tableone (version 0.5.0)

print.TableOne: Format and print the TableOne class objects

Description

This is the print method for the TableOne class objects created by CreateTableOne function.

Usage

## S3 method for class 'TableOne':
print(x, catDigits = 1, contDigits = 2, pDigits = 3,
  quote = FALSE, missing = FALSE, explain = TRUE, printToggle = TRUE,
  test = TRUE, noSpaces = FALSE, format = c("fp", "f", "p", "pf")[1],
  showAllLevels = FALSE, cramVars = NULL, exact = NULL,
  nonnormal = NULL, minMax = FALSE, ...)

Arguments

x

The result of a call to the CreateTableOne function.

catDigits

Number of digits to print for proportions. Default 1.

contDigits

Number of digits to print for continuous variables. Default 2.

pDigits

Number of digits to print for p-values. Default 3.

quote

Whether to show everything in quotes. The default is FALSE. If TRUE, everything including the row and column names are quoted so that you can copy it to Excel easily.

missing

Whether to show missing data information (not implemented yet, placeholder)

explain

Whether to add explanation to the variable names, i.e., (%) is added to the variable names when percentage is shown.

printToggle

Whether to print the output. If FLASE, no output is created, and a matrix is invisibly returned.

test

Whether to show the p-values. TRUE by default. If FALSE, only the numerical summaries are shown.

noSpaces

Whether to remove spaces added for alignment. Use this option if you prefer to align numbers yourself in other software.

format

The default is "fp" frequency (percentage). You can also choose from "f" frequency only, "p" percentage only, and "pf" percentage (frequency).

showAllLevels

Whether to show all levels. FALSE by default, i.e., for 2-level categorical variables, only the higher level is shown to avoid redundant information.

cramVars

A character vector to specify the two-level categorical variables, for which both levels should be shown in one row.

exact

A character vector to specify the variables for which the p-values should be those of exact tests. By default all p-values are from large sample approximation tests (chisq.test).

nonnormal

A character vector to specify the variables for which the p-values should be those of nonparametric tests. By default all p-values are from normal assumption-based tests (oneway.test).

minMax

Whether to use [min,max] instead of [p25,p75] for nonnormal variables. The default is FALSE.

...

For compatibility with generic. Ignored.

Value

• It is mainly for printing the result. But this function does return a matrix containing what you see in the output invisibly. You can assign it to an object to save it.

See Also

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

Examples

## Load
library(tableone)

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

## Make categorical variables factors
varsToFactor <- c("status","trt","ascites","hepato","spiders","edema","stage")
pbc[varsToFactor] <- lapply(pbc[varsToFactor], factor)

## Create Table 1 stratified by sex and trt
tableOne <- CreateTableOne(vars = c("time","status","age","ascites","hepato",
                                    "spiders","edema","bili","chol","albumin",
                                    "copper","alk.phos","ast","trig","platelet",
                                    "protime","stage"),
                           strata = c("sex","trt"), data = pbc)

## 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. cramVars can be used to
## show both levels for a 2-level categorical variables.
print(tableOne, nonnormal = c("bili","chol","copper","alk.phos","trig"),
      exact = c("status","stage"), cramVars = "hepato")

## 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 = "hepato", 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 = "hepato", quote = TRUE, noSpaces = TRUE)