Possible bug in lmer nested analysis with factors
On 16 Sep 2005, at 17:21, Sundar Dorai-Raj wrote:
My guess is he wants this:
c1 <- factor(c)
d1 <- factor(d)
m <- lmer(a ~ b + (1|c1:d1)+(1|c1))
which assumes d1 is nested within c1.
Take a look at Section 3 in the "MlmSoftRev" vignette:
library(mlmRev)
vignette("MlmSoftRev")
Ah, that vignette is extremely useful: it deserves to be more widely known. I mainly intended this reply to be a thank you to yourself and Harold. Unfortunately, there is (as always), one last thing that is still puzzling me: the df for fixed factors seems to vary between what I currently understand to be equivalent calls to lme and lmer, e.g: ------- a<-rnorm(36); b<-factor(rep(1:3,each=12)) c<-factor(rep(1:2,each=6,3)) d<-factor(rep(1:3,each=2,6)) c <- evalq(b:c)[,drop=T] #make unique factor levels d <- evalq(c:d)[,drop=T] #make unique factor levels summary(lme(a ~ b, random=~1|c/d)) # output includes estimates for fixed effects such as # Value Std.Error DF t-value p-value # (Intercept) 0.06908901 0.3318330 18 0.2082041 0.8374 # b2 0.13279084 0.4692828 3 0.2829655 0.7956 # b3 -0.26146698 0.4692828 3 -0.5571630 0.6163 # I understand the above lme model to be equivalent to summary(lmer(a ~ b + (1|c) +(1|c:d)) #but this gives fixed effects estimates with differing DF: # Estimate Std. Error DF t value Pr(>|t|) # (Intercept) 0.069089 0.331724 33 0.2083 0.8363 # b2 0.132791 0.469128 33 0.2831 0.7789 # b3 -0.261467 0.469128 33 -0.5573 0.5811 Again, many thanks for your help: even more so if you or anyone else can answer this last little niggle of mine. Yan