TableOne

Description

An R package that provides an easy way of exporting the descriptive table 1 that is commonly used in articles to a Word document for easy editing and copying to the article.

Installation

The package is still under active development and has not been submitted to the CRAN yet.

You can install the TableOne package from GitHub repository as follows:

Installation using R package devtools:

install.packages("devtools")
devtools::install_github("agapiospanos/TableOne")

Input data format

I will soon provide an excel file as a template for the input data format.

Usage example

The basic function of this package has the following syntax:

library(TableOne)
tableone(
  dichotomous = c('gender', 'hypertension'),
  group.col.name = 'hyperglycemia',
  control.value = 0,
  treatment.value = 1,
  import.col.names = c('age', 'gender', 'systbp', 'diastbp', 'hypertension'),
  output.var.names = c('Age', 'Females', 'Systolic Blood Pressure', 'Diastolic Blood Pressure', 'Hypertension')
)

List of arguments:

• import.col.names: Use a vector to specify the column names that will be loaded from the data.frame / excel
• output.var.names: Use a vector to specify the names of the variables. i.e. how the variables will appear in the exported table
• dichotomous: (optional) Use a vector to specify the column names that contain dichotomous data
• ordinal: (optional) Use a vector to specify the column names that contain ordinal data
• median.iqr: (optional) Use a vector to specify column names with continuous data for which the table will calculate median and IQR instead of mean and SD
• group.col.name: Specify which column contains the grouping variable.
• control.value: Specify the value that indicates the control group in the group.col.name
• treatment.value: Specify the value that indicated the treatment group in the group.col.name
• data: (optional) Pass a data.frame to this argument on case you want tableOne to load data from it instead of an excel file
• excel.path: (optional) Specify the path that the excel will be read from. In case you do not specify this argument, a pop up window will be displayed to choose the path
• export.path: (optional) Specify the path that the excel will be exported to. In case you do not specify this argument, a pop up window will be displayed to choose the path
• sheet: (optional) Specify the excel sheet number that you need to load data from. In case you do not specify this argument, the first sheet will be used
• tableone.col.names: (optional) A vector for the column names of the exported table. Default are: c('Variable', 'Treatment Group', 'Control Group', 'p-value', 'Mean Difference', 'OR', 'Test Stat.')
• export.filename (optional) the name of the file that will be exported. Do not include the .docx extension. (default filename is TableOne.docx)
• show.stats (optional) A vector that specifies which statistics will be displayed in the produced table One. By default it displays the MD, OR and Test Stat. value as additional statistics except from p-value
• export.word (optional) (default: TRUE) specify if you want to have a Word Document that contains the table one exported. Whether you export the table to Word or not, you will also get the results in a data.frame format after running the package.