[R-sig-eco] quadratic factor

[Simon Blomberg]

To include a quadratic term, use I(Dor^2) instead of Dor^2. The problem
is that R interprets Dor^2 as a formula term ie the main effect as well
as the second-order interaction of Dor with itself (which is just Dor).
Using the I() construct tells R to treat the enclosed expression as a
mathematical expression.

Cheers,

Simon.

On Thu, 2008-08-14 at 21:30 -0700, Lingbo Li wrote:
> Hello R expert,
> 
> I have fish length and corresponding otolith size at six times for 30 fish. Firstly, I use a linear mixed effect model to correlate the fish length (L) with otolith size in dorsal radius (Dor). Since the residuals are domeshaped, I then tried to add a quadratic factor. However, as the summary shown below, the quadratic factor was missing in the analysis. WHY?
> 
> Thank you very much.
> 
> Lingbo
> 
> 
> > back<-read.table("back.r", header=T)
> 
> > attach(back)
> 
> > names(back)
> 
> [1] "Fish"  "Treat" "Mark"  "L"     "Dor"   "Dis"   "Ven"   "Width"
> 
> > library(nlme)
> 
> > ldor.lme=lme(L~Dor, random=~1|Fish)
> 
> > ldor11.lme=lme(L~Dor+Dor^2, random=~1|Fish)
> 
> > summary(ldor11.lme)
> 
> Linear mixed-effects model fit by REML
> 
>  Data: NULL 
> 
>        AIC      BIC    logLik
> 
>   1539.336 1552.063 -765.6682
> 
>  
> 
> Random effects:
> 
>  Formula: ~1 | Fish
> 
>         (Intercept) Residual
> 
> StdDev:    31.90245 13.00981
> 
>  
> 
> Fixed effects: L ~ Dor + Dor^2 
> 
>                 Value Std.Error  DF  t-value p-value
> 
> (Intercept) -30.74635  9.775326 149 -3.14530   0.002
> 
> Dor         157.14556  3.157083 149 49.77556   0.000
> 
>  Correlation: 
> 
>     (Intr)
> 
> Dor -0.797
> 
>  
> 
> Standardized Within-Group Residuals:
> 
>         Min          Q1         Med          Q3         Max 
> 
> -2.47279716 -0.59191227 -0.09822955  0.49939862  3.12757256 
> 
>  
> 
> Number of Observations: 180 
> 
> Number of Groups: 30 
> 
> 
> 
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> 
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-- 
Simon Blomberg, BSc (Hons), PhD, MAppStat. 
Lecturer and Consultant Statistician 
Faculty of Biological and Chemical Sciences 
The University of Queensland 
St. Lucia Queensland 4072 
Australia
Room 320 Goddard Building (8)
T: +61 7 3365 2506
http://www.uq.edu.au/~uqsblomb
email: S.Blomberg1_at_uq.edu.au

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be extracted from a given body of data. - John Tukey.