Sort Hierarchical Tables

Source: R/sort_hierarchical.R

[Experimental]

This function is used to sort hierarchical tables. Options for sorting criteria are:

  1. Descending - within each section of the hierarchy table, event rate sums are calculated for each row and rows are sorted in descending order by sum (default).

  2. Alphanumeric - rows are ordered alphanumerically (i.e. A to Z) by label text. By default, tbl_hierarchical() sorts tables in alphanumeric order.

sort_hierarchical(x, ...)

# S3 method for class 'tbl_hierarchical'
sort_hierarchical(x, sort = everything() ~ "descending", ...)

# S3 method for class 'tbl_hierarchical_count'
sort_hierarchical(x, sort = everything() ~ "descending", ...)

# S3 method for class 'tbl_ard_hierarchical'
sort_hierarchical(x, sort = everything() ~ "descending", ...)

Arguments

x

(tbl_hierarchical, tbl_hierarchical_count, tbl_ard_hierarchical)
a hierarchical gtsummary table of class 'tbl_hierarchical', 'tbl_hierarchical_count', or 'tbl_ard_hierarchical'.

...

These dots are for future extensions and must be empty.

sort

(formula-list-selector, string)
a named list, a list of formulas, a single formula where the list element is a named list of functions (or the RHS of a formula), or a string specifying the types of sorting to perform at each hierarchy level. If the sort method for any variable is not specified then the method will default to "descending". If a single unnamed string is supplied it is applied to all hierarchy levels. For each variable, the value specified must be one of:

  • "alphanumeric" - at the specified hierarchy level, groups are ordered alphanumerically (i.e. A to Z) by variable_level text.

  • "descending" - at the specified hierarchy level, count sums are calculated for each row and rows are sorted in descending order by sum. If sort is "descending" for a given variable and n is included in statistic for the variable then n is used to calculate row sums, otherwise p is used. If neither n nor p are present in x for the variable, an error will occur.

Defaults to everything() ~ "descending".

Value

a gtsummary table of the same class as x.

Note

When sorting a table that includes an overall column add_overall() must be called to add the overall column before sort_hierarchical() is called.

Examples

theme_gtsummary_compact()
#> Setting theme "Compact"
ADAE_subset <- cards::ADAE |>
  dplyr::filter(AEBODSYS %in% c("SKIN AND SUBCUTANEOUS TISSUE DISORDERS",
                                "EAR AND LABYRINTH DISORDERS")) |>
  dplyr::filter(.by = AEBODSYS, dplyr::row_number() < 20)

tbl <-
  tbl_hierarchical(
    data = ADAE_subset,
    variables = c(AEBODSYS, AEDECOD),
    by = TRTA,
    denominator = cards::ADSL,
    id = USUBJID,
    overall_row = TRUE
  ) |>
  add_overall()

# Example 1 ----------------------------------------------
# Sort all variables by descending frequency (default)
sort_hierarchical(tbl)



  
Body System or Organ Class

    Dictionary-Derived Term		
      Overall

N = 2541		
      Placebo

N = 861		
      Xanomeline High Dose

N = 841		
      Xanomeline Low Dose

N = 841		
    
Number of patients with event
11 (4.3%)
3 (3.5%)
3 (3.6%)
5 (6.0%)
SKIN AND SUBCUTANEOUS TISSUE DISORDERS
7 (2.8%)
2 (2.3%)
2 (2.4%)
3 (3.6%)
    ERYTHEMA
4 (1.6%)
1 (1.2%)
0 (0%)
3 (3.6%)
    PRURITUS
3 (1.2%)
1 (1.2%)
0 (0%)
2 (2.4%)
    ACTINIC KERATOSIS
1 (0.4%)
0 (0%)
1 (1.2%)
0 (0%)
    PRURITUS GENERALISED
1 (0.4%)
0 (0%)
0 (0%)
1 (1.2%)
    RASH
1 (0.4%)
0 (0%)
1 (1.2%)
0 (0%)
EAR AND LABYRINTH DISORDERS
4 (1.6%)
1 (1.2%)
1 (1.2%)
2 (2.4%)
    VERTIGO
2 (0.8%)
0 (0%)
1 (1.2%)
1 (1.2%)
    CERUMEN IMPACTION
1 (0.4%)
0 (0%)
0 (0%)
1 (1.2%)
    EAR PAIN
1 (0.4%)
1 (1.2%)
0 (0%)
0 (0%)
    TINNITUS
1 (0.4%)
0 (0%)
0 (0%)
1 (1.2%)
1 n (%)
    

