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Standardize missing value display across all gtsummary table types

Source: R/clean_table.R
clean_table.Rd

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 = "---")

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".

Value

A gtsummary table object with standardized missing value display

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

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()



  
Characteristic
      Drug A

N = 981		
      Drug B

N = 1021		
    
age
46 (37, 60)
—
    Unknown
7
0
marker
—
0.52 (0.18, 1.21)
    Unknown
98
4
1 Median (Q1, Q3)
    

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



  

      Overall

N = 2001		
      Drug A

N = 981		
      Drug B

N = 1021		
      p-value2
    
age
0 (0, 45)
46 (37, 60)
—
<0.001
    Unknown
7
7
0

marker
0.52 (0.18, 1.21)
—
0.52 (0.18, 1.21)

    Unknown
102
98
4

1 Median (Q1, Q3)
    
2 Wilcoxon rank sum test; NA
    

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



  
Characteristic
      Drug A

N = 981		
      Drug B

N = 1021		
    
age
46 (37, 60)
???
    Unknown
7
0
marker
???
0.52 (0.18, 1.21)
    Unknown
98
4
1 Median (Q1, Q3)
    
# }