[R-sig-ME] Split plot design with repeated measures - model errors (nlme)
Anthony Rietl
anthony.rietl at gmail.com
Sat Sep 1 00:54:50 CEST 2012
Tom,
Thanks for your input. My treatments (nut & clip) were applied to the
entire tank and all 4 species within that tank, making it a true split
plot. Each treatment combination also had a replicate - for example, 2
tanks would have the treatment combination of 1(nut) and a(clip), and
so on for other treatments. I was not aware that spp*nut*clip*t would
give me main effect, 2-way, and 3-way interactions. Thanks for
pointing that out. However, if I run the model with spp*nut*clip*t,
removing all of the other interactions, I still get the same error
regarding singularity, making me think that the nested term is still a
problem.
Thanks,
Anthony
On Fri, Aug 31, 2012 at 5:29 PM, <Tom_Philippi at nps.gov> wrote:
> Anthony--
> You did not specify whether your nutrient and clipping treatments are
> applied to entire tanks, quadrants within tanks, or individual plants
> within quadrants, so I don't think anyone can suggest the proper model
> specification.
>
> Nonetheless, I suspect that the error message is because your formula
> specifies each main effect several times. Note that spp*nut*clip*t is not
> just the 4-way interaction, but each main effect, 2-way, and 3-way
> interaction. spp:nut:clip:t would be the 4-way interaction. See the
> documentation for formula, or any of relevant resources listed at:
> http://cran.r-project.org/other-docs.html
>
> Tom
>
>
>
>
>
> Anthony Rietl
> <anthony.rietl at gm
> ail.com> To
> Sent by: r-sig-mixed-models at r-project.org
> r-sig-mixed-model cc
> s-bounces at r-proje
> ct.org Subject
> [R-sig-ME] Split plot design with
> repeated measures - model errors
> 08/31/2012 05:12 (nlme)
> PM EST
>
>
>
>
>
>
>
>
>
> 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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>
--
Anthony Rietl
Graduate Student
Louisiana State University
Renewable Natural Resources
Baton Rouge, LA 70803
Office: (225) 578-1540
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