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Create a table of summary statistics using a custom summary function

Source: R/tbl_custom_summary.R
tbl_custom_summary.Rd

[Experimental]
The tbl_custom_summary() function calculates descriptive statistics for continuous, categorical, and dichotomous variables. This function is similar to tbl_summary() but allows you to provide a custom function in charge of computing the statistics (see Details).

Usage

tbl_custom_summary(
  data,
  by = NULL,
  label = NULL,
  stat_fns,
  statistic,
  digits = NULL,
  type = NULL,
  value = NULL,
  missing = c("ifany", "no", "always"),
  missing_text = "Unknown",
  missing_stat = "{N_miss}",
  include = everything(),
  overall_row = FALSE,
  overall_row_last = FALSE,
  overall_row_label = "Overall"
)

Arguments

data

(data.frame)
A data frame.

by

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

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.

stat_fns

(formula-list-selector)
Specifies the function to be used to compute the statistics (see below for details and examples). You can also use dedicated helpers such as ratio_summary() or proportion_summary().

statistic

(formula-list-selector)
Specifies summary statistics to display for each variable. The default is list(all_continuous() ~ "{median} ({p25}, {p75})", all_categorical() ~ "{n} ({p}%)"). See below for details.

digits

(formula-list-selector)
Specifies how summary statistics are rounded. Values may be either integer(s) or function(s). If not specified, default formatting is assigned via assign_summary_digits(). See below for details.

type

(formula-list-selector)
Specifies the summary type. Accepted value are c("continuous", "continuous2", "categorical", "dichotomous"). If not specified, default type is assigned via assign_summary_type(). See below for details.

value

(formula-list-selector)
Specifies the level of a variable to display on a single row. The gtsummary type selectors, e.g. all_dichotomous(), cannot be used with this argument. Default is NULL. See below for details.

missing, missing_text, missing_stat

Arguments dictating how and if missing values are presented:

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

(scalar logical)
Logical indicator to display an overall row. Default is FALSE. Use add_overall() to add an overall column.

overall_row_last

(scalar logical)
Logical indicator to display overall row last in table. Default is FALSE, which will display overall row first.

overall_row_label

(string)
String indicating the overall row label. Default is "Overall".

Value

A tbl_custom_summary object

Similarities with tbl_summary()

Please refer to the help file of tbl_summary() regarding the use of select helpers, and arguments include, by, type, value, digits, missing and missing_text.

stat_fns argument

The stat_fns argument specify the custom function(s) to be used for computing the summary statistics. For example, stat_fns = everything() ~ foo.

Each function may take the following arguments: foo(data, full_data, variable, by, type, ...)

  • data= is the input data frame passed to tbl_custom_summary(), subset according to the level of by or variable if any, excluding NA values of the current variable

  • full_data= is the full input data frame passed to tbl_custom_summary()

  • variable= is a string indicating the variable to perform the calculation on

  • by= is a string indicating the by variable from tbl_custom_summary=, if present

  • type= is a string indicating the type of variable (continuous, categorical, ...)

  • stat_display= a string indicating the statistic to display (for the statistic argument, for that variable)

The user-defined does not need to utilize each of these inputs. It's encouraged the user-defined function accept ... as each of the arguments will be passed to the function, even if not all inputs are utilized by the user's function, e.g. foo(data, ...) (see examples).

The user-defined function should return a one row dplyr::tibble() with one column per summary statistics (see examples).

statistic argument

The statistic argument specifies the statistics presented in the table. The input is a list of formulas that specify the statistics to report. For example, statistic = list(age ~ "{mean} ({sd})"). A statistic name that appears between curly brackets will be replaced with the numeric statistic (see glue::glue()). All the statistics indicated in the statistic argument should be returned by the functions defined in the stat_fns argument.

When the summary type is "continuous2", pass a vector of statistics. Each element of the vector will result in a separate row in the summary table.

For both categorical and continuous variables, statistics on the number of missing and non-missing observations and their proportions are also available to display.

  • {N_obs} total number of observations

  • {N_miss} number of missing observations

  • {N_nonmiss} number of non-missing observations

  • {p_miss} percentage of observations missing

  • {p_nonmiss} percentage of observations not missing

Note that for categorical variables, {N_obs}, {N_miss} and {N_nonmiss} refer to the total number, number missing and number non missing observations in the denominator, not at each level of the categorical variable.

It is recommended to use modify_footnote() to properly describe the displayed statistics (see examples).

Caution

The returned table is compatible with all gtsummary features applicable to a tbl_summary object, like add_overall(), modify_footnote() or bold_labels().

However, some of them could be inappropriate in such case. In particular, add_p() do not take into account the type of displayed statistics and always return the p-value of a comparison test of the current variable according to the by groups, which may be incorrect if the displayed statistics refer to a third variable.

