R: Markdown or HTML markup in `gtsummary` tables

Question

I have a table with variable names usually spelt with superscript or subscript numbers. I'm using R package {gtsummary} to automatically create the table from select columns of a data frame/tibble.

Say this is the tibble:

library(nycflights13)

lm_1 <- lm(arr_delay ~ air_time, flights)

tbl_1 <- tbl_regression(lm_1, exponentiate = F,
                        label = list(
                            air_time ~ "Air Time"
                        )) %>% 
    add_glance_source_note(include = c('r.squared'))

tbl_1

… but I need to write this as Air^time (HTML Air^time or Markdown Air~time~).

In {gtsummary}, specifying the label argument in HTML or Markdown doesn't work for me:

tbl_1 <- tbl_regression(lm_1, exponentiate = F,
                        label = list(
                            air_time ~ "Air^time",
                            sched_dep_time ~ "Departure^time^"
                        )) %>% 
    add_glance_source_note(include = c('r.squared'))

I've tried wrapping the strings in gt::html() or gt::md() but it didn't change anything:

tbl_1 <- tbl_regression(lm_1, exponentiate = F,
                        label = list(
                            air_time ~ html("Air^time"),
                            sched_dep_time ~ md("Departure^time^")
                        )) %>% 
    add_glance_source_note(include = c('r.squared'))

Would it be possible to use HTML and/or Markdown in gtsummary tables? Thanks!

user_8711276 · Answer

To 100% honest, I don't know why this solution works...but it does! The {gt} package has a function called fmt_markdown() that is meant to convert markdown syntax to the specified output type. BUT in your example, the markdown superscript is not recognized (more on why here https://github.com/rstudio/gt/issues/129#issuecomment-663753251). BUUUUT, when I apply that function to your HTML tag superscripts, they are recognized and you get the output you're looking for.

library(gtsummary)
library(nycflights13)

lm_1 <- lm(arr_delay ~ air_time + sched_dep_time , flights)

tbl_regression(lm_1, 
               label = list(air_time ~ "Air^time",
                            sched_dep_time ~ "Departure^time")) %>% 
  add_glance_source_note(include = 'r.squared') %>%
  as_gt() %>%
  gt::fmt_markdown(columns = vars(label))

R: Markdown or HTML markup in `gtsummary` tables

1 Answers