_Anova
   ) |>
     as.data.frame()
   #>             term       afex effectsize_anova_table effectsize_Anova diff
   #> 1         XBlock 0.03913943             0.03913943       0.03913943    0
   #> 2          Block 0.72727054             0.72727054       0.72727054    0
   #> 3   XBlock:Block 0.24689135             0.24689135       0.24689135    0
   #> 4              C 0.52735804             0.52735804       0.52735804    0
   #> 5       XBlock:C 0.53255624             0.53255624       0.53255624    0
   #> 6        Block:C 0.23034705             0.23034705       0.23034705    0
   #> 7 XBlock:Block:C 0.71927298             0.71927298       0.71927298    0

   ^{Created on 2026-03-27 with reprex v2.1.1}
3. mattansb commented on Mar 27, 2026

   

   mattansb

   on Mar 27, 2026

   Member

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   Fixed in #699
4. mattansb

   closed this as completedin d431017on Mar 29, 2026
5. mattansb

   added

   bug 🐜Something isn't workingSomething isn't working

   on Mar 29, 2026