Author

Joseph Larmarange

Examples

# Example 1 ----------------------------------
my_stats <- function(data, ...) {
  marker_sum <- sum(data$marker, na.rm = TRUE)
  mean_age <- mean(data$age, na.rm = TRUE)
  dplyr::tibble(
    marker_sum = marker_sum,
    mean_age = mean_age
  )
}

my_stats(trial)
#> # A tibble: 1 × 2
#>   marker_sum mean_age
#>        <dbl>    <dbl>
#> 1       174.     47.2

trial |>
  tbl_custom_summary(
    include = c("stage", "grade"),
    by = "trt",
    stat_fns = everything() ~ my_stats,
    statistic = everything() ~ "A: {mean_age} - S: {marker_sum}",
    digits = everything() ~ c(1, 0),
    overall_row = TRUE,
    overall_row_label = "All stages & grades"
  ) |>
  add_overall(last = TRUE) |>
  modify_footnote(
    all_stat_cols() ~ "A: mean age - S: sum of marker"
  ) |>
  bold_labels()



  
Characteristic
      Drug A

N = 981		
      Drug B

N = 1021		
      Overall

N = 2001		
    
All stages & grades
A: 47.0 - S: 94
A: 47.4 - S: 80
A: 47.2 - S: 174
T Stage





    T1
A: 44.1 - S: 19
A: 49.5 - S: 15
A: 46.8 - S: 35
    T2
A: 50.2 - S: 29
A: 46.4 - S: 29
A: 48.1 - S: 59
    T3
A: 48.8 - S: 21
A: 50.0 - S: 18
A: 49.4 - S: 39
    T4
A: 45.3 - S: 24
A: 44.3 - S: 18
A: 44.8 - S: 42
Grade





    I
A: 45.9 - S: 39
A: 46.4 - S: 31
A: 46.2 - S: 70
    II
A: 44.6 - S: 24
A: 50.3 - S: 19
A: 47.5 - S: 43
    III
A: 51.0 - S: 30
A: 45.7 - S: 30
A: 48.1 - S: 61
1 A: mean age - S: sum of marker
    

# Example 2 ----------------------------------
# Use `data[[variable]]` to access the current variable
mean_ci <- function(data, variable, ...) {
  test <- t.test(data[[variable]])
  dplyr::tibble(
    mean = test$estimate,
    conf.low = test$conf.int[1],
    conf.high = test$conf.int[2]
  )
}

trial |>
  tbl_custom_summary(
    include = c("marker", "ttdeath"),
    by = "trt",
    stat_fns = ~ mean_ci,
    statistic = ~ "{mean} [{conf.low}; {conf.high}]"
  ) |>
  add_overall(last = TRUE) |>
  modify_footnote(
    all_stat_cols() ~ "mean [95% CI]"
  )



  
Characteristic
      Drug A

N = 981		
      Drug B

N = 1021		
      Overall

N = 2001		
    
Marker Level (ng/mL)
1.02 [0.83; 1.20]
0.82 [0.65; 0.99]
0.92 [0.79; 1.04]
    Unknown
6
4
10
Months to Death/Censor
20.2 [19.2; 21.2]
19.0 [18.0; 20.1]
19.6 [18.9; 20.4]
1 mean [95% CI]
    

# Example 3 ----------------------------------
# Use `full_data` to access the full datasets
# Returned statistic can also be a character
diff_to_great_mean <- function(data, full_data, ...) {
  mean <- mean(data$marker, na.rm = TRUE)
  great_mean <- mean(full_data$marker, na.rm = TRUE)
  diff <- mean - great_mean
  dplyr::tibble(
    mean = mean,
    great_mean = great_mean,
    diff = diff,
    level = ifelse(diff > 0, "high", "low")
  )
}

trial |>
  tbl_custom_summary(
    include = c("grade", "stage"),
    by = "trt",
    stat_fns = ~ diff_to_great_mean,
    statistic = ~ "{mean} ({level}, diff: {diff})",
    overall_row = TRUE
  ) |>
  bold_labels()



  
Characteristic
      Drug A

N = 981		
      Drug B

N = 1021		
    
Overall
1.0173 (high, diff: 0.1014)
0.8208 (low, diff: -0.0952)
Grade



    I
1 (high, diff: 0)
1 (high, diff: 0)
    II
1 (low, diff: 0)
1 (low, diff: 0)
    III
1 (high, diff: 0)
1 (high, diff: 0)
T Stage



    T1
1 (low, diff: 0)
1 (low, diff: 0)
    T2
1 (high, diff: 0)
1 (high, diff: 0)
    T3
1 (high, diff: 0)
1 (high, diff: 0)
    T4
1 (high, diff: 0)
1 (low, diff: 0)
1 Mean (level, diff: diff)