Generate Table One Summary Statistics

Generates publication-ready descriptive statistics (Table 1) for selected variables from a REDCap project. Produces n (%), mean (SD), or median (IQR) based on variable type and distribution. Supports stratification by grouping variables and filtering of records.

The function automatically handles character-stored numeric data (common in REDCap) by attempting numeric conversion. Missing values are properly handled and reported.

Usage

generate_table_one(
  project,
  vars = NULL,
  strata = NULL,
  filter = NULL,
  cat_vars = NULL,
  cont_vars = NULL,
  non_normal = NULL,
  include_missing = TRUE,
  test = FALSE,
  test_type = "auto",
  digits = 1,
  output_format = "data.frame",
  datatable = FALSE
)

Arguments

project

A redcap_project object

vars

Character vector of variable names to include in the table. If NULL, all non-ID fields are included (default: NULL)

strata

Character vector of variable name(s) to stratify by (default: NULL for no stratification)

filter

Character vector of filter expressions to subset data (e.g., c("age > 18", "consent == 1")). Uses standard R logical expressions. Multiple filters are combined with AND logic. For security, only data frame operations are allowed - system calls and file operations are blocked (default: NULL)

cat_vars

Character vector of variables to force as categorical (overrides auto-detection)

cont_vars

Character vector of variables to force as continuous (overrides auto-detection). Character data will be converted to numeric if possible.

non_normal

Character vector of continuous variables to display as median (IQR) instead of mean (SD) (default: NULL)

include_missing

Logical. Include missing data counts (default: TRUE)

test

Logical. Include statistical tests comparing strata (default: FALSE)

test_type

Character. Type of test: "auto" (default), "parametric", "nonparametric"

digits

Numeric. Number of decimal places for continuous variables (default: 1)

output_format

Character. Output format: "data.frame" (default), "kable", "gt", "flextable"

datatable

Logical. Return output as a DT datatable (default: FALSE)

Value

A data frame or formatted table object depending on output_format

Examples

if (FALSE) { # \dontrun{
project <- redcap_project()

# Basic table with all variables
table_one <- generate_table_one(project)

# Filtered and stratified
table_one <- generate_table_one(
  project,
  filter = c("withdrawn != 1", "consent_complete == 1"),
  strata = "treatment_group"
)

# Force variable types
table_one <- generate_table_one(
  project,
  vars = c("age", "gender", "bmi", "study_group"),
  cat_vars = c("gender", "study_group"),
  cont_vars = c("age", "bmi"),
  non_normal = "bmi",
  test = TRUE
)
} # }