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ARD summary table

Source: R/tbl_ard_summary.R
tbl_ard_summary.Rd

[Experimental]
The tbl_ard_summary() function tables descriptive statistics for continuous, categorical, and dichotomous variables. The functions accepts an ARD object.

Usage

tbl_ard_summary(
  cards,
  by = NULL,
  statistic = list(all_continuous() ~ "{median} ({p25}, {p75})", all_categorical() ~
    "{n} ({p}%)"),
  type = NULL,
  label = NULL,
  missing = c("no", "ifany", "always"),
  missing_text = "Unknown",
  missing_stat = "{N_miss}",
  include = everything(),
  overall = FALSE
)

Arguments

cards

(card)
An ARD object of class "card" typically created with cards::ard_*() functions.

by

(tidy-select)
A single column from data. Summary statistics will be stratified by this variable. Default is NULL

statistic

(formula-list-selector)
Used to specify the summary statistics for each variable. Each of the statistics must be present in card as no new statistics are calculated in this function. The default is list(all_continuous() ~ "{median} ({p25}, {p75})", all_categorical() ~ "{n} ({p}%)").

type

(formula-list-selector)
Specifies the summary type. Accepted value are c("continuous", "continuous2", "categorical", "dichotomous"). Continuous summaries may be assigned c("continuous", "continuous2"), while categorical and dichotomous cannot be modified.

label

(formula-list-selector)
Used to override default labels in summary table, e.g. list(age = "Age, years"). The default for each variable is the column label attribute, attr(., 'label'). If no label has been set, the column name is used.

missing, missing_text, missing_stat

Arguments dictating how and if missing values are presented:

  • missing: must be one of c("no", "ifany", "always")

  • missing_text: string indicating text shown on missing row. Default is "Unknown"

  • missing_stat: statistic to show on missing row. Default is "{N_miss}". Possible values are N_miss, N_obs, N_nonmiss, p_miss, p_nonmiss

include

(tidy-select)
Variables to include in the summary table. Default is everything()

overall

(scalar logical)
When TRUE, the cards input is parsed into two parts to run tbl_ard_summary(cards_by) |> add_overall(cards_overall). Can only by used when by argument is specified. Default is FALSE.

Value

a gtsummary table of class "tbl_ard_summary"

Details

There are three types of additional data that can be included in the ARD to improve the default appearance of the table.

  1. Attributes: When attributes are included, the default labels will be the variable labels, when available. Attributes can be included in an ARD with cards::ard_attributes() or ard_stack(.attributes = TRUE).

  2. Missing: When missing results are included, users can include missing counts or rates for variables with tbl_ard_summary(missing = c("ifany", "always")). The missing statistics can be included in an ARD with cards::ard_missing() or ard_stack(.missing = TRUE).

  3. Total N: The total N is saved internally when available, and it can be calculated with cards::ard_total_n() or ard_stack(.total_n = TRUE).

Examples

library(cards)

ard_stack(
  data = ADSL,
  ard_categorical(variables = "AGEGR1"),
  ard_continuous(variables = "AGE"),
  .attributes = TRUE,
  .missing = TRUE,
  .total_n = TRUE
) |>
  tbl_ard_summary()



  
Characteristic
      Overall1
    
Pooled Age Group 1

    65-80
144 (56.7%)
    <65
33 (13.0%)
    >80
77 (30.3%)
Age
77.0 (70.0, 81.0)
1 n (%); Median (Q1, Q3)
    

ard_stack(
  data = ADSL,
  .by = ARM,
  ard_categorical(variables = "AGEGR1"),
  ard_continuous(variables = "AGE"),
  .attributes = TRUE,
  .missing = TRUE,
  .total_n = TRUE
) |>
  tbl_ard_summary(by = ARM)



  
Characteristic
      Placebo1
      Xanomeline High Dose1
      Xanomeline Low Dose1
    
Pooled Age Group 1





    65-80
42 (48.8%)
55 (65.5%)
47 (56.0%)
    <65
14 (16.3%)
11 (13.1%)
8 (9.5%)
    >80
30 (34.9%)
18 (21.4%)
29 (34.5%)
Age
76.0 (69.0, 82.0)
76.0 (70.5, 80.0)
77.5 (71.0, 82.0)
1 n (%); Median (Q1, Q3)
    

ard_stack(
  data = ADSL,
  .by = ARM,
  ard_categorical(variables = "AGEGR1"),
  ard_continuous(variables = "AGE"),
  .attributes = TRUE,
  .missing = TRUE,
  .total_n = TRUE,
  .overall = TRUE
) |>
  tbl_ard_summary(by = ARM, overall = TRUE)



  
Characteristic
      Overall1
      Placebo1
      Xanomeline High Dose1
      Xanomeline Low Dose1
    
Pooled Age Group 1







    65-80
144 (56.7%)
42 (48.8%)
55 (65.5%)
47 (56.0%)
    <65
33 (13.0%)
14 (16.3%)
11 (13.1%)
8 (9.5%)
    >80
77 (30.3%)
30 (34.9%)
18 (21.4%)
29 (34.5%)
Age
77.0 (70.0, 81.0)
76.0 (69.0, 82.0)
76.0 (70.5, 80.0)
77.5 (71.0, 82.0)
1 n (%); Median (Q1, Q3)