[R-sig-ME] Split plot design with repeated measures - model errors (nlme)

[I.M.S.White]

This is standard split-plot design.  The lme model formula is

fixed = ch4 ~ nut*clip*spp, random = ~1|tank, ...

Specify the treatment structure as fixed formula, plot structure as  
random. Here the plot structure is simple, mainplots (tanks), and  
subplots within mainplots. The latter does not need to be specified  
because it is residual, fitted always by default.



Quoting Anthony Rietl <anthony.rietl at gmail.com> on Fri, 31 Aug 2012  
17:12:52 -0500:

> 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
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>



::::::::::::::::::::::::::::::::::::::::::
: I.White                                :
: University of Edinburgh                :
: Ashworth Laboratories, West Mains Road :
: Edinburgh EH9 3JT                      :
: Tel 0131 650 5490  Fax 0131 650 6564   :
::::::::::::::::::::::::::::::::::::::::::

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.