[SOLVED] Bug report when emmeans() is used along with fct_na_value_to

This is an MRE that shows an inconsistency in the use of emmeans() along with fct_na_value_to_level(). It wasn't easy to get the why of the error from my initial code ;)

I prefer to put it here instead on GitHub because I don't know which package can fix the behavior.

What do you think? Thank you

# I was dealing with na values in some factors and I decided to use the fct_na_value_to_level() function
warpbreaks2 <- warpbreaks |> 
  dplyr::mutate(
    tension_na_value = forcats::fct_na_level_to_value(tension, "L"), # just to simulate some missing values in my datatset
    tension_na_level = forcats::fct_na_value_to_level(tension_na_value, "missing"), # I want to make the missing values explicit for my later model
    tension_na_level2 = forcats::fct_na_value_to_level(tension_na_value) # this is another try, without renaming the new explicit level
  )

# For your information
levels(warpbreaks2$tension_na_level)
#> [1] "M"       "H"       "missing"
levels(warpbreaks2$tension_na_level2)
#> [1] "M" "H" NA

# First try : everything is ok
lm(breaks ~ wool * tension_na_level, data = warpbreaks2) |> 
  emmeans::emmeans (~ wool | tension_na_level)
#> tension_na_level = M:
#>  wool emmean   SE df lower.CL upper.CL
#>  A      24.0 3.65 48     16.7     31.3
#>  B      28.8 3.65 48     21.4     36.1
#> 
#> tension_na_level = H:
#>  wool emmean   SE df lower.CL upper.CL
#>  A      24.6 3.65 48     17.2     31.9
#>  B      18.8 3.65 48     11.4     26.1
#> 
#> tension_na_level = missing:
#>  wool emmean   SE df lower.CL upper.CL
#>  A      44.6 3.65 48     37.2     51.9
#>  B      28.2 3.65 48     20.9     35.6
#> 
#> Confidence level used: 0.95

# Second try throws an error. the behaviour of emmeans() is not consistant, but maybe it's an issue with how fct_na_value_to_level() is written?
lm(breaks ~ wool * tension_na_level2, data = warpbreaks2) |> 
  emmeans::emmeans (~ wool | tension_na_level2)
#> Error in X[, nm, drop = FALSE]: indice hors limites

^{Created on 2024-07-08 with reprex v2.1.1}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.1 (2024-06-14)
#>  os       Manjaro Linux
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  C
#>  ctype    fr_FR.UTF-8
#>  tz       Indian/Reunion
#>  date     2024-07-08
#>  pandoc   3.1.11 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/x86_64/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package      * version  date (UTC) lib source
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#>  [1] /home/annadoizy/R/x86_64-pc-linux-gnu-library/4.4
#>  [2] /usr/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Bug report when emmeans() is used along with fct_na_value_to_level()