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Hierarchical ARD Statistics

Source: R/ard_hierarchical.R
ard_hierarchical.Rd

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.

Usage 

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_fn = NULL,
  stat_label = everything() ~ default_stat_labels(),
  id = NULL,
  ...
)

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

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_fn

(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.

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 |> dplyr::rename(TRTA = ARM)
)
#> {cards} data frame: 2178 x 13
#>    group1 group1_level group2 group2_level variable variable_level stat_name
#> 1    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL F…         n
#> 2    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL F…         N
#> 3    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL F…         p
#> 4    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL F…         n
#> 5    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL F…         N
#> 6    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL F…         p
#> 7    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL H…         n
#> 8    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL H…         N
#> 9    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL H…         p
#> 10   TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIOVEN…         n
#>    stat_label  stat
#> 1           n     1
#> 2           N    86
#> 3           % 0.012
#> 4           n     0
#> 5           N    86
#> 6           %     0
#> 7           n     1
#> 8           N    86
#> 9           % 0.012
#> 10          n     1
#> ℹ 2168 more rows
#> ℹ Use `print(n = ...)` to see more rows
#> ℹ 4 more variables: context, fmt_fn, warning, error

ard_hierarchical_count(
  data = ADAE,
  variables = c(AESOC, AEDECOD),
  by = TRTA
)
#> {cards} data frame: 726 x 13
#>    group1 group1_level group2 group2_level variable variable_level stat_name
#> 1    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL F…         n
#> 2    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL F…         n
#> 3    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIAL H…         n
#> 4    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIOVEN…         n
#> 5    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      ATRIOVEN…         n
#> 6    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      BRADYCAR…         n
#> 7    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      BUNDLE B…         n
#> 8    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      BUNDLE B…         n
#> 9    TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      CARDIAC …         n
#> 10   TRTA      Placebo  AESOC    CARDIAC …  AEDECOD      CARDIAC …         n
#>    stat_label stat
#> 1           n    1
#> 2           n    0
#> 3           n    2
#> 4           n    1
#> 5           n    2
#> 6           n    4
#> 7           n    1
#> 8           n    2
#> 9           n    0
#> 10          n    1
#> ℹ 716 more rows
#> ℹ Use `print(n = ...)` to see more rows
#> ℹ 4 more variables: context, fmt_fn, warning, error