tableone (version 0.5.0)

tableone-package: Create "Table 1" to describe baseline characteristics

Description

This package creates "Table 1", i.e., description of baseline patient characteristics, which is essential in every medical research. This package provides functions to create such summaries for continuous and categorical variables, optionally with subgroup comparisons. The package was insipired by and based on descriptive statistics functions in Deducer, a Java-based GUI package by Ian Fellows. This package does not require GUI or Java, and intended for command-line users.

See Also

CreateTableOne, print.TableOne, summary.TableOne, CreateContTable, print.ContTable, summary.ContTable, CreateCatTable, print.CatTable, summary.CatTable, ShowRegTable

Examples

## Load
library(tableone)

## Load Mayo Clinic Primary Biliary Cirrhosis Data
library(survival)
data(pbc)
## Check variables
head(pbc)

## List numerically coded categorical variables for later conversion.
## Factor variables are automatically handled as categorical variables.
factorVars <- c("status","trt","ascites","hepato","spiders","edema","stage")

## Create a variable list
dput(names(pbc))    # This shows a character vector-creating syntax.
vars <- c("time","status","age","sex","ascites","hepato",
          "spiders","edema","bili","chol","albumin",
          "copper","alk.phos","ast","trig","platelet",
          "protime","stage")

## Create Table 1 stratified by trt. Use factorVars to convert numerically
## coded categorical variables as factors without changing the dataset.
tableOne <- CreateTableOne(vars = vars, strata = c("trt"), data = pbc,
                           factorVars = factorVars)

## Just typing the object name will invoke the print.TableOne method
tableOne

## Specifying nonnormal variables will show the variables appropriately,
## and show nonparametric test p-values. Specify variables in the exact
## argument to obtain the exact test p-values. For two-level categorical
## variables specified in cramVars, both levels are shown. Use minMax
## argument to show median [min, max] for nonnormal variables.
print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
      exact = c("status","stage"), cramVars = "sex")

## Use the summary.TableOne method for detailed summary
summary(tableOne)

## See the categorical part only using $ operator
tableOne$CatTable
summary(tableOne$CatTable)

## See the continuous part only using $ operator
tableOne$ContTable
summary(tableOne$ContTable)

## If your work flow includes copying to Excel and Word when writing manuscripts,
## you may benefit from the quote argument. This will quote everything so that
## Excel does not mess up the cells.
print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
      exact = c("status","stage"), cramVars = "sex", quote = TRUE)

## If you want to center-align values in Word, use noSpaces option.
print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
      exact = c("status","stage"), cramVars = "sex", quote = TRUE, noSpaces = TRUE)