Creates publication-ready summary tables for categorical data grouped, by visit

Usage

summaryByVisitCategorical(
  data,
  vars = NULL,
  group = NULL,
  labels = NULL,
  stat_cat = "n_percent",
  visit = "visit",
  order = NULL,
  visitgroup = NULL,
  digits_cat = 1,
  missing_percent = TRUE,
  missing = TRUE,
  missing_text = "Missing",
  add_n = FALSE,
  overall = FALSE,
  as_flex_table = FALSE,
  border = TRUE,
  word_output = FALSE,
  file_path = paste0("SummaryByVisit_", format(Sys.Date(), "%Y%m%d"), ".docx")
)

Arguments

data: A data frame or tibble containing the data to be summarized.
vars: Continuous variables to include in the summary table. Need to be specified with quotes, e.g. "grade" or c("grade", "stage"). 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. A maximum of 3 groups are currently supported.
labels: A list containing the labels that should be used for the variables in the table. If NULL, labels are automatically taken from the dataset. If no label present, the variable name is taken.
stat_cat: Summary statistic to display for categorical variables. Options include "n", "n_N" and "n_percent" (default).
visit: Name of the stratum for which summary statistics are displayed by line. Typically, this would be "visit".
order: A numerical variable defining the visit order.
visitgroup: A grouping variable for the stratum for which summary statistics are displayed by line. Must be an ordered factor. Typically, this would be a visit group such as e.g., baseline, follow-up etc.
digits_cat: Digits for summary statistics of categorical variables. Default to 1.
missing_percent: Indicates whether percentages for missings are shown (TRUE, default) or not (FALSE) for categorical variables. If "both", then both options are displayed next to each other.
missing: Logical. If TRUE (default), the missing values are shown.
missing_text: String indicating text shown on missing row. Default to "Missing".
add_n: Logical. If TRUE, an additional column with the total number of non-missing observations for each variable is added.
overall: Logical. If TRUE, an additional column with the total is added to the table. Ignored, if no groups are defined. 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_path: Character string. Specify the path 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_strata_nested_stack", "tbl_stack", "gtsummary"). Optionally returns a .docx file in the specified folder.