- the difference between t-tests and Z-tests (as pointed out by @vkehayas); t-tests account for the uncertainty in the estimate of the standard error, so should be preferred to Z-tests where available.
- the fact that
summary.lme
by default adjusts the residual standard error for ML estimates (whileglht
doesn't); ML estimation in general gives a slightly downward-biased estimate of the standard error (by a factor $\sqrt{(n-p)/n}$), so this adjustment should be preferred where available. This is theadjustSigma
parameter ofsummary.lme
:
Both of these adjustments should in general make little difference unless your sample is small, but both adjustSigma=TRUE
and t-tests rather than Z-test are technically more correct, so in a pinch you should probably accept the results of summary(.)
rather than those of glht()
.
If you have a factor with more than two levels (so that you need to summarize the joint significance of multiple parameters), you can use anova()
, which uses F tests (the analog of t-tests) and includes an adjustSigma
option: if you want to do more complicated post hoc testing (e.g. Tukey pairwise comparisons), you will probably need to use glht()
and accept that your answers will be slightly anticonservative/optimistic.