# Example 2 ----------------------------------------------
# Sort all variables alphanumerically
sort_hierarchical(tbl, sort = everything() ~ "alphanumeric")



  
Body System or Organ Class

    Dictionary-Derived Term		
      Overall

N = 2541		
      Placebo

N = 861		
      Xanomeline High Dose

N = 841		
      Xanomeline Low Dose

N = 841		
    
Number of patients with event
11 (4.3%)
3 (3.5%)
3 (3.6%)
5 (6.0%)
EAR AND LABYRINTH DISORDERS
4 (1.6%)
1 (1.2%)
1 (1.2%)
2 (2.4%)
    CERUMEN IMPACTION
1 (0.4%)
0 (0%)
0 (0%)
1 (1.2%)
    EAR PAIN
1 (0.4%)
1 (1.2%)
0 (0%)
0 (0%)
    TINNITUS
1 (0.4%)
0 (0%)
0 (0%)
1 (1.2%)
    VERTIGO
2 (0.8%)
0 (0%)
1 (1.2%)
1 (1.2%)
SKIN AND SUBCUTANEOUS TISSUE DISORDERS
7 (2.8%)
2 (2.3%)
2 (2.4%)
3 (3.6%)
    ACTINIC KERATOSIS
1 (0.4%)
0 (0%)
1 (1.2%)
0 (0%)
    ERYTHEMA
4 (1.6%)
1 (1.2%)
0 (0%)
3 (3.6%)
    PRURITUS
3 (1.2%)
1 (1.2%)
0 (0%)
2 (2.4%)
    PRURITUS GENERALISED
1 (0.4%)
0 (0%)
0 (0%)
1 (1.2%)
    RASH
1 (0.4%)
0 (0%)
1 (1.2%)
0 (0%)
1 n (%)
    

# Example 3 ----------------------------------------------
# Sort `AEBODSYS` alphanumerically, `AEDECOD` by descending frequency
sort_hierarchical(tbl, sort = list(AEBODSYS = "alphanumeric", AEDECOD = "descending"))



  
Body System or Organ Class

    Dictionary-Derived Term		
      Overall

N = 2541		
      Placebo

N = 861		
      Xanomeline High Dose

N = 841		
      Xanomeline Low Dose

N = 841		
    
Number of patients with event
11 (4.3%)
3 (3.5%)
3 (3.6%)
5 (6.0%)
EAR AND LABYRINTH DISORDERS
4 (1.6%)
1 (1.2%)
1 (1.2%)
2 (2.4%)
    VERTIGO
2 (0.8%)
0 (0%)
1 (1.2%)
1 (1.2%)
    CERUMEN IMPACTION
1 (0.4%)
0 (0%)
0 (0%)
1 (1.2%)
    EAR PAIN
1 (0.4%)
1 (1.2%)
0 (0%)
0 (0%)
    TINNITUS
1 (0.4%)
0 (0%)
0 (0%)
1 (1.2%)
SKIN AND SUBCUTANEOUS TISSUE DISORDERS
7 (2.8%)
2 (2.3%)
2 (2.4%)
3 (3.6%)
    ERYTHEMA
4 (1.6%)
1 (1.2%)
0 (0%)
3 (3.6%)
    PRURITUS
3 (1.2%)
1 (1.2%)
0 (0%)
2 (2.4%)
    ACTINIC KERATOSIS
1 (0.4%)
0 (0%)
1 (1.2%)
0 (0%)
    PRURITUS GENERALISED
1 (0.4%)
0 (0%)
0 (0%)
1 (1.2%)
    RASH
1 (0.4%)
0 (0%)
1 (1.2%)
0 (0%)
1 n (%)
    

reset_gtsummary_theme()