Re: [R] nls not solving
Here is a reply by Bart: Yes you're right (I should have taken off my glasses and looked closer). However, the argument is essentially the same: Suppose you have a solution with a,b,k,l. Then for any positive c, [a+b-bc] + [bc] + (bc) *exp(kl')exp(-kx) is also a solution, where l' = l - log(c)/k . Cheers, Bert (Feel free to post this correction if you like) This is from me: The problem with dropping the l parameter is that it is supposed to account for the lag component. This equation was published in the literature and has been being solved in SAS. When I put it in excel, it solves, but not very well as it comes to a different solution for each time that I change the starting values. As such, I'm not sure how SAS solves for it and I'm not sure what I should do about the equation. Maybe I should just drop the parameter a. Thanks for the help. -- View this message in context: http://r.789695.n4.nabble.com/nls-not-solving-tp3328647p3329936.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nls not solving
On 2011-03-01 06:38, Schatzi wrote: Here is a reply by Bart: Yes you're right (I should have taken off my glasses and looked closer). However, the argument is essentially the same: Suppose you have a solution with a,b,k,l. Then for any positive c, [a+b-bc] + [bc] + (bc) *exp(kl')exp(-kx) is also a solution, where l' = l - log(c)/k . Cheers, Bert (Feel free to post this correction if you like) This is from me: The problem with dropping the l parameter is that it is supposed to account for the lag component. This equation was published in the literature and has been being solved in SAS. When I put it in excel, it solves, but not very well as it comes to a different solution for each time that I change the starting values. As such, I'm not sure how SAS solves for it and I'm not sure what I should do about the equation. Maybe I should just drop the parameter a. Thanks for the help. When you say 'published in the literature' you should provide a reference; you may be misinterpreting what's published. If SAS provides a 'solution', then there's an added assumption being made (perhaps 'l' is being fixed?). What Excel does is of little interest. 'Dropping' the parameter 'a' is equivalent to setting a=0. You could also set, say, a = -10 or l = 50, or ... The point is that, as Bert says, the model is nonidentifiable. Peter Ehlers __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] nls not solving
I am running the following nls equation. I tried it with data that excel was fitting and got the error: singular gradient matrix at initial parameter estimates I thought it was due to a low number of points (6), but when I create a dataset, I get the same problem. If I remove the parameter a, then it can find a solution. Does anyone know what I can do to fit this model? vardata- rnorm(73,mean=0,sd=5) x-0:72 a-1 b-50 k-0.05 l-5 startt-c(a,b,k,l) yf-a+b*(1-exp(-k*(x-l))) y-yf+vardata nmodel-nls(y~a+b*(1-exp(-k*(x-l))), start=list(a=1,b=50,k=0.05,l=5)) -- View this message in context: http://r.789695.n4.nabble.com/nls-not-solving-tp3328647p3328647.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nls not solving
By the way, sorry about the reposts. I subscribed but wasn't sure what was happening. Hopefully this worked. -- View this message in context: http://r.789695.n4.nabble.com/nls-not-solving-tp3328647p3328659.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nls not solving
Well, since no one else has replied, let me state the obvious: The model is nonidentifiable. It is of the form: y = a + b(1 - exp(kl)) - b exp(-kx) Suppose you have a solution. Suppose with your solution, a + b(1 -exp(kl)) = C, say. Then a = C - b(1-exp(kl)). Hence you have generated an infinite number of pairs a,l by solving for one in terms of the other that give the exact same solution. That is, the model is nonidentifiable. Whence your error. Removing a or l makes the model identifiable. -- Bert On Mon, Feb 28, 2011 at 12:23 PM, Schatzi adele_thomp...@cargill.com wrote: I am running the following nls equation. I tried it with data that excel was fitting and got the error: singular gradient matrix at initial parameter estimates I thought it was due to a low number of points (6), but when I create a dataset, I get the same problem. If I remove the parameter a, then it can find a solution. Does anyone know what I can do to fit this model? vardata- rnorm(73,mean=0,sd=5) x-0:72 a-1 b-50 k-0.05 l-5 startt-c(a,b,k,l) yf-a+b*(1-exp(-k*(x-l))) y-yf+vardata nmodel-nls(y~a+b*(1-exp(-k*(x-l))), start=list(a=1,b=50,k=0.05,l=5)) -- View this message in context: http://r.789695.n4.nabble.com/nls-not-solving-tp3328647p3328647.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nls not solving
I am not sure how you simplified the model to: y = a + b(1 - exp(kl)) - b exp(-kx) I tried simplifying it but only got to: y = a + b - b * exp(kl) * exp(-kx) I agree that the model must not be identifiable. That makes sense, especially given that removing either a or l makes the model work. Can you please further explain the math though as I am not understanding it? I do not see you obtained your equation and when I tried to solve using your equation I got quite different numbers. Thank you. -- View this message in context: http://r.789695.n4.nabble.com/nls-not-solving-tp3328647p3328862.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nls not solving
On 2011-02-28 14:14, Schatzi wrote:
I am not sure how you simplified the model to:
y = a + b(1 - exp(kl)) - b exp(-kx)
I tried simplifying it but only got to:
y = a + b - b * exp(kl) * exp(-kx)
I agree that the model must not be identifiable. That makes sense,
especially given that removing either a or l makes the model work. Can you
please further explain the math though as I am not understanding it? I do
not see you obtained your equation and when I tried to solve using your
equation I got quite different numbers. Thank you.
You can obviously write your function as
f - f(x, A, B, K) {A - B * exp(-Kx)}
i.e. in terms of *3* parameters. In that form,
it's apple pie for nls().
fm - nls(y ~ f(x, A, B, K),
start = list(A = 50, B = 60, K = 1)
coef(fm)
xx - seq(0, 72, length = 101)
yy - predict(fm, newdata = list(x = xx))
plot(x, y)
lines(xx, yy, col = red)
Peter Ehlers
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