gtsummmary::modify_header() with overall column - r

Question

I would like to modify the column header formatting in a {gtsummary} table with a categorical varible (two levels) and an overall column, as in With gtsummary, is it possible to have N on a separate row to the column name?. I'm having trouble figuring out the correct gtsummary variable name to access the various column names. I currently have a workaround in which I first modify the categorical levels headers, and then add the overall and modify it. However, I'm wondering if there is a better way to do this in a single modify_header line. Reprex with various attempts below.
library(gtsummary)
library(dplyr)
# Shorten trial for examples
trial <- select(trial, trt, age)
# Modify headers
trial %>%
tbl_summary(by = trt) %>%
modify_header(update = all_stat_cols() ~ "**{level}**<br>N = {N}") %>%
as_kable()
Characteristic
Drug AN = 200
Drug BN = 200
Age
46 (37, 59)
48 (39, 56)
Unknown
7
4
# Adding overall before modifying stats columns doesn't work with {level} or {label}
try(
trial %>%
tbl_summary(by = trt) %>%
add_overall() %>%
modify_header(update = all_stat_cols() ~ "**{level}**<br>N = {N}") %>%
as_kable()
)
#> Error in eval(parse(text = text, keep.source = FALSE), envir) :
#> object 'level' not found
try(
trial %>%
tbl_summary(by = trt) %>%
add_overall() %>%
modify_header(update = all_stat_cols() ~ "**{label}**<br>N = {N}") %>%
as_kable()
)
#> Error in eval(parse(text = text, keep.source = FALSE), envir) :
#> object 'label' not found
# Adding overall before modifying stats columns does work with plain text
trial %>%
tbl_summary(by = trt) %>%
add_overall() %>%
modify_header(update = all_stat_cols() ~ "**THIS WORKS**<br>N = {N}") %>%
as_kable()
Characteristic
THIS WORKSN = 200
THIS WORKSN = 200
THIS WORKSN = 200
Age
47 (38, 57)
46 (37, 59)
48 (39, 56)
Unknown
11
7
4
# And with {column} but then gives the gtsummary backend column name
trial %>%
tbl_summary(by = trt) %>%
add_overall() %>%
modify_header(update = all_stat_cols() ~ "**{column}**<br>N = {N}") %>%
as_kable()
Characteristic
stat_0N = 200
stat_1N = 200
stat_2N = 200
Age
47 (38, 57)
46 (37, 59)
48 (39, 56)
Unknown
11
7
4
# Adding overall after modifying stats columns does work, but need to change label separately
trial %>%
tbl_summary(by = trt) %>%
modify_header(update = all_stat_cols() ~ "**{level}**<br>N = {N}") %>%
add_overall(col_label = "**Overall**<br>N = {N}") %>%
as_kable()
Characteristic
OverallN = 200
Drug AN = 200
Drug BN = 200
Age
47 (38, 57)
46 (37, 59)
48 (39, 56)
Unknown
11
7
4
Created on 2021-08-20 by the reprex package (v2.0.0)

Answer 1

The issue you are running into is that all_stat_cols(), by default, selects the overall column and the other columns. Depending on whether you're assigning a label to the overall or split columns, you'll want to use slightly different syntax.
Example below!
library(gtsummary)
tbl <-
trial %>%
select(trt, age) %>%
tbl_summary(by = trt, missing = "no") %>%
add_overall() %>%
modify_header(
update = list(all_stat_cols(FALSE) ~ "**{level}**<br>N = {n}",
stat_0 ~ "**Overall**<br>N = {N}"))
show_header_names(tbl)
#> i As a usage guide, the code below re-creates the current column headers.
#> modify_header(update = list(
#> label ~ "**Characteristic**",
#> stat_0 ~ "**Overall**<br>N = 200",
#> stat_1 ~ "**Drug A**<br>N = 98",
#> stat_2 ~ "**Drug B**<br>N = 102"
#> ))
#>
#>
#> Column Name Column Header
#> ------------ -----------------------
#> label **Characteristic**
#> stat_0 **Overall**<br>N = 200
#> stat_1 **Drug A**<br>N = 98
#> stat_2 **Drug B**<br>N = 102
Created on 2021-08-20 by the reprex package (v2.0.1)