baseline_table {clinpubr} | R Documentation |
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,
...
)
Arguments
data |
A data frame. |
var_types |
An object from class |
strata |
A variable to stratify the table. Overwrites the strata variable in |
vars |
A vector of variables to include in the table. |
factor_vars |
A vector of factor variables. Overwrites the factor variables in |
exact_vars |
A vector of variables to test for exactness. Overwrites the exact variables in |
nonnormal_vars |
A vector of variables to test for normality. Overwrites the nonnormal variables in |
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
|
p_adjust_method |
The method to use for p-value adjustment for pairwise comparison. Default is "BH".
See |
smd |
A logical value indicating whether to include SMD in the table. Passed to |
... |
Additional arguments passed to |
Value
A list containing the baseline table and accompanying tables.
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, filename = "baselineV2.csv")
print(paste0("files saved to: ", getwd()))
},
clean = FALSE
)