desc_facvar: Summarise categorical variables
In vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox

desc_facvar

R Documentation

Summarise categorical variables

Description

Summarize categorical data and handle output format.

Usage

desc_facvar(
  .data,
  vf,
  format = "n_/N_ (pc_%)",
  digits = 0,
  pad_width = 12,
  ncat_max = 20,
  export_raw_values = FALSE
)

Arguments

`.data`	A data.frame, where `vf` are column names of categorical variables
`vf`	A character vector
`format`	A character string, formatting options.
`digits`	A numeric. Number of digits for the percentage (passed to interval formatting function).
`pad_width`	A numeric. Minimum character length of value output (passed to `stringr::str_pad()`).
`ncat_max`	A numeric. How many levels should be allowed for all variables? See details.
`export_raw_values`	A logical. Should the raw values be exported?

Details

Many other packages provide tools to summarize data. This one is just the package author's favorite. Important format inputs are

n_ number of patients with the categorical variable at said level
N_ the first quartile number of patients with an available value for this variable
pc_ percentage of n / N

The format argument should contain at least the words "n_", "N_", and optionally "pc_". ncat_max ensures that you didn't provided a continuous variable to desc_facvar(). If you have many levels for one of your variables, set to Inf or high value. Equivalent for continuous data is desc_cont().

Value

A data.frame with columns

var the variable name
level the level of the variable
value the formatted value with possible number of cases n_, number of available cases N_, and percentage pc_, depending on format argument.
n_avail the number of cases with available data for this variable.

Examples

df1 <-
  data.frame(
    smoke_status = c("smoker", "non-smoker",
           "smoker", "smoker",
           "smoker", "smoker",
           "non-smoker"
           ),
   hypertension = c(1, 1, 0, 1, 1, 1, 1),
    age = c(60, 50, 56, 49, 75, 69, 85),
    bmi = c(18, 30, 25, 22, 23, 21, 22)
  )

# Use default formatting
desc_facvar(.data = df1, vf = c("hypertension", "smoke_status"))

# Use custom formatting
desc_facvar(.data = df1,
           vf = c("hypertension", "smoke_status"),
           format = "n_ out of N_, pc_%",
           digits = 1)

# You might want to export raw values, to run plotting or
# other formatting functions

desc_facvar(.data = df1,
            vf = c("hypertension", "smoke_status"),
            export_raw_values = TRUE)

vigicaen documentation built on April 3, 2025, 8:55 p.m.