geom_pwc() with emmeans_test method

[DariuszMajerek]

During my research I encounter an issue with geom_pwc() with emmeans_test method when I want to extract means from defined lmer model. Let say I build the following model:

library(ggpubr)
library(tidyverse)
library(rstatix)
library(datarium)
library(lme4)

df_long <- anxiety %>% 
  pivot_longer(cols = t1:t3, names_to = "time", values_to = "score")

mod <- lmer(score ~ group * time + (1 | id), data = df_long)

I want to estimate marginal means by:

emmeans_test(df_long, ~ group, ref.group = "grp1", model = mod)

the result is following:

NOTE: Results may be misleading due to involvement in interactions
# A tibble: 2 × 9
  term  .y.   group1 group2    df statistic       p  p.adj p.adj.signif
* <chr> <chr> <chr>  <chr>  <dbl>     <dbl>   <dbl>  <dbl> <chr>       
1 group group grp1   grp2    42.0      1.11 0.272   0.543  ns          
2 group group grp1   grp3    42.0      2.92 0.00557 0.0111 *  

But when I try to plot the results of test on boxplot I have a problem. Let say I do it in this way:

df_long %>% 
  ggboxplot(x = "group", y = "score", color = "group")+
  geom_pwc(method = "emmeans_test", ref.group = "grp1")

this gives me

which is wrong with the comparison with the results of the tests. So I tried:

df_long %>% 
  ggboxplot(x = "group", y = "score", color = "group")+
  geom_pwc(method = "emmeans_test", ref.group = "grp1",
           method.args = list(model = mod))

and this gives me the following error:

Warning message:
Computation failed in `stat_pwc()`.
Caused by error in `emmeans::emmeans()`:
! No variable named x in the reference grid

Please help :)

session_info()

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.0 (2024-04-24)
 os       macOS Sonoma 14.5
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Warsaw
 date     2024-06-03
 rstudio  2024.04.1+748 Chocolate Cosmos (desktop)
 pandoc   3.1.11 @ /opt/homebrew/bin/pandoc

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package      * version  date (UTC) lib source
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 [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library