In shannonpileggi/gtreg: Regulatory Tables for Clinical Research

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(gtreg)
library(dplyr)
library(gt)
gtsummary::theme_gtsummary_compact()

Overview

In general, use modify_header() and modify_spanning_header() to specify how headers should be modified; use in conjunction with column selectors to specify which column headers to modify. Use show_header_names() on a saved table object to display a usage guide for modifying headers.

To specify footnotes and captions, use modify_footnote() and modify_caption().

For all modify_ functions, formatting is applied via markdown and glue syntax can be used to insert summary statistics. In addition, a return carriage inserts a line break when preceded by two spaces: \n.

AE tables

For adverse event tables functions tbl_ae(), tbl_ae_focus(), and tbl_ae_count(), use the {gtreg} column selectors all_ae_cols(), all_overall_cols(), all_unknown_cols(), and all_cols_in_strata() to specify which columns to apply formatting.

tibble::tribble(
  ~`Selector`,                                     ~`AE`, ~`Overall`, ~`Unknown`, 
  "`all_ae_cols()`",                                "✔️",   "",        "",        
  "`all_overall_cols()`",                           "",    "✔️",       "",        
  "`all_unknown_cols()`",                           "",    "",         "✔️" ,
  "`all_ae_cols(overall = TRUE, unknown = TRUE)`",  "✔️",  "✔️",       "✔️"   
  )  %>%
  gt::gt() %>%
  gt::cols_align(
    align = "center",
    columns = c(AE, Overall, Unknown)
  ) %>%
  gt::tab_header(
    title = md("**{gtreg} column selectors and resulting columns selected.**")
  ) %>%
  cols_width(
    2:4 ~ px(80)
  ) %>% 
  tab_stubhead(label = "Selector") %>% 
  fmt_markdown(1)

#| fig.cap: > 
#|   Demonstration of `modify_` functions used with {gtreg} column selectors.
#| fig.alt: > 
#|   Left hand side code, right hand side output table. Gif contains 8 frames
#|   that sequentially builds a table.
knitr::include_graphics("misc/gtreg-modify.gif")

Additionally, the all_cols_in_strata() selector can be used with modify_spanning_header() to apply differing modifications within strata.

tbl_ae() without strata

tbl1 <- df_adverse_events %>%
  # create a missing value to demonstrate unknown columns
  mutate(grade = ifelse(dplyr::row_number() == 1L, NA, grade)) %>%
  tbl_ae(
    id = patient_id,
    ae = adverse_event,
    soc = system_organ_class,
    by = grade
  ) %>%
  add_overall(across = 'by') %>% 
  bold_labels()

Unmodified

# show_header_names(tbl1)
tbl1

Modified

tbl1 %>%
  modify_header(
    label ~ "**Event**",
    all_ae_cols() ~ "**Grade {by}**",
    all_overall_cols() ~ "**Total**",
    all_unknown_cols() ~ "**Unknown Grade**"
  ) %>%
  modify_spanning_header(
    all_ae_cols(TRUE, TRUE) ~ "**All cohorts**, N = {N}"
  ) 

tbl_ae() with strata

tbl2 <-
  df_adverse_events %>%
    tbl_ae(
      id = patient_id,
      soc = system_organ_class,
      ae = adverse_event,
      strata = trt,
      by = grade
    ) %>%
  bold_labels()

Unmodified

# show_header_names(tbl2)
tbl2

Modified

tbl2 %>% 
  modify_header(all_ae_cols() ~ "**Grade {by}**") %>%
  modify_spanning_header(all_ae_cols() ~ "**{strata}**  \n{style_percent(p)}% ({n}/{N})") %>%
  modify_caption("My caption: N = {N}")  %>%
  modify_footnote(label = "My footnote: N = {N}") 

tbl2 %>%
  modify_spanning_header(
      all_cols_in_strata("Drug A") ~ "**Control Group**  \n{style_percent(p)}% ({n}/{N})",
      all_cols_in_strata("Drug B") ~ "**Experimental Group**  \n{style_percent(p)}% ({n}/{N})"
    )

Summary tables

For tbl_reg_summary(), the modify_header() and modify_spanning_header() functions work with the {gtsummary} column selectors like all_stat_cols() to specify formatting of table headers.

tbl_reg_summary(), without overall

tbl3 <-
  df_patient_characteristics %>% 
  select(trt, marker, discontinued) %>% 
  tbl_reg_summary(
    by = trt
  ) %>% 
  bold_labels()

Unmodified

# show_header_names(tbl3)
tbl3

Modified

tbl3 %>% 
  modify_header(
    all_stat_cols() ~ "**{level}**, N = {n}/{N} ({style_percent(p)}%)"
    )

tbl_reg_summary(), with overall

tbl4 <-
  df_patient_characteristics %>% 
  select(trt, marker, discontinued) %>% 
  tbl_reg_summary(
    by = trt
  ) %>% 
  add_overall(last = TRUE) %>% 
  bold_labels()

Unmodified

# show_header_names(tbl4)
tbl4

Modified

tbl4 %>% 
  modify_header(
    list(
      stat_1 ~ "**Control Group**  \n N = {n}",
      stat_2 ~ "**Experimental Group**  \n N = {n}",
      stat_0 ~ "**Overall**  \n N = {N}"
    )) 

shannonpileggi/gtreg documentation built on Feb. 23, 2025, 3:04 p.m.