Introduction

Another one of the most common tables in medical literature includes summary statistics for a set of variables paired across two time points. Locally at Mayo, the SAS macro %paired was written to create summary tables with a single call. With the increasing interest in R, we have developed the function paired() to create similar tables within the R environment.

This vignette is light on purpose; paired() piggybacks off of tableby, so most documentation there applies here, too.

Simple Example

The first step when using the paired() function is to load the arsenal package. We can’t use mockstudy here because we need a dataset with paired observations, so we’ll create our own dataset.

library(arsenal)
dat <- data.frame(
  tp = paste0("Time Point ", c(1, 2, 1, 2, 1, 2, 1, 2, 1, 2)),
  id = c(1, 1, 2, 2, 3, 3, 4, 4, 5, 6),
  Cat = c("A", "A", "A", "B", "B", "B", "B", "A", NA, "B"),
  Fac = factor(c("A", "B", "C", "A", "B", "C", "A", "B", "C", "A")),
  Num = c(1, 2, 3, 4, 4, 3, 3, 4, 0, NA),
  Ord = ordered(c("I", "II", "II", "III", "III", "III", "I", "III", "II", "I")),
  Lgl = c(TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE),
  Dat = as.Date("2018-05-01") + c(1, 1, 2, 2, 3, 4, 5, 6, 3, 4),
  stringsAsFactors = FALSE
)

To create a simple table stratified by time point, use a formula= statement to specify the variables that you want summarized and the id= argument to specify the paired observations.

p <- paired(tp ~ Cat + Fac + Num + Ord + Lgl + Dat, data = dat, id = id, signed.rank.exact = FALSE)
summary(p)

The third column shows the difference between time point 1 and time point 2. For categorical variables, it reports the percent of observations from time point 1 which changed in time point 2.

NAs

Note that by default, observations which do not have both timepoints are removed. This is easily changed using the na.action = na.paired("<arg>") argument. For example:

p <- paired(tp ~ Cat + Fac + Num + Ord + Lgl + Dat, data = dat, id = id,
            signed.rank.exact = FALSE, na.action = na.paired("fill"))
summary(p)

For more details, see the help page for na.paired().

Available Function Options

args(paired.control)

## function (diff = TRUE, numeric.test = "paired.t", cat.test = "mcnemar", 
##     ordered.test = "signed.rank", date.test = "paired.t", mcnemar.correct = TRUE, 
##     signed.rank.exact = NULL, signed.rank.correct = TRUE, ...) 
## NULL

args(arsenal:::summary.tableby)

## function (object, ..., labelTranslations = NULL, text = FALSE, 
##     title = NULL, pfootnote = FALSE, term.name = "") 
## NULL