tbl_merge: sort variables alphabetically in merged tbl_regression models {gtsummary}-CodePudding

Consider the example below:

library(tidyverse)
library(gtsummary)

    t1 <- trial %>%
      na.exclude() %>%
      lm(marker ~ age   ttdeath, .) %>%
      tbl_regression()
    t2 <- trial %>%
      na.exclude() %>%
      lm(marker ~ age   response   death, .) %>%
      tbl_regression()
    t3 <- trial %>%
      na.exclude() %>%
      lm(marker ~ age   stage   death, .) %>%
      tbl_regression()
    t4 <- trial %>%
      na.exclude() %>%
      lm(marker ~ stage   grade   death, .) %>%
      tbl_regression()
    
    tbl_merge(list(t1, t2, t3 ,t4))

In the characteristic tab, variables are only alphabetically within a particular model. For example, when looking only at Table 1 is fine, it's A-M-T.

However, when looking at mutiple tables at once, the order is not alphabetical. Is there a way to sort variables alphabetically within all the tables?

E.g. Age, Grade, Months to Death/Censor, Patient Died...

I assume the way to do this is by gtsummary::modify_table_body into dplyr::arrange, but I don't know how to do it exactly.

Any help would be appreciated. Thanks in advance.

Edit: actually, anyway to manually modify the order of variables would be helpful as well, ignore this if it's too difficult.

Edit2: I forgot to mention that there's glance statistics involved as well, such as add_glance_table(adj.r.squared) %>% modify_table_body(~.x %>% arrange(row_type == "glance_statistic")) (which is not in this example), so I imagine there is a possibility that the sorting of variables messes with the order of glance statistics as well. Excuse me for making this complicated, but it would be extremely helpful.

CodePudding user response：

You're correct that modify_table_body() is the way to go. You'll first want to arrange the order to put the glance table at the bottom, then you arrange by "var_label" to put the variables in alphabetical order. "var_label" is a column in .$table_body. Example below!

library(gtsummary)
packageVersion("gtsummary")
#> [1] '1.5.0'

t1 <- trial %>%
  lm(marker ~ age   ttdeath, .) %>%
  tbl_regression() %>%
  add_glance_table(adj.r.squared)
t2 <- trial %>%
  lm(marker ~ age   response   death, .) %>%
  tbl_regression() %>%
  add_glance_table(adj.r.squared)
t3 <- trial %>%
  lm(marker ~ age   stage   death, .) %>%
  tbl_regression() %>%
  add_glance_table(adj.r.squared)
t4 <- trial %>%
  lm(marker ~ stage   grade   death, .) %>%
  tbl_regression() %>%
  add_glance_table(adj.r.squared)

tbl <- 
  tbl_merge(list(t1, t2, t3 ,t4)) %>%
  modify_table_body(
    ~.x %>% 
      dplyr::arrange(
        row_type == "glance_statistic", # sort glance table to bottom
        var_label                       # sort by the variable label (a hidden column) 
      )
  )

^{Created on 2021-12-19 by the}