# How to properly perform “change from baseline” (pre-post) analysis adjusting for pre using lme4 in R?

Let's assume I have the following data set, consisting of pre (t1) and post (t2) measurements. I want to check, if there is a significant effect over time (t1, t2).

d <- structure(list(pre = c(1, 2, 2.3, 1.3, 4.4, 3.4, 5.3, 2.2, 4.4,
3.3, 5.5, 7, 8.8, 3.3, 6, 7.7, 2.2), post = c(2, 4.3, 7.1, 8.1,
5.3, 4.3, 3.2, 5.7, 6.5, 4.4, 6.6, 7, 9.9, 6.6, 6, 6.6, 8.8),
diff = c(1, 2.3, 4.8, 6.8, 0.899999999999999, 0.9, -2.1,
3.5, 2.1, 1.1, 1.1, 0, 1.1, 3.3, 0, -1.1, 6.6)), .Names = c("pre",
"post", "diff"), row.names = c(NA, -17L), class = "data.frame")


It was tempting to use the paired t.test:

> t.test(d$$pre, d$$post, paired = TRUE)

Paired t-test

data:  d$$pre and d$$post
t = -3.1952, df = 16, p-value = 0.005634
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-3.1605916 -0.6394084
sample estimates:
mean of the differences
-1.9


Then I quickly checked, whether I can reproduce this using lm()

> summary(lm( (post-pre) ~ 1, data=d))

Call:
lm(formula = (post - pre) ~ 1, data = d)

Residuals:
Min     1Q Median     3Q    Max
-4.0   -1.0   -0.8    1.4    4.9

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept)   1.9000     0.5946   3.195  0.00563 **
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 2.452 on 16 degrees of freedom


OK. It works. Now, I wanted to adjust for the pre value, as it is accepted in analysing data from observational trials. I cannot use t.test any more, so I switched to lm(). First, I switched to the long format (no third-party packages):

dl <- reshape(data=d, idvar="subj", varying = c("pre", "post"), times=c("pre", "post"), v.name=c("value"), direction="long", new.row.names = 1:100)


With result:

> rbind(head(dl,3), tail(dl,3))
diff time value subj
1.pre    1.0  pre   1.0    1
2.pre    2.3  pre   2.0    2
3.pre    4.8  pre   2.3    3
15.post  0.0 post   6.0   15
16.post -1.1 post   6.6   16
17.post  6.6 post   8.8   17


Now I also added the "pre" to the data.frame

dl$$pre <- c(d$$pre, d\$pre)


And did this:

> summary(lme4::lmer(value ~ time + pre + (1|subj), data=dl))
singular fit
Linear mixed model fit by REML ['lmerMod']
Formula: value ~ time + pre + (1 | subj)
Data: dl

REML criterion at convergence: 126.5

Scaled residuals:
Min      1Q  Median      3Q     Max
-2.2960 -0.5785 -0.1819  0.4949  2.5783

Random effects:
Groups   Name        Variance  Std.Dev.
subj     (Intercept) 1.097e-15 3.313e-08
Residual             2.449e+00 1.565e+00
Number of obs: 34, groups:  subj, 17

Fixed effects:
Estimate Std. Error t value
(Intercept)   3.3254     0.6244   5.326
timepre      -1.9000     0.5368  -3.539
pre           0.6543     0.1202   5.442

Correlation of Fixed Effects:
(Intr) timepr
timepre -0.430
pre     -0.794  0.000
convergence code: 0
singular fit


Then, I calculated the CI for the mean difference (mm holds the result of lmer):

> confint(mm, method="Wald")
2.5 %     97.5 %
.sig01              NA         NA
.sigma              NA         NA
(Intercept)  2.1016860  4.5491895
timepre     -2.9521169 -0.8478831
pre          0.4186819  0.8899503


The CI for "timepre" is shorter than the CI returned by the paired t.test, which is expected. The estimate for the difference is (ignoring the sign) 1.9, t is now much larger (I believe due to pre included).

Now, my question is, do I do it properly? I need just "paired t.test adjusted for pre" and a CI.

By the way, in clinical research, often data like this is summarized by: mean_t1, mean_t2, difference, CI_for_difference, CI_adj_for_pre. But how can we report the difference of means and report the CI for that, if these are paired data? This is rather mean of differences, isn't it?

What you have done here is correct ! The confidence interval is smaller due to conditioning on baseline. The mistake a lot of people make is to regress the change on baseline which is very bad due to mathematical coupling which can invoke bias.

There are quite a few questions on Cross Validated with answers that go into this is depth. For example:
Is there a mathematical proof for change being correlated with baseline value

Also related is my answer here:
Difference between Repeated measures ANOVA, ANCOVA and Linear mixed effects model

Also, specifically regarding ANCOVA, see my answer here:
Is ANCOVA correct here?

For more background and further detail this is a very good paper on the topic:
Tu YK, Gilthorpe MS. Revisiting the relation between change and initial value: a review and evaluation. Stat Med. 2007;26(2):443-457. doi:10.1002/sim.2538
https://pubmed.ncbi.nlm.nih.gov/16526009/

• "which is very bad due to mathematical coupling which can invoke bias" It could be very good to expand this statement with more reasoning or references. – ttnphns Aug 4 '20 at 13:24
• Asking, because there exists also opposite statement that it is sane to regress (or ANCOVA) the change (the difference) on baseline. – ttnphns Aug 4 '20 at 13:28
• @ttnphns ANCOVA can also be biased if subjects are not randomised to the groups. I wrote a long answer on this, with references, not long ago. I will try to find it and add a link to my answer. Thanks ! – Robert Long Aug 4 '20 at 13:43
• Thanks. If you collect even more links, relevant to the baseline controversy, bring them in either. Thanks again. – ttnphns Aug 4 '20 at 14:37
• Does this answer your question ? If so, please consider marking it as the accepted answer, and if not please let us know why. – Robert Long Aug 21 '20 at 12:09