[R-sig-ME] Split plot design with repeated measures - model errors (nlme)
Anthony Rietl
anthony.rietl at gmail.com
Sat Sep 1 02:50:03 CEST 2012
Dennis,
Thanks for the response. For clarification, the treatments are
assigned to tanks at random. For example, all 18 tanks were randomly
assigned a nutrient treatment (1, 2, or 3) and randomly assigned a
clip treatment (a, b, or c). That gives 9 combinations, each
replicated once in a total of 18 tanks. After trying the model you
suggest (m1 <- lme(ch4 ~ t * spp * nut * clip, random = ~ 1 | tank/nut
* clip/spp,
> data = ch4data) I get another error - "Error in getGroups.data.frame(dataMix, groups) : Invalid formula for groups"
If I run the model without specifying nut*clip nested within tank, the
model runs leaving me to still suspect that I am still unclear how to
specify my nesting correctly. This is the model that runs - ch4.model
<- lme(ch4 ~ t * spp * nut * clip, random = ~ 1 | tank, data =
ch4data)
I will look through Pinheiro and Bates (2000), thanks for pointing me to it.
Anthony
On Fri, Aug 31, 2012 at 6:50 PM, Dennis Murphy <djmuser at gmail.com> wrote:
> Hi:
>
> It's not clear to me how nut and clip are assigned. Are two tanks assigned
> to each nut/clip combination at random? If so, then the df breakdown in the
> ANOVA should look something like
>
> Whole plot: (tank level)
>
> nut 2
> clip 2
> nut * clip 4
> Error(WP) 9
>
> Split plot: (section level)
>
> variety 3
> variety * nut 6
> variety* clip 6
> 3fi 12
> Error (SP) 27
>
> Split-split plot: (occasion level)
>
> Occasion 1
> (Cross occasion with everything above, same degrees of freedom)
>
> Occasion is equivalent to a split-split plot factor when the #occasions = 2,
> since you can only get a compound symmetric covariance structure in that
> case. That's how I'd analyze it, something like
>
> m1 <- lme(ch4 ~ t * spp * nut * clip, random = ~ 1 | tank/nut * clip/spp,
> data = ch4data)
>
> For reference, see the split-plot example starting on p.45 of Pinheiro and
> Bates (2000). I'm not sure about the correctness of the random effects
> specification, but check out the example to see how split-plot designs are
> programmed in lme(). I'd try it out myself, but no data were provided...
>
> HTH,
> Dennis
>
> On Fri, Aug 31, 2012 at 3:54 PM, Anthony Rietl <anthony.rietl at gmail.com>
> wrote:
>>
>> 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
>> >
>> > _______________________________________________
>> > R-sig-mixed-models at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> >
>> >
>>
>>
>>
>> --
>> Anthony Rietl
>> Graduate Student
>> Louisiana State University
>> Renewable Natural Resources
>> Baton Rouge, LA 70803
>> Office: (225) 578-1540
>>
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>
--
Anthony Rietl
Graduate Student
Louisiana State University
Renewable Natural Resources
Baton Rouge, LA 70803
Office: (225) 578-1540
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