gtsummary + R Markdown

The {gtsummary} package was written to be a companion to the {gt} package from RStudio. But not all output types are supported by the {gt} package. Therefore, we have made it possible to print {gtsummary} tables with various engines.

Output Types

Here’s a summary of the various R Markdown output types and the print engines that support them.

Print Engine	Function	HTML	PDF	RTF	Word
gt	`as_gt()`
kable	`as_kable()`
flextable	`as_flex_table()`
kableExtra	`as_kable_extra()`
huxtable	`as_hux_table()`
tibble	`as_tibble()`

#> Warning: `columns = vars(...)` has been deprecated in gt 0.3.0:
#> * please use `columns = c(...)` instead

#> Warning: `columns = vars(...)` has been deprecated in gt 0.3.0:
#> * please use `columns = c(...)` instead

Key
	Output fully supported
	Formatted output, but missing indentation, footnotes, spanning headers
	No formatted output
	Output not supported
	Under development

Any {gtsummary} table can be converted to one of the types in the table above. For example, the code below prints a {gtsummary} table as a {flextable} table, instead of the default {gt} table.

tbl_summary(trial) %>%
  as_flex_table()

Default Printer

Tables printed with {gtsummary} can be seamlessly integrated into R markdown documents. Currently, {gt} supports HTML output, with LaTeX and RTF planned for the future. The table below summarizes the default print engine utilized for {gtsummary} tables for various R Markdown output formats.

Output Type	Default Engine	Details
HTML	{gt}	{gt} output is fully supported with HTML output.
PDF	kable	You may force printing with {gt} by converting a {gtsummary} object to {gt} with `as_gt()`, e.g. `tbl_summary(trial) %>% as_gt()`. PDF output is under development in the {gt} package. You may get a gorgeous table, but you may also get an error or a malformed table.
RTF	kable	You may force printing with {gt} by converting a {gtsummary} object to {gt} with `as_gt()`, e.g. `tbl_summary(trial) %>% as_gt()`. RTF output is under development in the {gt} package. You may get a gorgeous table, but you may also get an error or a malformed table.
Word	flextable	{flextable} is the default print engine for Word output, as {gt} does not support Word. If {flextable} is not installed, kable is used.

When a table is printed with kintr::kable() the resulting table is less full featured compared to a table printed with {gt}. For example, the table will not contain footnotes, spanning headers, or row indentation.

Example R Markdown Report

An example R markdown report using {gtsummary} has been included with the package. To open the example file, run the following command in the R console.

library(gtsummary)
system.file(package = "gtsummary") %>%
  file.path("rmarkdown_example/gtsummary_rmarkdown_html.Rmd") %>%
  file.edit()

LaTeX

To print {gtsummary} tables using LaTeX, utilize one of the supporting print engines.

# build gtsummary table
tbl <- tbl_summary(trial)

# using the {gt} package
as_gt(tbl) %>% gt::as_latex()

# using the {huxtable} package
as_hux_table(tbl) %>% huxtable::to_latex()

# using the {kableExtra} package
as_kable_extra(tbl, format = "latex")

# using the knitr::kable function
as_kable(tbl, format = "latex")

Images

Use the {gt} package’s gt::gtsave() function to save images of {gtsummary} tables.

tbl_summary(trial) %>%    # build gtsummary table
  as_gt() %>%             # convert to gt table
  gt::gtsave(             # save table as image
    filename = "my_table_image.png"
  )

Tips

When printing {gt} or {gtsummary} tables in a loop, use print() and results = 'asis' in the R markdown chunk.

```{r loop_print, results = 'asis'}
for (i in 1) {
  tbl <- tbl_summary(trial)   # build gtsummary table
  print(tbl)                  # print table
}
```

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