tbl_hierarchical: Hierarchical Table

In gtsummary: Presentation-Ready Data Summary and Analytic Result Tables

Hierarchical Table

Description

This is an preview of this function. There will be changes in the coming releases, and changes will not undergo a formal deprecation cycle.

Use these functions to generate hierarchical tables.

• tbl_hierarchical(): Calculates rates of events (e.g. adverse events) utilizing the denominator and id arguments to identify the rows in data to include in each rate calculation. If variables contains more than one variable and the last variable in variables is an ordered factor, then rates of events by highest level will be calculated.

• tbl_hierarchical_count(): Calculates counts of events utilizing all rows for each tabulation.

Usage

tbl_hierarchical(
  data,
  variables,
  by = NULL,
  id = NULL,
  denominator = NULL,
  include = everything(),
  statistic = "{n} ({p})",
  overall_row = FALSE,
  label = NULL
)

tbl_hierarchical_count(
  data,
  variables,
  by = NULL,
  denominator = NULL,
  include = everything(),
  overall_row = FALSE,
  label = NULL
)

Arguments

data	(data.frame) a data frame.
variables	(tidy-select) character vector or tidy-selector of columns in data used to create a hierarchy. Hierarchy will be built with variables in the order given.
by	(tidy-select) a single column from data. Summary statistics will be stratified by this variable. Default is NULL.
id	(tidy-select) argument used to subset data to identify rows in data to calculate event rates in tbl_hierarchical().
denominator	(data.frame, integer) used to define the denominator and enhance the output. The argument is required for tbl_hierarchical() and optional for tbl_hierarchical_count(). The denominator argument must be specified when id is used to calculate event rates.
include	(tidy-select) variables from hierarchy for which summary statistics should be returned (on the variable label rows) Including the last element of hierarchy has no effect since each level has its own row for this variable. The default is everything().
statistic	(string) used to specify the summary statistics to display for all variables in tbl_hierarchical(). The default is "{n} ({p})".
overall_row	(scalar logical) whether an overall summary row should be included at the top of the table. The default is FALSE.
label	(formula-list-selector) used to override default labels in hierarchical table, e.g. list(AESOC = "System Organ Class"). The default for each variable is the column label attribute, attr(., 'label'). If no label has been set, the column name is used.

Value

a gtsummary table of class "tbl_hierarchical" (for tbl_hierarchical()) or "tbl_hierarchical_count" (for tbl_hierarchical_count()).

Overall Row

An overall row can be added to the table as the first row by specifying overall_row = TRUE. Assuming that each row in data corresponds to one event record, this row will count the overall number of events recorded when used in tbl_hierarchical_count(), or the overall number of patients recorded with any event when used in tbl_hierarchical().

A label for this overall row can be specified by passing an overall element in label. If no overall label has been set and overall_row = TRUE, "Total number of patients with any event" will be used by tbl_hierarchical() and "Total number of events" will be used by tbl_hierarchical_count().

Examples

ADAE_subset <- cards::ADAE |>
  dplyr::filter(
    AESOC %in% unique(cards::ADAE$AESOC)[1:5],
    AETERM %in% unique(cards::ADAE$AETERM)[1:5]
  )

# Example 1 - Event Rates --------------------
tbl_hierarchical(
  data = ADAE_subset,
  variables = c(AESOC, AETERM),
  by = TRTA,
  denominator = cards::ADSL |> mutate(TRTA = ARM),
  id = USUBJID,
  overall_row = TRUE
)

# Example 2 - Rates by Highest Severity ------
tbl_hierarchical(
  data = ADAE_subset |> mutate(AESEV = factor(AESEV, ordered = TRUE)),
  variables = c(AESOC, AESEV),
  by = TRTA,
  id = USUBJID,
  denominator = cards::ADSL |> mutate(TRTA = ARM),
  include = AESEV,
  label = list(AESEV = "Highest Severity")
)

# Example 3 - Event Counts -------------------
tbl_hierarchical_count(
  data = ADAE_subset,
  variables = c(AESOC, AETERM, AESEV),
  by = TRTA,
  overall_row = TRUE
)

gtsummary documentation built on Oct. 5, 2024, 1:06 a.m.