[R-sig-eco] nested mixed model?

[ONKELINX, Thierry]

I aggree with Luciano. You should take the individual into account. The
point is only relevant as a random effect if you have multiple records
per point.

I would use something like lme(response ~ species, data=tooth,
random=~1|individual/bone/tooth) 

HTH,

Thierry

------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium

Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium

tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be

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say what the experiment died of.
~ Sir Ronald Aylmer Fisher

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~ Roger Brinner

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-----Oorspronkelijk bericht-----
Van: r-sig-ecology-bounces at r-project.org
[mailto:r-sig-ecology-bounces at r-project.org] Namens Luciano Selzer
Verzonden: woensdag 3 februari 2010 13:59
Aan: Mauricio Cifuentes
CC: r-sig-ecology at r-project.org
Onderwerp: Re: [R-sig-eco] nested mixed model?

Hi, I'm by no means an expert, just an PhD student. But in my humble
opinion shouldn't you consider the individual effect? I think that the
microtexture could be influenced by this.
Luciano


2010/2/3 Mauricio Cifuentes <mcifuent at gmail.com>

> Hi everybody,
>
> I am trying to fit a model in R using the lme() function. I would like

> to have your opinion about what I did and if there are better ways to 
> resolve this analysis. First Let me explain you how look the data that

> we are analyzing. We want to compare the tooth microtexture of four 
> species of ungulates.
>
> For that we have taken pictures in eight different points within each 
> tooth of one individual. We used as many teeth as were available for 
> each individual taken in account their position and at the same time 
> separating them by the place they were located (mandible: down tooth;
> maxilla: upper tooth).
>
> I am not an expert, but until here the model looks as nested design, 
> please let me know if I am wrong. In summary we have the following 
> hierarchy arrangement:
>
> Species (4 species) > bone(mandible or maxilla) > tooth > points 
> within each tooth (8 points).
>
> I have fitted this model using: lme(response ~ species, data=tooth,
> random=~1|bone/tooth/points,na.action=na.omit)
>
> I will be really grateful if you can give me your opinion about that.
>
> Best wishes
>
> Mauro
>
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> R-sig-ecology at r-project.org
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>

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