Title: Produces Publication-Ready Summary Tables
Version: 0.1.1
Description: Produces tables with descriptive statistics for continuous, categorical and dichotomous variables. It is largely based on the package 'gtsummary'; Sjoberg DD et al. (2021) <doi:10.32614/RJ-2021-053>.
License: LGPL-3
Encoding: UTF-8
RoxygenNote: 7.3.2
Imports: Hmisc, cardx, dplyr, gtsummary (≥ 2.3.0), forcats, labelled, purrr, rlang, tidyr, flextable, officer
Suggests: knitr, tidyverse, survival
VignetteBuilder: knitr
URL: https://github.com/SAKK-Statistics/summarySCI/
BugReports: https://github.com/SAKK-Statistics/summarySCI/issues
NeedsCompilation: no
Packaged: 2025-10-09 12:20:09 UTC; charlottemi
Author: Sämi Schär [aut], Charlotte Micheloud [cre, aut]
Maintainer: Charlotte Micheloud <Charlotte.Micheloud@swisscancerinstitute.ch>
Depends: R (≥ 4.1.0)
Repository: CRAN
Date/Publication: 2025-10-15 20:00:02 UTC

Geometric mean

Description

This function return the geometric mean

Usage

geom_mean(x, na.rm = TRUE)

Arguments

x

Numeric vector

Value

Geometric mean

Get the labels from a dataset

Description

This function get the labels from a dataset

Usage

get_labels(data, vars)

Arguments

data

Dataset

vars

Variables of interest

Value

The labels

Standard error

Description

This function return the standard error

Usage

se(x)

Arguments

x

Numeric vector

Value

standard error

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

Description

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

Usage

summaryByVisit(
  data,
  vars = NULL,
  group = NULL,
  labels = NULL,
  stat_cont = "median_range",
  visit = "visit",
  order = NULL,
  visitgroup = NULL,
  digits_cont = 1,
  add_n = FALSE,
  overall = FALSE,
  as_flex_table = TRUE,
  border = TRUE,
  word_output = FALSE,
  file_name = 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. "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. 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_cont

Summary statistic to display for continuous variables. Options include "median_IQR", "median_range" (default), "mean_sd", "mean_se" and "geomMean_sd".

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_cont

Digits for summary statistics and CI of continuous variables. Default to 1.

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_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_strata_nested_stack", "tbl_stack", "gtsummary"). Optionally returns a .docx file in the specified folder.

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")
)

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.

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")
)

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".

Value

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

Examples


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"))