In the non-formula signature of the t.test function t.test(x, y, paired=T), I'm assuming that the data are assumed paired as ordered in the two inputs (x and y in the documentation).
However, in the formula signature t.test(values ~ groups, df, paired=T), how does the function associate observations in the two groups as pairs? By order?
In the reprex below, I create a dataframe with paired before and after data. Then I put it in long form (as would be suitable for the t.test function) in two ways: 1) list "before" group in order of observation, then list "after" group in order of observation. 2) list all the data in no particular order.
I run a paired t-test on both data sets. It's pretty obvious that in case 2 the function has absolutely no way of knowing which "after" observation goes with which "before" observation. Can I assume that the t.test function understands the data as entered in case 1, that is the "before" and "after" data are both in order of observation?
I couldn't find anything about this in the documentation or any examples online. Because there is no argument for a key that links observations in the two groups, the t.test function is making some kind of assumption.
library(tidyverse)
df = data.frame(
observation = 1:20,
before = rnorm(20, 10, 2),
after = rnorm(20, 10.2, 2.3)
)
print.data.frame(df)
#> observation before after
#> 1 1 10.930157 11.818216
#> 2 2 10.870749 10.699232
#> 3 3 9.603120 14.384484
#> 4 4 9.615291 8.777045
#> 5 5 6.714043 9.506421
#> 6 6 9.063117 5.574887
#> 7 7 8.152260 10.357455
#> 8 8 8.256237 8.660646
#> 9 9 12.641977 7.511760
#> 10 10 11.010290 9.391047
#> 11 11 12.545197 9.072856
#> 12 12 12.606526 9.110687
#> 13 13 8.659088 12.445071
#> 14 14 8.958959 10.783168
#> 15 15 11.635443 6.926802
#> 16 16 6.922437 12.419453
#> 17 17 10.326176 10.416757
#> 18 18 7.680960 9.836573
#> 19 19 9.458365 8.083777
#> 20 20 7.235837 12.094290
df_long =
df %>%
pivot_longer(
cols = c("before", "after"),
names_to = "time",
values_to="fabulousness"
)
print.data.frame(df_long)
#> observation time fabulousness
#> 1 1 before 10.930157
#> 2 1 after 11.818216
#> 3 2 before 10.870749
#> 4 2 after 10.699232
#> 5 3 before 9.603120
#> 6 3 after 14.384484
#> 7 4 before 9.615291
#> 8 4 after 8.777045
#> 9 5 before 6.714043
#> 10 5 after 9.506421
#> 11 6 before 9.063117
#> 12 6 after 5.574887
#> 13 7 before 8.152260
#> 14 7 after 10.357455
#> 15 8 before 8.256237
#> 16 8 after 8.660646
#> 17 9 before 12.641977
#> 18 9 after 7.511760
#> 19 10 before 11.010290
#> 20 10 after 9.391047
#> 21 11 before 12.545197
#> 22 11 after 9.072856
#> 23 12 before 12.606526
#> 24 12 after 9.110687
#> 25 13 before 8.659088
#> 26 13 after 12.445071
#> 27 14 before 8.958959
#> 28 14 after 10.783168
#> 29 15 before 11.635443
#> 30 15 after 6.926802
#> 31 16 before 6.922437
#> 32 16 after 12.419453
#> 33 17 before 10.326176
#> 34 17 after 10.416757
#> 35 18 before 7.680960
#> 36 18 after 9.836573
#> 37 19 before 9.458365
#> 38 19 after 8.083777
#> 39 20 before 7.235837
#> 40 20 after 12.094290
df_long_not_paired =
df_long %>%
arrange(fabulousness)
print.data.frame(df_long_not_paired)
#> observation time fabulousness
#> 1 6 after 5.574887
#> 2 5 before 6.714043
#> 3 16 before 6.922437
#> 4 15 after 6.926802
#> 5 20 before 7.235837
#> 6 9 after 7.511760
#> 7 18 before 7.680960
#> 8 19 after 8.083777
#> 9 7 before 8.152260
#> 10 8 before 8.256237
#> 11 13 before 8.659088
#> 12 8 after 8.660646
#> 13 4 after 8.777045
