Prior to the steps below, enter the data as appropriate for the analyses (described elsewhere). As always, the following commands should be typed directly in the R console window.
Get the sample sizes, means, and standard deviations for the variables.
lapply(PairedData, function(x) c(length(x), mean(x), sd(x)))
Test the mean difference for statistical significance and get its confidence interval.
t.test(Outcome2,Outcome1,paired=TRUE)
Also, you can change the width of the confidence interval if desired.
t.test(Outcome2,Outcome1,paired=TRUE,conf.level=.99)