lme4 Question

Hello Ben,

My name is Aimee Tallian and I am a Ph.D. student at Utah State
University. I have a question about you package, 'lme4'.

I have ran a bunch of analyses a while back in version 1.0-6, and
have since updated to version 1.1-7. I have gone back to the
initial analyses since I updated the package, and the results have
changed. Everything is mostly the same except for the standard
errors and p-values. What was significant is not anymore in several
cases, even though the code and data are the exact same. See output
below:

*Output (lme4_1.0-6) *

[image: Inline image 1]


*Output (lme4_1.1-7) Same output in versions 1.1-6 / 1.1-5* [image:
Inline image 2]


This statement is the only real change associated with SE that I
found between the versions that I have been using:

*From the news for version 1.1-4*: Standard errors of fixed effects
are now computed from the approximate Hessian by default (see the
use.hessian argument in vcov.merMod); this gives better (correct)
answers when the estimates of the random- and fixed-effect
parameters are correlated (Github #47)

I dug into the subject and it appears that this is the cause of my
inflated SE and p-values. I tried: summary(a1fit1,
use.hessian=FALSE), and as you suggested in the pdf manual, this
returned my results from before.

So, this is suggesting that my previous results are incorrect and
that I should use the estimates from the newer version (which means
a full start over)? Or is there justification for using my previous
results and using the hessian = FALSE command? I.e., how do I know
if my fixed and random effect parameters are correlated?

I really appreciate any advice you might have on the subject!

Thanks,

Aimee