Re: [R] Help specifying a non-linear model in nlsLM()

Prof J C Nash (U30A) Wed, 17 Dec 2014 03:48:32 -0800

nlsLM and nls share a numerical gradient approximation and pop up the"singular gradient" quite often at the start. Package nlmrt and a veryalpha nls14 (not on CRAN) try to use analytic derivatives for theJacobian (most optimization folk will say singular Jacobian rather thansingular gradient), so you might be better off with nlxb from nlmrt.BUT ... it works on expressions, not functions.

Or you could provide your own Jacobian and make sure it is not singularat the start.

Both nlsLM and nlxb/nlfb will generally be OK once they get started dueto the Marquardt adjustment to the Jacobian to avoid singularity.


JN


On 14-12-17 06:00 AM, r-help-requ...@r-project.org wrote:

Message: 9 Date: Tue, 16 Dec 2014 08:24:45 -0800 From: Bert Gunter
<gunter.ber...@gene.com> To: Chandrasekhar Rudrappa
<chandr...@gmail.com> Cc: "r-help@r-project.org" <r-help@r-project.org>
Subject: Re: [R] Help specifying a non-linear model in nlsLM()
Message-ID:
<cack-te30269-jbc4roh24whycv2mrsorqcekurn+vzhvurm...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8 Suitable help may not be
possible. I suspect that either your function/code is funky (is the
function smooth, non-infinite near your starting value?) or you are
overparameterized. If the latter, the remedy may depend on the nature of
your data, which you have not shared. While you may receive some help
here (there are some pretty smart optimizers who monitor the list), I
suggest you try a statistical site like stats.stackexchange.com for
help, as this appears to be primarily a statistics issue, not an R
programming one. Cheers, Bert Bert Gunter Genentech Nonclinical
Biostatistics (650) 467-7374 "Data is not information. Information is
not knowledge. And knowledge is certainly not wisdom." Clifford Stoll On
Tue, Dec 16, 2014 at 6:26 AM, Chandrasekhar Rudrappa
<chandr...@gmail.com> wrote:

>Dear All,
>
>I am trying to fit the following model in nlsLM():
>
>fn5 <- function(x, T, t1, w_inf, Lt0){
>S<-function(x, T, t1){
>x+(1-T)/(2*pi)*sin(2*pi*(x-t1)/(1-T))
>}
>F <- function(x, T, t1){
>t2 <- t1 + (1-T)/2
>t3 <- t1 + (1+T)/2
>t.factorial <- x%%1
>floor(x)*(1-T) + S(t.factorial, T, t1)*(0<=t.factorial & t.factorial<t2) +
>S(t2, T, t1)*(t2<=t.factorial & t.factorial<t3) +
>S(t.factorial-T, T, t1)*(t3<=t.factorial & t.factorial<1)
>}
>return(w_inf - (w_inf - Lt0)*exp(-(2/30)*(F(x,T,t1)-F(7,T,t1))))
>}
>fn6<- y~fn5(x, T, t1, w_inf, Lt0)
>startval<-c(x=x, T=0.035, t1=0.359, w_inf=135, Lt0=47)
>(nlsktm1 <- nlsLM(fn6, start=startval, lower=c(x=x, T=0.0135, t1=0.259,
>w_inf=131, Lt0=41), jac=NULL, trace=T, data=ktm,
>control=nls.control(maxiter=10)))
>
>When I run the above script, the following error is displayed:
>
>Error in nlsModel(formula, mf, start, wts) :
>   singular gradient matrix at initial parameter estimates
>In addition: Warning message:
>In nls.lm(par = start, fn = FCT, jac = jac, control = control, lower =
>lower,  :
>   lmdif: info = 0. Improper input parameters.
>
>Suitable help is requested.
>--
>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
>
>         [[alternative HTML version deleted]]
>
>______________________________________________
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>and provide commented, minimal, self-contained, reproducible code.


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Re: [R] Help specifying a non-linear model in nlsLM()

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