In shannonpileggi/gtreg: Regulatory Tables for Clinical Research

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

Setup

# install.packages("gtreg")
library(gtreg)
library(gtsummary)

Overview

As {gtreg} is built upon {gtsummary}, you can use the same methods you would use for {gtsummary} to output tables to various formats. A {gtreg} table can be exported with {gt}, {flextable}, {huxtable}, {kableExtra}, knitr::kable(), and as a tibble. See the print engines available in {gtsummary} for details.

Here, we share approaches to common requests and recommendations for each output type.

Example table

table1 <- 
  df_adverse_events %>% 
  tbl_ae(
    id = patient_id,
    id_df = df_patient_characteristics,
    ae = adverse_event,
    soc = system_organ_class, 
    by = grade
  ) %>% 
  modify_header(
    all_ae_cols() ~ "**Grade {by}**"
    ) %>%
  bold_labels()

Example outputs

HTML

The default output type is HTML.

table1

Word

Leverage the {flextable} package for word output.

table1 %>%  
  as_flex_table() %>% 
  flextable::save_as_docx(path = "misc/ae_table.docx")

Excel

Leverage the {huxtable} package for excel output.

table1 %>%  
 as_hux_xlsx(
   file = "misc/ae_table.xlsx"
   )

PDF

Leverage the {kableExtra} package for styled PDF output.

To export to PDF, create a new .Rmd or .qmd document with a PDF output type. The YAML shown here is for .Rmd. You can then use as_kable_extra() to convert the table to the LaTeX required for pdf rendering, and kable_styling() for extra styling of the table. For more pdf styling options, see the blog post Report Ready PDF tables with rmarkdown, knitr, kableExtra, and LaTeX.

---
output: pdf_document
---
<stuff>  

```r
table1 %>% 
  as_kable_extra(
    booktabs = TRUE
  ) %>% 
  kableExtra::kable_styling(
    latex_options = "striped",
    stripe_color = "gray!15"
  )
```