Hierarchical ARD Statistics

Source: R/ard_hierarchical.R

Functions ard_hierarchical() and ard_hierarchical_count() are primarily helper functions for ard_stack_hierarchical() and ard_stack_hierarchical_count(), meaning that it will be rare a user needs to call ard_hierarchical()/ard_hierarchical_count() directly.

Performs hierarchical or nested tabulations, e.g. tabulates AE terms nested within AE system organ class.

  • ard_hierarchical() includes summaries for the last variable listed in the variables argument, nested within the other variables included.

  • ard_hierarchical_count() includes summaries for all variables listed in the variables argument each summary nested within the preceding variables, e.g. variables=c(AESOC, AEDECOD) summarizes AEDECOD nested in AESOC, and also summarizes the counts of AESOC.

ard_hierarchical(data, ...)

ard_hierarchical_count(data, ...)

# S3 method for class 'data.frame'
ard_hierarchical(
  data,
  variables,
  by = dplyr::group_vars(data),
  statistic = everything() ~ c("n", "N", "p"),
  denominator = NULL,
  fmt_fun = NULL,
  stat_label = everything() ~ default_stat_labels(),
  id = NULL,
  fmt_fn = deprecated(),
  ...
)

# S3 method for class 'data.frame'
ard_hierarchical_count(
  data,
  variables,
  by = dplyr::group_vars(data),
  fmt_fun = NULL,
  stat_label = everything() ~ default_stat_labels(),
  fmt_fn = deprecated(),
  ...
)

Arguments

data

(data.frame)
a data frame

...

Arguments passed to methods.

variables

(tidy-select)
variables to perform the nested/hierarchical tabulations within.

by

(tidy-select)
variables to perform tabulations by. All combinations of the variables specified here appear in results. Default is dplyr::group_vars(data).

statistic

(formula-list-selector)
a named list, a list of formulas, or a single formula where the list element one or more of c("n", "N", "p", "n_cum", "p_cum") (on the RHS of a formula).

denominator

(data.frame, integer)
used to define the denominator and enhance the output. The argument is required for ard_hierarchical() and optional for ard_hierarchical_count().

  • the univariate tabulations of the by variables are calculated with denominator, when a data frame is passed, e.g. tabulation of the treatment assignment counts that may appear in the header of a table.

  • the denominator argument must be specified when id is used to calculate the event rates.

fmt_fun

(formula-list-selector)
a named list, a list of formulas, or a single formula where the list element is a named list of functions (or the RHS of a formula), e.g. list(mpg = list(mean = \(x) round(x, digits = 2) |> as.character())).

stat_label

(formula-list-selector)
a named list, a list of formulas, or a single formula where the list element is either a named list or a list of formulas defining the statistic labels, e.g. everything() ~ list(n = "n", p = "pct") or everything() ~ list(n ~ "n", p ~ "pct").

id

(tidy-select)
an optional argument used to assert there are no duplicates within the c(id, variables) columns.

fmt_fn

[Deprecated]

Value

an ARD data frame of class 'card'

Examples

ard_hierarchical(
  data = ADAE |>
    dplyr::slice_tail(n = 1L, by = c(USUBJID, TRTA, AESOC, AEDECOD)),
  variables = c(AESOC, AEDECOD),
  by = TRTA,
  id = USUBJID,
  denominator = ADSL
)
#> # An ARD data frame: 2,178 × 13
#>    group1 group1_level group2 group2_level     variable variable_level stat_name
#>    <chr>  <list>       <chr>  <list>           <chr>    <list>         <chr>    
#>  1 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL FIBRIL… n        
#>  2 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL FIBRIL… N        
#>  3 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL FIBRIL… p        
#>  4 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL FLUTTER n        
#>  5 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL FLUTTER N        
#>  6 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL FLUTTER p        
#>  7 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL HYPERT… n        
#>  8 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL HYPERT… N        
#>  9 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL HYPERT… p        
#> 10 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIOVENTRICU… n        
#> # ℹ 2,168 more rows
#> # ℹ 6 more variables: context <chr>, stat_label <chr>, stat <list>,
#> #   fmt_fun <list>, warning <list>, error <list>

ard_hierarchical_count(
  data = ADAE,
  variables = c(AESOC, AEDECOD),
  by = TRTA
)
#> # An ARD data frame: 726 × 13
#>    group1 group1_level group2 group2_level     variable variable_level stat_name
#>    <chr>  <list>       <chr>  <list>           <chr>    <list>         <chr>    
#>  1 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL FIBRIL… n        
#>  2 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL FLUTTER n        
#>  3 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIAL HYPERT… n        
#>  4 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIOVENTRICU… n        
#>  5 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  ATRIOVENTRICU… n        
#>  6 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  BRADYCARDIA    n        
#>  7 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  BUNDLE BRANCH… n        
#>  8 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  BUNDLE BRANCH… n        
#>  9 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  CARDIAC DISOR… n        
#> 10 TRTA   Placebo      AESOC  CARDIAC DISORDE… AEDECOD  CARDIAC FAILU… n        
#> # ℹ 716 more rows
#> # ℹ 6 more variables: context <chr>, stat_label <chr>, stat <list>,
#> #   fmt_fun <list>, warning <list>, error <list>