#> 14 14 before 8.958959
#> 15 6 before 9.063117
#> 16 11 after 9.072856
#> 17 12 after 9.110687
#> 18 10 after 9.391047
#> 19 19 before 9.458365
#> 20 5 after 9.506421
#> 21 3 before 9.603120
#> 22 4 before 9.615291
#> 23 18 after 9.836573
#> 24 17 before 10.326176
#> 25 7 after 10.357455
#> 26 17 after 10.416757
#> 27 2 after 10.699232
#> 28 14 after 10.783168
#> 29 2 before 10.870749
#> 30 1 before 10.930157
#> 31 10 before 11.010290
#> 32 15 before 11.635443
#> 33 1 after 11.818216
#> 34 20 after 12.094290
#> 35 16 after 12.419453
#> 36 13 after 12.445071
#> 37 11 before 12.545197
#> 38 12 before 12.606526
#> 39 9 before 12.641977
#> 40 3 after 14.384484
df_long_paired =
df_long %>%
arrange(desc(time))
print.data.frame(df_long_paired)
#> observation time fabulousness
#> 1 1 before 10.930157
#> 2 2 before 10.870749
#> 3 3 before 9.603120
#> 4 4 before 9.615291
#> 5 5 before 6.714043
#> 6 6 before 9.063117
#> 7 7 before 8.152260
#> 8 8 before 8.256237
#> 9 9 before 12.641977
#> 10 10 before 11.010290
#> 11 11 before 12.545197
#> 12 12 before 12.606526
#> 13 13 before 8.659088
#> 14 14 before 8.958959
#> 15 15 before 11.635443
#> 16 16 before 6.922437
#> 17 17 before 10.326176
#> 18 18 before 7.680960
#> 19 19 before 9.458365
#> 20 20 before 7.235837
#> 21 1 after 11.818216
#> 22 2 after 10.699232
#> 23 3 after 14.384484
#> 24 4 after 8.777045
#> 25 5 after 9.506421
#> 26 6 after 5.574887
#> 27 7 after 10.357455
#> 28 8 after 8.660646
#> 29 9 after 7.511760
#> 30 10 after 9.391047
#> 31 11 after 9.072856
#> 32 12 after 9.110687
#> 33 13 after 12.445071
#> 34 14 after 10.783168
#> 35 15 after 6.926802
#> 36 16 after 12.419453
#> 37 17 after 10.416757
#> 38 18 after 9.836573
#> 39 19 after 8.083777
#> 40 20 after 12.094290
df_long_not_paired %>%
t.test(fabulousness ~ time, ., paired=T)
#>
#> Paired t-test
#>
#> data: fabulousness by time
#> t = 2.0289, df = 19, p-value = 0.05672
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#> -0.007878376 0.506318062
#> sample estimates:
#> mean of the differences
#> 0.2492198
df_long_paired %>%
t.test(fabulousness ~ time, ., paired=T)
#>
#> Paired t-test
#>
#> data: fabulousness by time
#> t = 0.3422, df = 19, p-value = 0.736
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#> -1.27509 1.77353
#> sample estimates:
#> mean of the differences
#> 0.2492198
Created on 2020-11-24 by the reprex package (v0.3.0)
When I run this multiple times, I frequently see false positives in the case where I have scrambled the group order.
So to find out exactly how this is done, we can look at the source code.
stats:::t.test.formula gives us:
g <- factor(mf[[-response]])
where mf is the model frame and response is the response variable. g is then the grouping variable from your formula (LHS).
Then, later, we see the creation of an object DATA which is the spliting of mf on the basis of the grouping variable g. This data is then passed to stats:::t.test.default without any changing of the order.
DATA <- setNames(split(mf[[response]], g), c("x", "y"))
We can then look into stats:::t.test.default, focusing on wherever paired data is mentioned.
if (paired) { x <- x - y y <- NULL } nx <- length(x) mx <- mean(x) vx <- var(x)
From this we see that t.test.default simply calculates the difference between pairs and then does a single-sample t-test on the difference.
From all of this together we understand that the order of the observations must be correct in order to have the correct pairs.