I want to run a linear mixed model (LMM) testing the effects of two continuous variables (FD and FI) over time (Year:FD, Year:FI) on my response variable (QMD). For LMMs I typically use lmer4 but as in this model the variance increases over time, I want to use nlme to weight the model variance by year (using VarIdent=Year). However, when I run the ANOVA table of the model, it seems something is not correct. The Denonminator degrees of freedom (DenDF) do not seem correct.
When I compare the estimated DenDF of lmer (lme4) and lme (nlme) models, they are very different. The other estimates vary also, but I assumed this was because, as I said before, in the lme model I weighted the variance by year. Do you know why the two models report so different DenDFs?
Here the lmer model without weighting the variance by year
mod_lmer <- lmer (QMD ~ FD*Year + FI*Year + (1|Block) + (1|Plot), data=QMD_data, REML=TRUE)
Now, running the lme model - following BenBolker's approach to include crossed random factors in lme models - enter link description here
mod_lme = lme (QMD ~ FdisPC1 * Inv + CWM_PC1 * Inv,
random=list(Dummy = pdBlocked(list(pdIdent(~Plot-1),
pdIdent(~Block-1)))),
data=QMD_data,
weights = varIdent(form = ~1 | Inv),method="REML",control =list(msMaxIter = 1000, msMaxEval = 1000))
Does someone know why the estimated DenDF are so different from each other? Also, I realized that when in lmer model the DenDF for FDisPC1 and CWM_PC1 are different than the rest of the variables (34), in lme model both have the same DenDF that the other effects (1591)


anova()for the olderlmefunction doesn't even try to take those problems into account. See this page for approximations used inlmermodels. – EdM May 19 '23 at 16:03