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Sort Hierarchical Tables

Source: R/sort_hierarchical.R
sort_hierarchical.Rd

[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.

Usage

sort_hierarchical(x, ...)

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

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

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

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".

by_level

(scalar)
an optional single level of the table's by variable used to restrict the counts used for "descending" sorting. When supplied, "descending" sorts rank rows by the count sums observed only in the specified by level (e.g. by_level = "Placebo" sorts by the counts in the "Placebo" arm), rather than by the sums across all by levels. Has no effect on variables sorted "alphanumeric", and cannot be used when x has no by variable. Because gtsummary hierarchical tables allow only a single by variable, a scalar level is supplied here (rather than the named list used by cards::sort_ard_hierarchical()).

Defaults to NULL, in which case count sums are calculated across all by levels.

Value

a gtsummary table of the same class as x.

Details

If you do not want to display rates for a hierarchy variable from table x but you would like to sort by descending frequency for that variable, the recommended method is to keep the variable in include when calling tbl_hierarchical() so that rates for this variable are available, sort the table as needed using sort_hierarchical(), and then finally remove these rates from the table using modify_table_body().

For example, to remove rates from the AESOC rows in hierarchy table x, you can call:

x |>
  modify_table_body(
    \(df) mutate(df, dplyr::across(all_stat_cols(), ~ifelse(variable %in% "AESOC", NA, .)))
  )

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.

See also

filter_hierarchical()

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 (%)
    

# Example 4 ----------------------------------------------
# Sort by descending frequency within the "Placebo" arm only
sort_hierarchical(tbl, by_level = "Placebo")



  
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%)
    EAR PAIN
1 (0.4%)
1 (1.2%)
0 (0%)
0 (0%)
    CERUMEN IMPACTION
1 (0.4%)
0 (0%)
0 (0%)
1 (1.2%)
    TINNITUS
1 (0.4%)
0 (0%)
0 (0%)
1 (1.2%)
    VERTIGO
2 (0.8%)
0 (0%)
1 (1.2%)
1 (1.2%)
1 n (%)
    

reset_gtsummary_theme()