[R-sig-ME] Split plot design with repeated measures - model errors (nlme)
Anthony Rietl
anthony.rietl at gmail.com
Sat Sep 1 00:12:52 CEST 2012
Forgive me if this has been answered, but after extensive searching I
have found nothing to help me. Here is a brief overview of the
experiment:
-I have 18 tanks, each of which are split into 4 sections, each
section has a different specie of wetland plant. Tank is my whole plot
factor. Variety, or species (spp), is my split plot factor.
-I have 2 treatments, each at three levels. Nutrient addition (nut)
and clipping (clip)
-I am measuring methane (ch4) emission as my response variable. I
measured methane on 2 occasions, represented by variable t for time.
Data Structure
>str(ch4data)
'data.frame': 144 obs. of 6 variables:
$ tank: Factor w/ 18 levels "1","2","3","4",..: 1 1 1 1 2 2 2 2 3 3 ...
$ spp : Factor w/ 4 levels "Emac","Ewal",..: 4 2 3 1 3 4 1 2 1 4 ...
$ nut : Factor w/ 3 levels "1","2","3": 2 2 2 2 1 1 1 1 3 3 ...
$ clip: Factor w/ 3 levels "a","b","c": 3 3 3 3 2 2 2 2 2 2 ...
$ t: Factor w/ 2 levels "1","2": 1 1 1 1 1 1 1 1 1 1 ...
$ ch4 : num 0.382 1.642 1.529 0.245 11.482 ...
Model
ch4.model = lme(fixed = ch4 ~ spp+nut+clip+t + spp*nut+spp*clip+spp*t
+ nut*clip+nut*t + clip*t + spp*nut*clip + spp*nut*clip*t
+(nut*clip)%in%tank, random= ~1|tank, data=ch4data)
this gives the following error
Error in MEEM(object, conLin, control$niterEM) : Singularity in
backsolve at level 0, block 1
Specifically, my questions are as follows: What is wrong with the fit
of my model and what does this error mean? What in my model is
singular? Have I over specified the model? I think the problem is with
nesting the nut*clip interaction within tank, but I'm not sure.
Additional help with fitting this model correctly would be much
appreciated. I am new to R, so please take that into account.
Thanks,
Anthony
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