summaryLevels

Collapses factor levels from multiple columns into one and creates summary table.

Usage

summaryLevels(
  data,
  vars = NULL,
  group = NULL,
  label = NULL,
  levels = NULL,
  stat_cat = "n_percent",
  test = FALSE,
  test_cat = "fisher.test",
  ci = FALSE,
  ci_cat = "wilson",
  conf_level = 0.95,
  digits_cat = 0,
  overall = FALSE,
  as_flex_table = TRUE,
  border = TRUE,
  word_output = FALSE,
  file_name = paste0("SummaryLevels_", format(Sys.Date(), "%Y%m%d"), ".docx")
)

Arguments

data

A data frame or tibble containing the data to be summarized.

vars

Variables to include in the summary table. Need to be specified with quotes, e.g. "score" or c("score", "age_cat"). Default to all variables present in the data except group.

group

A single column from data. Need to be specified with quotes, e.g. "treatment". Summary statistics will be stratified according to this variable. Default to NULL.

label

A label for the new variable to be created. If no label present, the variable name is taken.

levels

= A vector containing the values indicating presence of the factor level. Included by default are "1", "yes", "Yes".

stat_cat

Summary statistic to display for categorical variables. Options include "n_percent" (default) and "n", and "n_N".

test

Logical. Indicates whether p-values are displayed (TRUE) or not (FALSE). Default to FALSE

test_cat

Test type used to calculated the p-value for categorical variables. Only used if test = TRUE. Options include "fisher.test" (default), "chisq.test", "chisq.test.no.correct". If NULL, the function decides itself: "chisq.test.no.correct" for categorical variables with all expected cell counts >=5, and "fisher.test" for categorical variables with any expected cell count <5.

ci

Logical. Indicates whether CI are displayed (TRUE) or not (FALSE). Default to FALSE.

ci_cat

Confidence interval method for categorical variables. Options include "wilson" (default), "wilson.no.correct", "clopper.pearson", "wald", "wald.no.correct", "agresti.coull" and "jeffreys". If NULL, no CI will be displayed.

conf_level

Numeric. Confidence level. Default to 0.95.

digits_cat

Numeric. Digits for summary statistics and CI of categorical variables. Default to 0.

overall

Logical. If TRUE, an additional column with the total is added to the table. Default to FALSE.

as_flex_table

Logical. If TRUE (default) the gtsummary object is converted to a flextable object. Useful when rendering to Word.

border

Logical. If TRUE, a border will be drawn around the table. Only available if flex_table = TRUE. Default is TRUE.

word_output

Logical. If TRUE, the table is also saved in a word document.

file_name

Character string. Specify the name of the Word document containing the table. Only used when word_output is TRUE. Needs to end with ".docx".

Value

A table of class "flextable" or c("tbl_stack", "gtsummary"). Optionally returns a .docx file in the specified folder.