sumExtras (version 1.0.0)

clean_table: Standardize missing value display across all gtsummary table types

Description

Replaces various missing value representations with a consistent symbol (default "---") so it is easier to tell actual data from missing or undefined values.

Works with all gtsummary table types, including stacked tables (tbl_strata) and survey-weighted summaries (tbl_svysummary). Handles tables with or without the standard var_type column.

Usage

clean_table(tbl, symbol = "---")

Value

A gtsummary table object with standardized missing value display

Arguments

tbl

A gtsummary table object (e.g., from tbl_summary(), tbl_svysummary(), tbl_regression(), or tbl_strata())

symbol

Character string to replace missing values with. Default is "---" (em-dash style). Common alternatives: "\u2014" (em-dash), "\u2013" (en-dash), "--", or "N/A".

Details

The function uses gtsummary::modify_table_body() to transform character columns and replace missing, undefined, and zero-valued patterns with a consistent symbol. Matched patterns include:

• Literal NA and Inf / -Inf values

• Count/percent pairs: "0 (0%)", "0 (NA%)", "0 (NA)", "NA (0)", "NA (NA)"

• Decimal variants: "0.00 (0.00)", "0.00% (0.00)", "0% (0.000)"

• Paired values: "NA, NA"

• Confidence intervals: "NA (NA, NA)", "0% (0.000) (0%, 0%)", "0.00 (0.00) (0.00, 0.00)", and similar zero-CI patterns

Replacing these patterns with a single symbol keeps the table easier to read.

Note: The function checks for the presence of var_type column before applying modify_missing_symbol(). This allows it to work with tbl_strata objects which use var_type_1, var_type_2, etc. instead of var_type.

See Also

• gtsummary::modify_table_body() for general table body modifications

• extras() which includes clean_table() in its styling pipeline

Examples

# \donttest{
# Basic usage - clean missing values in summary table
demo_trial <- gtsummary::trial |>
  dplyr::mutate(
    age = dplyr::if_else(trt == "Drug B", 0, age),
    marker = dplyr::if_else(trt == "Drug A", NA, marker)
  ) |>
  dplyr::select(trt, age, marker)

demo_trial |>
  gtsummary::tbl_summary(by = trt) |>
  clean_table()

# Used inside extras() automatically
demo_trial |>
  gtsummary::tbl_summary(by = trt) |>
  extras()

# Custom missing symbol
demo_trial |>
  gtsummary::tbl_summary(by = trt) |>
  clean_table(symbol = "???")
# }