[R-sig-eco] help with a suitable code to fit a complicated non-linear model in R

[Mollie Brooks]

Dear Dr. Chandrasekhar,

Writing code for that model looks like a non-trivial undertaking. Maybe someone else has more time to invest.

I would check to see if code was published with the 2009 paper. If not, I would recommend contacting the authors to ask for code. The paper would get more citations if they provide code. 
 
You can find general advice on fitting non-linear models in the following paper (let me know if you need a copy)
Bolker, B. M., B. Gardner, M. Maunder, C. W. Berg, M. Brooks, L. Comita, E. Crone, S. Cubaynes, T. Davies, P. de Valpine, J. Ford, O. Gimenez, M. Kery, E. J. Kim, C. Lennert-Cody, A. Magnusson, S. Martell, J. Nash, A. Nielsen, J. Regetz, H. Skaug, and E. Zipkin. 2013. Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS. Methods in Ecology and Evolution:1–12.

Cheers,
Mollie


------------------------
Mollie Brooks, PhD
Postdoctoral Researcher, Population Ecology Research Group
Institute of Evolutionary Biology & Environmental Studies, University of Zürich
http://www.popecol.org/team/mollie-brooks/


> On 6Dec 2014, at 6:22, Chandrasekhar Rudrappa <chandratr at gmail.com> wrote:
> 
> Dear All,
> 
> 
> I have to fit the following model to growth data of Hevea (rubber) trees:
> 
> *a=a-(a-b)exp(-(2/p)(F(t)-F(t0))).*  Where *F(t)=t+(A/2pi)(sin 2pi(t-t1))*,
> 
> *F(t0)=t0+(A/2pi)(sin 2pi(t0-t1)), t1* signifies the maximum point of
> *f(t)*. Thus the equation becomes:
> 
> *a=a-(a-b)exp(-(2/p)(t+(A/2pi)(sin 2pi(t-t1)))- (t0+(A/2pi)(sin
> 2pi(t0-t1))))*
> 
> Up to this step, I have succeeded very well.
> 
> 
> 
> *My problem is with the following model for which I need help. *
> 
> 
> 
> The same equation is further developed into a seasonal cessation model by
> deriving equivalent equations to replace *F(t)*. For the purpose of
> seasonal cessation model *F(t)* is derived as:
> 
> 
> 
> *            n(1-T)+S(t-n)               (n<=t<n+t2),  *
> 
> *F(t) =  n(1-T)+S(t2)                 (n+t2<=t<n+t3),         *
> 
> *            n(1-T)+S(t-n-T)           (n+t3<=t<n+1),*
> 
> 
> 
> where *S(t)=t+((1-T)/(2pi))(sin 2pi((t-t1)/(1-T))),* n=integral part of t,
> 
> 
> 
> *t2=t1+(1-T)/2,  t3=t1+(1+T)/2  , T=no growth period. *Similarly the above
> equations have to be modified *for F(to).* These have to be integrated in
> to:
> 
> 
> 
> *a=a-(a-b)exp(-(2/p)(F(t)-F(t0))).*
> 
> 
> 
> Kindly help with a suitable code to fit the above model to my data.
> 
> 
> 
> References: 1. Akamine, T (1993). A New Standard Formula for Seasonal
> Growth of Fish in Population Dynamics. Nippon Suisan Gakkaishi
> 59(11):1857-1863.
> 
> 2.  Akamine, T (2009). Non-linear and graphical methods for fish stock
> analysis with statistical modelling. Aqua-BioScience Monographs VOL. 2 NO. 3
> :1-45.
> 
> 
> -- 
> Dr. TR Chandrasekhar, M.Sc., M. Tech., Ph. D.,
> Sr. Scientist
> Rubber Research Institute of India
> Hevea Breeding Sub Station
> Kadaba - 574 221
> DK Dt., Karnataka
> Phone-Land: 08251-214336
> Mobile: 9448780118
> 
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> 
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