clinpubr (version 1.1.1)

baseline_table: Create a baseline table for a dataset.

Description

Create a baseline table and a table of missing values. If the strata variable has more than 2 levels, a pairwise comparison table will also be created.

Usage

baseline_table(
  data,
  var_types = NULL,
  strata = NULL,
  vars = NULL,
  factor_vars = NULL,
  exact_vars = NULL,
  nonnormal_vars = NULL,
  seed = NULL,
  omit_missing_strata = FALSE,
  save_table = FALSE,
  filename = NULL,
  multiple_comparison_test = TRUE,
  p_adjust_method = "BH",
  smd = FALSE,
  ...
)

Value

A list containing the baseline table and accompanying tables.

Arguments

data

A data frame.

var_types

An object from class var_types returned by get_var_types function.

strata

A variable to stratify the table. Overwrites the strata variable in var_types.

vars

A vector of variables to include in the table.

factor_vars

A vector of factor variables. Overwrites the factor variables in var_types.

exact_vars

A vector of variables to test for exactness. Overwrites the exact variables in var_types.

nonnormal_vars

A vector of variables to test for normality. Overwrites the nonnormal variables in var_types.

seed

A seed for the random number generator. This seed can be set for consistent simulation when performing fisher exact tests.

omit_missing_strata

A logical value indicating whether to omit missing values in the strata variable.

save_table

A logical value indicating whether to save the result tables.

filename

The name of the file to save the table. The file names for accompanying tables will be the same as the main table, but with "_missing" and "_pairwise" appended.

multiple_comparison_test

A logical value indicating whether to perform multiple comparison tests. Variables in factor_vars and exact_vars are tested with pairwise chisq.test or fisher.test, and other variables are tested with rstatix::dunn_test() or rstatix::games_howell_test().

p_adjust_method

The method to use for p-value adjustment for pairwise comparison. Default is "BH". See ?p.adjust.methods.

smd

A logical value indicating whether to include SMD in the table. Passed to tableone::print.TableOne().

...

Additional arguments passed to tableone::print.TableOne().

Examples

withr::with_tempdir(
  {
    data(cancer, package = "survival")
    var_types <- get_var_types(cancer, strata = "sex")
    baseline_table(cancer, var_types = var_types, filename = "baseline.csv")

    # baseline table with pairwise comparison
    cancer$ph.ecog_cat <- factor(cancer$ph.ecog,
      levels = c(0:3),
      labels = c("0", "1", ">=2", ">=2")
    )
    var_types <- get_var_types(cancer, strata = "ph.ecog_cat")
    baseline_table(cancer, var_types = var_types, save_table = TRUE, filename = "baseline.csv")
    print(paste0("files saved to: ", getwd()))
  },
  clean = FALSE
)