summaryLevels: summaryLevels

Description

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")
)

Value

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

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".