Grouping Rows in GTSummary

Question

I am trying to group some rows/variables (both categorical and continuous) to help with the table readability in a large dataset.

Here is the dummy dataset:

library(gtsummary)
library(tidyverse)
library(gt)
set.seed(11012021)

# Create Dataset
PIR <- 
  tibble(
    siteidn = sample(c("1324", "1329", "1333", "1334"), 5000, replace = TRUE, prob = c(0.2, 0.45, 0.15, 0.2)) %>% factor(),
    countryname = sample(c("NZ", "Australia"), 5000, replace = TRUE, prob = c(0.3, 0.7)) %>% factor(),
    hospt = sample(c("Metropolitan", "Rural"), 5000, replace = TRUE, prob = c(0.65, 0.35)) %>% factor(),
    age = rnorm(5000, mean = 60, sd = 20),
    apache2 = rnorm(5000, mean = 18.5, sd=10),
    apache3 = rnorm(5000, mean = 55, sd=20),
    mechvent = sample(c("Yes", "No"), 5000, replace = TRUE, prob = c(0.4, 0.6)) %>% factor(),
    sex = sample(c("Female", "Male"), 5000, replace = TRUE) %>% factor(),
    patient = TRUE
  ) %>%
  mutate(patient_id = row_number())%>% 
  group_by(
    siteidn) %>% mutate(
      count_site = row_number() == 1L) %>%
  ungroup()%>% 
  group_by(
    patient_id) %>% mutate(
      count_pt = row_number() == 1L) %>%
  ungroup()

Then I use the following code to generate my table:

t1 <- PIR %>% 
  select(patientn = count_pt, siten = count_site, age, sex, apache2, apache3,  apache2, mechvent, countryname) %>% 
  tbl_summary(
    by = countryname,
    missing = "no", 
    statistic = list(
      patientn ~ "{n}",
      siten ~ "{n}",
      age ~ "{mean} ({sd})",
      apache2 ~ "{mean} ({sd})",
      mechvent ~ "{n} ({p}%)",
      sex ~ "{n} ({p}%)",
      apache3 ~ "{mean} ({sd})"),
    label = list(
      siten = "Number of ICUs",
      patientn = "Number of Patients",
      age = "Age",
      apache2 = "APACHE II Score",
      mechvent = "Mechanical Ventilation",
      sex = "Sex",
      apache3 = "APACHE III Score")) %>% 
  modify_header(stat_by = "**{level}**") %>%
  add_overall(col_label = "**Overall**")
  
t2 <- PIR %>% 
  select(patientn = count_pt, siten = count_site, age, sex, apache2, apache3,  apache2, mechvent, hospt) %>% 
  tbl_summary(
    by = hospt,
    missing = "no", 
     statistic = list(
      patientn ~ "{n}",
      siten ~ "{n}",
      age ~ "{mean} ({sd})",
      apache2 ~ "{mean} ({sd})",
      mechvent ~ "{n} ({p}%)",
      sex ~ "{n} ({p}%)",
      apache3 ~ "{mean} ({sd})"),
    label = list(
      siten = "Number of ICUs",
      patientn = "Number of Patients",
      age = "Age",
      apache2 = "APACHE II Score",
      mechvent = "Mechanical Ventilation",
      sex = "Sex",
      apache3 = "APACHE III Score")) %>%  
  modify_header(stat_by = "**{level}**")

tbl <-
  tbl_merge(
    tbls = list(t1, t2),
    tab_spanner = c("**Country**", "**Hospital Type**")
  ) %>%
  modify_spanning_header(stat_0_1 ~ NA) %>%
  modify_footnote(everything() ~ NA)

This produces the following table:

I would like to group certain rows together for ease of reading. Ideally, I would like the table to look like this:

I have attempted using the gt package, with the following code:

tbl <-
  tbl_merge(
    tbls = list(t1, t2),
    tab_spanner = c("**Country**", "**Hospital Type**")
  ) %>%
  modify_spanning_header(stat_0_1 ~ NA) %>%
  modify_footnote(everything() ~ NA) %>% 
as_gt() %>%  
  gt::tab_row_group(
    group = "Severity of Illness Scores",
    rows = 7:8) %>%  
  gt::tab_row_group(
    group = "Patient Demographics",
    rows = 3:6) %>%  
  gt::tab_row_group(
    group = "Numbers",
    rows = 1:2)

This produces the desired table:

There are a couple of issues I'm having with the way that I'm doing this.

1. When I try to use the row names (variables), an error message comes up (Can't subset columns that don't exist...). Is there a way to do this by using the variable names? With larger tables, I am getting into some trouble with using the row numbers method of assigning row names. This is particularly true when there is a single variable that loses its place as it's moved to the end to account for the grouped rows.

2. Is there a way to do this prior to piping into tbl_summary? Although I like the output of this table, I use Word as my output document for statistical reports and would like the ability to be able to format the tables in Word if need be (or by my collaborators). I usually use gtsummary::as_flextable for table output.

Thanks again,

Ben

Answer 1

I think I might have a solution for this (thanks, obviously, to Daniel Sjoberg and team providing us with the modify_table_body function)

All you need to do is edit the underlying data frame to add a variable with your desired grouping row using modify_table_body, and then put it in the position you want it to be in, like this:

library(gtsummary)
library(dplyr)
packageVersion("gtsummary")

trial%>%
 select(age, stage, grade)%>%
 tbl_summary()%>%
 modify_table_body(
  ~.x %>% 
  
  # add your variable
  rbind(
    tibble(
      variable="Demographics",
      var_type=NA,
      var_label = "Demographics",
      row_type="label",
      label="Demographics",
      stat_0= NA))%>% # expand the components of the tibble as needed if you have more columns
  
  # can add another one
    rbind(
      tibble(
        variable="Tumor characteristics",
        var_type=NA,
        var_label = "Tumor characteristics",
        row_type="label",
        label="Tumor characteristics",
        stat_0= NA))%>%  
    
  # specify the position you want these in
    
  arrange(factor(variable, levels=c("Demographics",
                                    "age",
                                    "Tumor characteristics",
                                    "stage",
                                    "grade"))))%>%

# and you can then indent the actual variables
modify_column_indent(columns=label, rows=variable%in%c("age",
                                                      "stage",
                                                      "grade"))%>%

# and double indent their levels
modify_column_indent(columns=label, rows= (variable%in%c("stage",
                                                      "grade") 
                                             & row_type=="level"),
                     double_indent=T)