I am trying to use glmer
to model coral recruitment and get the error "Error: Invalid grouping factor specification, Site" when I run the model after re-scaling the variables. Help greatly appreciated
m1<-glmer(Tot~cs.Tile(Tile)+cs.Coral_T(Coral_T)+cs.Sponge(Sponge)+
cs.Turf(Turf)+cs.Acro(Acro)+cs.Por(Por)+cs.Poc(Poc)+
cs.Mer(Mer)+cs.Agar(Agar)+cs.Fav(Fav)+
cs.Den(Den)+cs.Sid(Sid)+cs.CCA(CCA)+cs.Soft(Soft)+
(1|Site),
family=poisson, data=data)
I have 16 variables and 368 obs:
str(data)
'data.frame': 368 obs. of 16 variables:
$ Site : Factor w/ 25 levels "Eight","Eighteen",..: 10 10 10 10 10 10 10 10 10 10 ...
$ Tile : int 1 2 3 4 5 6 7 8 9 10 ...
$ Tot : int 28 24 17 13 29 19 6 13 14 4 ...
$ Coral_T: num 32.6 32.6 32.6 32.6 32.6 ...
$ Sponge : num 0.206 0.206 0.206 0.206 0.206 ...
$ Turf : num 32.3 32.3 32.3 32.3 32.3 ...
$ Acro : num 3.45 3.45 3.45 3.45 3.45 ...
$ Por : num 1.15 1.15 1.15 1.15 1.15 ...
$ Poc : num 0 0 0 0 0 0 0 0 0 0 ...
$ Mer : num 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 ...
$ Agar : num 24.2 24.2 24.2 24.2 24.2 ...
$ Fav : num 1.02 1.02 1.02 1.02 1.02 ...
$ Den : num 1.18 1.18 1.18 1.18 1.18 ...
$ Sid : int 0 0 0 0 0 0 0 0 0 0 ...
$ CCA : num 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 ...
$ Soft : num 0 0 0 0 0 0 0 0 0 0 ...
I encountered the same error in a call to
update.merMod
, also after re-scaling variables. After digging down through thetraceback()
stack and rummaging around with what I found there using both the scaled and un-scaled datasets, I found that the issue arose in the creation of the model frame, and occurred because my scaling and centering algorithm failed to account forNA
values in the original variables. I originally performed the centering/scaling as follows:There were a few
NA
values in one of those variables, and scaling and centering it in this way resulted in an empty (allNA
) vector incsData
. This subsequently (and silently) led to the return of an empty frame frommodel.frame()
. Though the empty frame was what tripped the error, it (the error) came about because of my (mis)handling theNA
values in my variables during the re-scaling. Settingna.rm=TRUE
for the calls tosd()
andmean()
solved the issue for me: