I'm trying to use
lme from the
nlme package to replicate results from
aov for repeated measures ANOVAs. I've done this for a single-factor repeated measures experiment and for a two-factor experiment with one between-subjects factor and one within-subjects factor, but I'm having trouble doing it for a two-factor experiment with two within-subjects factors.
An example is shown below.
B are fixed-effect factors and
subject is a random-effect factor.
set.seed(1) d <- data.frame( Y = rnorm(48), subject = factor(rep(1:12, 4)), A = factor(rep(1:2, each=24)), B = factor(rep(rep(1:2, each=12), 2))) summary(aov(Y ~ A*B + Error(subject/(A*B)), data=d)) # Standard repeated measures ANOVA library(nlme) # Attempts: anova(lme(Y ~ A*B, data=d, random = ~ 1 | subject)) # not same as above anova(lme(Y ~ A*B, data=d, random = ~ 1 | subject/(A+B))) # gives error
I could not see an explanation of this in the Pinheiro and Bates book, but I may have overlooked it.