R t-test Grouping factor must have exactly 2 levels error

The problem is that your grouping variable has more than two levels, when the t.test requires that you cannot have more than two levels.

Here is a reproduction of your error:

library(tidyverse)


##This will reproduce your error

##Create some fake data
data_test <- tibble(measure = c(rnorm(100,30,5),rnorm(100,15,5)),
       group = factor(rep(c("A","B","C"),c(95,95,10))))


table(data_test$group) ##Notice that you have three levels

#Try to run the test
t.test(measure~group, data = data_test, paired = TRUE)

Here is an example that will run

##This will not result in a error, because you only have two groups

data_test2 <- tibble(measure = c(rnorm(100,30,5),rnorm(100,15,5)),
                    group = factor(rep(c("A","B"),c(100,100))))

table(data_test$group) ##Notice that you have the required two levels
t.test(measure~group, data = data_test2,paired = TRUE) ##Test will now run

Takeaway: Check the number of levels in your data. If there are more than two, recode or delete them.