gtsummary (version 1.5.1)

as_kable_extra: Convert gtsummary object to a kableExtra object

Description

Function converts a gtsummary object to a knitr_kable + kableExtra object. This allows the customized formatting available via knitr::kable and kableExtra; as_kable_extra() supports arguments in knitr::kable(). as_kable_extra() output via gtsummary supports bold and italic cells for table bodies. Users creating pdf output should specify as_kable_extra(format = "latex").

Usage

as_kable_extra(
  x,
  include = everything(),
  return_calls = FALSE,
  strip_md_bold = TRUE,
  fmt_missing = TRUE,
  ...
)

Arguments

x

Object created by a function from the gtsummary package (e.g. tbl_summary or tbl_regression)

include

Commands to include in output. Input may be a vector of quoted or unquoted names. tidyselect and gtsummary select helper functions are also accepted. Default is everything().

return_calls

Logical. Default is FALSE. If TRUE, the calls are returned as a list of expressions.

strip_md_bold

When TRUE, all double asterisk (markdown language for bold weight) in column labels and spanning headers are removed.

fmt_missing

Logical argument adding the missing value formats.

...

Additional arguments passed to knitr::kable

Value

A kableExtra object

PDF via LaTeX Tips

This section discusses options intended for use with

• output: pdf_document in yaml of .Rmd.

• as_kable_extra(format = "latex")

Custom column names

In pdf output, column names do not currently inherit formatting applied in gtsummary tables. However, custom column names can be achieved with the col.names argument as shown in Example 2, including attributes such as bold formatting, italic formatting, and line breaks. Doing so requires the escape = FALSE argument; however, when using escape = FALSE special latex characters like \ and % will need to be escaped prior to entering as_kable_extra(). Using escape = FALSE when the gtsummary table has special LaTeX characters will result in the error "LaTeX failed to compile..."

Additional table styling

Additional styling is available through knitr::kable() and kableExtra::kable_styling() as shown in Example 3, which implements row striping and repeated column headers in the presence of page breaks.

Example Output

Example 1 (html)

Example 1 (pdf)

Example 2 (pdf)

Example 3 (pdf)

See Also

Other gtsummary output types: as_flex_table(), as_gt(), as_hux_table(), as_kable(), as_tibble.gtsummary()

Examples

# NOT RUN {
# Example 1 (general) -------------------------------------------------------
as_kable_extra_ex1_gen <-
  trial %>%
  select(trt, age, stage) %>%
  tbl_summary(by = trt) %>%
  bold_labels() %>%
  as_kable_extra()

# Example 2 (PDF via LaTeX) -------------------------------------------------
custom_names <- c(
   "\\textbf{Characteristic}",
   "\\textbf{Drug A}\n\\textit{N = 98}",
   "\\textbf{Drug B}\n\\textit{N = 102}"
)
as_kable_extra_ex2_pdf <-
  trial %>%
  select(trt, age, stage) %>%
  tbl_summary(
     by = trt,
     statistic = list(all_categorical() ~ "{n} ({p}\\%)")
  ) %>%
  bold_labels() %>%
  modify_footnote(
     update = all_stat_cols() ~ "Median (IQR); n (%)"
  ) %>%
  as_kable_extra(
     format = "latex",
     col.names = kableExtra::linebreak(custom_names, align = "c"),
     escape = FALSE
  )

# Example 3 (PDF via LaTeX) -------------------------------------------------
as_kable_extra_ex3_pdf <-
trial %>%
  select(trt, age, stage) %>%
  tbl_summary(by = trt) %>%
  bold_labels() %>%
  as_kable_extra(
    format = "latex",
    booktabs = TRUE,
    longtable = TRUE,
    linesep = ""
  ) %>%
  kableExtra::kable_styling(
    position = "left",
    latex_options = c("striped", "repeat_header"),
    stripe_color = "gray!15"
  )
# }