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Modify Abbreviations

Source: R/modify_abbreviation.R
modify_abbreviation.Rd

All abbreviations will be coalesced when printing the final table into a single specialized source note.

Usage

modify_abbreviation(
  x,
  abbreviation,
  text_interpret = c("md", "html", "none"),
  prefix = NULL,
  sep1 = NULL,
  sep2 = NULL
)

remove_abbreviation(x, abbreviation = NULL)

Arguments

x

(gtsummary)
A gtsummary object

abbreviation

(character)
a character vector of one or more abbreviations to add. In remove_abbreviation(), the default value is NULL, which will remove all abbreviation source notes; otherwise a character vector of abbreviations to remove.

text_interpret

(string)
String indicates whether text will be interpreted with gt::md() or gt::html(). Must be "md" (default), "html", or "none". "none" applies no interpretation, rendering the text verbatim (useful when the text contains markdown-significant characters). Applies to tables printed with {gt}.

prefix, sep1, sep2

(character)
optional arguments controlling how the abbreviation source note is assembled as paste0(prefix, sep1, paste(abbreviations, collapse = sep2)).

  • prefix is a character vector of length two giving the leading text, as c(singular, plural). The first element is used when a single abbreviation is present and the second when multiple abbreviations are present. Pass c("", "") to omit the leading text. Defaults to NULL, in which case the theme element "modify_abbreviation-arg:prefix" is used, falling back to the translated default c("Abbreviation", "Abbreviations"). Unlike the default, a user-supplied prefix is used as-is and is not translated.

  • sep1 is a string giving the separator between the prefix and the abbreviations. Defaults to NULL, in which case the theme element "modify_abbreviation-arg:sep1" is used, falling back to the default ": ". It is omitted when the resolved prefix is empty.

  • sep2 is a string giving the separator placed between abbreviations. Defaults to NULL, in which case the theme element "modify_abbreviation-arg:sep2" is used, falling back to the default ", ".

Value

Updated gtsummary object

See also

Footnotes vs Source Notes vs Abbreviations

Examples

# Example 1 ----------------------------------
tbl_summary(
  trial,
  by = trt,
  include = age,
  type = age ~ "continuous2"
) |>
  modify_table_body(~dplyr::mutate(.x, label = sub("Q1, Q3", "IQR", x = label))) |>
  modify_abbreviation("IQR = Interquartile Range")



  
Characteristic
      Drug A

N = 98		
      Drug B

N = 102		
    
Age



    Median (IQR)
46 (37, 60)
48 (39, 56)
    Unknown
7
4
Abbreviation: IQR = Interquartile Range
    

# Example 2 ----------------------------------
lm(marker ~ trt, trial) |>
  tbl_regression() |>
  remove_abbreviation("CI = Confidence Interval")



  
Characteristic
      Beta
      95% CI
      p-value
    
Chemotherapy Treatment





    Drug A
—
—

    Drug B
-0.20
-0.44, 0.05
0.12

# Example 3 ----------------------------------
# add multiple abbreviations at once and customize the prefix and separator
tbl_summary(
  trial,
  by = trt,
  include = age,
  type = age ~ "continuous2"
) |>
  modify_table_body(~dplyr::mutate(.x, label = sub("Q1, Q3", "IQR", x = label))) |>
  modify_abbreviation(
    c("IQR = Interquartile Range", "SD = Standard Deviation"),
    prefix = c("Key", "Keys"),
    sep2 = "; "
  )



  
Characteristic
      Drug A

N = 98		
      Drug B

N = 102		
    
Age



    Median (IQR)
46 (37, 60)
48 (39, 56)
    Unknown
7
4
Keys: IQR = Interquartile Range; SD = Standard Deviation