theme_gtsummary {gtsummary}

Available gtsummary themes

Description

The following themes are available to use within the gtsummary package. Print theme elements with theme_gtsummary_journal(set_theme = FALSE) |> print(). Review the themes vignette for details.

Usage

theme_gtsummary_journal(
  journal = c("jama", "lancet", "nejm", "qjecon"),
  set_theme = TRUE
)

theme_gtsummary_compact(set_theme = TRUE, font_size = NULL)

theme_gtsummary_printer(
  print_engine = c("gt", "kable", "kable_extra", "flextable", "huxtable", "tibble"),
  set_theme = TRUE
)

theme_gtsummary_language(
  language = c("de", "en", "es", "fr", "gu", "hi", "is", "ja", "kr", "mr", "nl", "no",
    "pt", "se", "zh-cn", "zh-tw"),
  decimal.mark = NULL,
  big.mark = NULL,
  iqr.sep = NULL,
  ci.sep = NULL,
  set_theme = TRUE
)

theme_gtsummary_continuous2(
  statistic = "{median} ({p25}, {p75})",
  set_theme = TRUE
)

theme_gtsummary_mean_sd(set_theme = TRUE)

theme_gtsummary_eda(set_theme = TRUE)

Arguments

journal

String indicating the journal theme to follow. One of c("jama", "lancet", "nejm", "qjecon"). Details below.

set_theme

(scalar logical)
Logical indicating whether to set the theme. Default is TRUE. When FALSE the named list of theme elements is returned invisibly

font_size

(scaler numeric)
Numeric font size for compact theme. Default is 13 for gt tables, and 8 for all other output types

print_engine

String indicating the print method. Must be one of "gt", "kable", "kable_extra", "flextable", "tibble"

language

(string)
String indicating language. Must be one of "de" (German), "en" (English), "es" (Spanish), "fr" (French), "gu" (Gujarati), "hi" (Hindi), "is" (Icelandic),"ja" (Japanese), "kr" (Korean), "nl" (Dutch), "mr" (Marathi), "no" (Norwegian), "pt" (Portuguese), "se" (Swedish), "zh-cn" (Chinese Simplified), "zh-tw" (Chinese Traditional)

If a language is missing a translation for a word or phrase, please feel free to reach out on GitHub with the translated text.

decimal.mark

(string)
The character to be used to indicate the numeric decimal point. Default is "." or getOption("OutDec")

big.mark

(string)
Character used between every 3 digits to separate hundreds/thousands/millions/etc. Default is ",", except when decimal.mark = "," when the default is a space.

iqr.sep

(string)
String indicating separator for the default IQR in tbl_summary(). If ⁠decimal.mark=⁠ is NULL, ⁠iqr.sep=⁠ is ", ". The comma separator, however, can look odd when decimal.mark = ",". In this case the argument will default to an en dash

ci.sep

(string)
String indicating separator for confidence intervals. If ⁠decimal.mark=⁠ is NULL, ⁠ci.sep=⁠ is ", ". The comma separator, however, can look odd when decimal.mark = ",". In this case the argument will default to an en dash

statistic

Default statistic continuous variables

Themes

• theme_gtsummary_journal(journal)

  • "jama" The Journal of the American Medical Association

    • Round large p-values to 2 decimal places; separate confidence intervals with "ll to ul".

    • tbl_summary() Doesn't show percent symbol; use em-dash to separate IQR; run add_stat_label()

    • tbl_regression()/tbl_uvregression() show coefficient and CI in same column

  • "lancet" The Lancet

    • Use mid-point as decimal separator; round large p-values to 2 decimal places; separate confidence intervals with "ll to ul".

    • tbl_summary() Doesn't show percent symbol; use em-dash to separate IQR

  • "nejm" The New England Journal of Medicine

    • Round large p-values to 2 decimal places; separate confidence intervals with "ll to ul".

    • tbl_summary() Doesn't show percent symbol; use em-dash to separate IQR

  • "qjecon" The Quarterly Journal of Economics

    • tbl_summary() all percentages rounded to one decimal place

    • tbl_regression(),tbl_uvregression() add significance stars with add_significance_stars(); hides CI and p-value from output

      • For flaxtable and huxtable output, the coeficient's standard error is placed below. For gt, it is placed to the right.

• theme_gtsummary_compact()

  • tables printed with gt, flextable, kableExtra, or huxtable will be compact with smaller font size and reduced cell padding

• theme_gtsummary_printer(print_engine)

  • Use this theme to permanently change the default printer.

• theme_gtsummary_continuous2()

  • Set all continuous variables to summary type "continuous2" by default

• theme_gtsummary_mean_sd()

  • Set default summary statistics to mean and standard deviation in tbl_summary()

  • Set default continuous tests in add_p() to t-test and ANOVA

• theme_gtsummary_eda()

  • Set all continuous variables to summary type "continuous2" by default

  • In tbl_summary() show the median, mean, IQR, SD, and Range by default

Use reset_gtsummary_theme() to restore the default settings

Review the themes vignette to create your own themes.

See Also

Themes vignette

set_gtsummary_theme(), reset_gtsummary_theme()

Examples

# Setting JAMA theme for gtsummary
theme_gtsummary_journal("jama")
# Themes can be combined by including more than one
theme_gtsummary_compact()

trial |>
  select(age, grade, trt) |>
  tbl_summary(by = trt) |>
  as_gt()

# reset gtsummary themes
reset_gtsummary_theme()