When a reference row is added, rather than creating a new term <code class="notranslat

OK it has been fixed: <div class="snippet-clipboard-content notranslate position-r

Update the new term for reference rows about broom.helpers HOT 3 CLOSED

ddsjoberg commented on July 19, 2024

Update the new term for reference rows

from broom.helpers.

Comments (3)

larmarange commented on July 19, 2024 1

Should be noted, that then you specify manually a treatment contrast, R is not using anymore the level but the position of it. But it remains explicit and the label column is still correct.

library(broom.helpers)
library(gtsummary)

mod <- glm(age ~ grade, data = trial, family = gaussian, contrasts = list(grade = contr.treatment(3, base = 2)))

mod %>%
  tidy_and_attach() %>%
  tidy_identify_variables() %>%
  tidy_add_variable_labels() %>%
  tidy_add_reference_rows() %>%
  tidy_add_header_rows() %>% 
  select(variable, term, reference_row, label, header_row)

#> # A tibble: 5 x 5
#>   variable term        reference_row label       header_row
#>   <chr>    <chr>       <lgl>         <chr>       <lgl>     
#> 1 <NA>     (Intercept) NA            (Intercept) NA        
#> 2 grade    <NA>        NA            Grade       TRUE      
#> 3 grade    grade1      FALSE         I           FALSE     
#> 4 grade    gradeII     TRUE          II          FALSE     
#> 5 grade    grade3      FALSE         III         FALSE

from broom.helpers.

larmarange commented on July 19, 2024

The issue with "gradeI" is that naming convention is valid only for contr.treatment, while contr.sum and contr.SAS adopt another approach (with the number instead of the level instead of its value).

However, should be possible to do something. I just need to reread properly the code

from broom.helpers.

larmarange commented on July 19, 2024

OK it has been fixed:

library(broom.helpers)
library(gtsummary)

mod <- glm(age ~ grade, data = trial, family = gaussian)

mod %>%
  tidy_and_attach() %>%
  tidy_identify_variables() %>%
  tidy_add_variable_labels() %>%
  tidy_add_reference_rows() %>%
  tidy_add_header_rows() %>% 
  select(variable, term, reference_row, label, header_row)
#> # A tibble: 5 x 5
#>   variable term        reference_row label       header_row
#>   <chr>    <chr>       <lgl>         <chr>       <lgl>     
#> 1 <NA>     (Intercept) NA            (Intercept) NA        
#> 2 grade    <NA>        NA            Grade       TRUE      
#> 3 grade    gradeI      TRUE          I           FALSE     
#> 4 grade    gradeII     FALSE         II          FALSE     
#> 5 grade    gradeIII    FALSE         III         FALSE

from broom.helpers.

Recommend Projects