summaryTable: Creates publication-ready summary tables

Description

Creates publication-ready summary tables based on the gtsummary package.

Usage

summaryTable(
  data,
  vars = NULL,
  group = NULL,
  labels = NULL,
  stat_cont = "median_range",
  stat_cat = "n_percent",
  continuous_as = "continuous",
  dichotomous_as = "dichotomous",
  value = NULL,
  test = FALSE,
  test_cont = "wilcox.test",
  test_cat = "fisher.test",
  ci = FALSE,
  ci_cont = "wilcox.test",
  ci_cat = "wilson",
  conf_level = 0.95,
  digits_cont = 1,
  digits_cat = 0,
  missing = TRUE,
  missing_percent = TRUE,
  missing_text = "Missing",
  overall = FALSE,
  add_n = TRUE,
  as_flex_table = TRUE,
  border = TRUE,
  word_output = FALSE,
  file_name = paste0("SummaryTable_", format(Sys.Date(), "%Y%m%d"), ".docx")
)

Value

A table of class "flextable" or c("tbl_summary", "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. "age" or c("age", "response"). 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.
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_cont: Summary statistic to display for continuous variables. Options include "median_IQR", "median_range" (default), "mean_sd", "mean_se" and "geomMean_sd".
stat_cat: Summary statistic to display for categorical variables. Options include "n_percent" (default) and "n", and "n_N".
continuous_as: Type for the continuous variables. Can either be "continuous" (default) or "categorical".
dichotomous_as: Type for the dichotomous variables. Can either be "categorical" (default, one row per level) or "dichotomous" (only one row with reference level (see argument value), only works if missing = "FALSE" or missing_percent = FALSE.
value: Specifies the reference level of a variable to display on a single row. Default is NULL. The syntax is as follows: value = list(varname ~ "level to show").
test: Logical. Indicates whether p-values are displayed (TRUE) or not (FALSE). Default to FALSE
test_cont: Test type used to calculate the p-value for continuous variables. Only used if test = TRUE. Options include "t.test", "oneway.test", "kruskal.test", "wilcox.test" (default), "paired.t.test", "paired.wilcox.test"
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_cont: Confidence interval method for continuous variables. Only used if ci = TRUE. Options include "t.test" and "wilcox.test" (default).
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_cont: Numeric. Digits for summary statistics and CI of continuous variables. Default to 1.
digits_cat: Numeric. Digits for summary statistics and CI of categorical variables. Default to 0.
missing: Logical. If TRUE (default), the missing values are shown.
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_text: String indicating text shown on missing row. Default to "Missing".
overall: Logical. If TRUE, an additional column with the total is added to the table. Default to FALSE.
add_n: Logical. If TRUE (default), an additional column with the total number of non-missing observations for each variable is added.
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".

Examples

Run this code


library(survival)
data("cancer")
summaryTable(data = cancer,vars = c("inst", "time","age", "ph.ecog"),
             labels = list(inst = "Institution code",
                           time = "Time",
                           age = "Age",
                           ph.ecog = "ECOG score"))

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