Re: [R] How to put factor variables in an nls formula ?

From: François Morneau <francois.morneau_at_cirad.fr>
Date: Sat 20 Aug 2005 - 04:05:35 EST

Le 11:12 19/08/2005,Douglas Bates écrit:
>On 8/18/05, François Morneau <francois.morneau@cirad.fr> wrote:
> > Hello,
> >
> > I want to fit a Gompertz model for tree diameter growth that depends on a 4
> > levels edaphic factor ('Drain') and I don't manage to introduce the factor
> > variable in the formula.
> > Dinc is the annual diameter increment and D is the Diameter.
> >
> > >treestab
> > > Dinc D Drain
> > [1,] 0.03 26.10 2
> > [2,] 0.04 13.05 1
> > [3,] 0.00 24.83 1
> > [4,] 0.00 15.92 4
> > [5,] 0.00 12.25 4
> > [6,] 0.00 11.78 4
> > [7,] 0.00 16.87 4
> > [8,] 0.00 15.12 4
> > [9,] -0.01 13.53 4
> > [10,] 0.04 16.55 3
> > [11,] 0.025 16.07 3
> > [12,] 0.00 30.24 3
> > [13,] 0.06 15.28 2
> > etc…
> > >contrasts(Drain)<-contr.sum(4)
> > >mymodel<-nls(Dinc~r*(1+Drain)*D*log(Asym/D), data=treestab,
> start=list(r=0.05,
> > Asym=40))
> >
> > Error in numericDeriv(form[[3]], names(ind), env) :
> > Missing value or an infinity produced when evaluating the model
> > In addition: Warning messages:
> > 1: + not meaningful for factors in: Ops.factor(1, Drain)
> > 2: + not meaningful for factors in: Ops.factor(1, Drain)
>
>It is not clear to me what you are trying to do. Can you give us a
>bit more information such as how many parameter estimates you expect
>to obtain and what they would represent?

I'm trying to estimate the effect of the edaphic factor 'Drain' on tree diameter growth. The relationship between diameter 'D' and diameter increment 'Dinc' follow a Gompertz model written : Dinc= r D log(Asym/D) where 'r' is a parameter related to growth speed and 'Asym' is the diameter max where growth stops.

My hypothesis is that 'Asym' doesn't change according to edaphic condition but 'r' does. So I'd like to estimate 'Asym' and four 'r'i parameters for each level i of 'Drain' with 'r'i= r0 + effect of 'Drain'i

I hope this is helpful...

> >
> > Do I need to use another function instead of nls to correctly include the
> > factor 'Drain' ?
> >
> > Thanks,
> >
> > François

François Morneau
UMR Écologie des Forêts de Guyane
Kourou, French Guiana



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