R: Format and print 'CatTable' class objects

print.CatTable {tableone}

R Documentation

Format and print `CatTable` class objects

Description

print method for the CatTable class objects created by CreateCatTable function.

Usage

## S3 method for class 'CatTable'
print(
  x,
  digits = 1,
  pDigits = 3,
  quote = FALSE,
  missing = FALSE,
  explain = TRUE,
  printToggle = TRUE,
  noSpaces = FALSE,
  format = c("fp", "f", "p", "pf")[1],
  showAllLevels = FALSE,
  cramVars = NULL,
  dropEqual = FALSE,
  test = TRUE,
  exact = NULL,
  smd = FALSE,
  CrossTable = FALSE,
  formatOptions = list(scientific = FALSE),
  ...
)

Arguments

`x`	Object returned by `CreateCatTable` function.
`digits`	Number of digits to print in the table.
`pDigits`	Number of digits to print for p-values (also used for standardized mean differences).
`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.
`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 FALSE, no output is created, and a matrix is invisibly returned.
`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.
`dropEqual`	Whether to drop " = second level name" description indicating which level is shown for two-level categorical variables.
`test`	Whether to show p-values. TRUE by default. If FALSE, only the numerical summaries are shown.
`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).
`smd`	Whether to show standardized mean differences. FALSE by default. If there are more than one contrasts, the average of all possible standardized mean differences is shown. For individual contrasts, use `summary`.
`CrossTable`	Whether to show the cross table objects held internally using gmodels::CrossTable function. This will give an output similar to the PROC FREQ in SAS.
`formatOptions`	A list of options, which will be passed to `format`. Can be used to modify the `big.mark`, `decimal.mark`, `big.interval` etc. The default is `list(scientific = FALSE)`. The options digits, nsmall, justify and trim are not available. (Experimental)
`...`	For compatibility with generic. Ignored.

Value

A matrix object containing what you see is also invisibly returned. This can be assinged a name and exported via write.csv.

Author(s)

Kazuki Yoshida, Alexander Bartel

Examples


## Load
library(tableone)

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

## Create an overall table for categorical variables
catVars <- c("status","ascites","hepato","spiders","edema","stage")
catTableOverall <- CreateCatTable(vars = catVars, data = pbc)

## Simply typing the object name will invoke the print.CatTable method,
## which will show the sample size, frequencies and percentages.
## For 2-level variables, only the higher level is shown for simplicity.
catTableOverall

## If you need to show both levels for some 2-level factors, use cramVars
print(catTableOverall, cramVars = "hepato")

## Use the showAllLevels argument to see all levels for all variables.
print(catTableOverall, showAllLevels = TRUE)

## You can choose form frequencies ("f") and/or percentages ("p") or both.
## "fp" frequency (percentage) is the default. Row names change accordingly.
print(catTableOverall, format = "f")
print(catTableOverall, format = "p")

## To further examine the variables, use the summary.CatTable method,
## which will show more details.
summary(catTableOverall)

## The table can be stratified by one or more variables
catTableBySexTrt <- CreateCatTable(vars = catVars,
                                   strata = c("sex","trt"), data = pbc)

## print now includes p-values which are by default calculated by chisq.test.
## It is formatted at the decimal place specified by the pDigits argument
## (3 by default). It does <0.001 for you.
catTableBySexTrt

## The exact argument toggles the p-values to the exact test result from
## fisher.test. It will show which ones are from exact tests.
print(catTableBySexTrt, exact = "ascites")

## summary now includes both types of p-values
summary(catTableBySexTrt)

## 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(catTableBySexTrt, exact = "ascites", quote = TRUE)

## If you want to center-align values in Word, use noSpaces option.
print(catTableBySexTrt, exact = "ascites", quote = TRUE, noSpaces = TRUE)

[Package tableone version 0.13.2 Index]

Format and print CatTable class objects