I have been attempting to estimate the periodic contribution of an effect to some data but have not been able to fit a sine wave within R. It would be nice to start by being able to fit a sine wave with an amplitude and frequency. x<-seq(0,20,by=0.5) y<-2*sin(2*pi*.5*x) #amplitude =2, frequency=0.5 # This failed to converge r<-nls(y ~ A*sin(2*pi*F*x), start=list(A = 1, F = 1), trace=T) # even this gave a max iteration error r<-nls(y ~ A*sin(2*pi*F*x), start=list(A = 1, F = .5), trace=T) I have a feeling I am approaching this incorrectly. Thank you all very much for the guidance. Jon R 2.7.0 mac os 10.5 Jon Loehrke Graduate Research Assistant Department of Fisheries Oceanography School for Marine Science and Technology University of Massachusetts 200 Mill Road, Suite 325 Fairhaven, MA 02719 jloehrke at umassd.edu T 508-910-6393 F 509-910-6396
fitting periodic 'sine wave' model
4 messages · Jon Loehrke, Gabor Grothendieck, Charilaos Skiadas +1 more
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On Tue, Jun 10, 2008 at 10:25 AM, Jon Loehrke <jloehrke at umassd.edu> wrote:
I have been attempting to estimate the periodic contribution of an effect to some data but have not been able to fit a sine wave within R. It would be nice to start by being able to fit a sine wave with an amplitude and frequency. x<-seq(0,20,by=0.5) y<-2*sin(2*pi*.5*x) #amplitude =2, frequency=0.5 # This failed to converge r<-nls(y ~ A*sin(2*pi*F*x), start=list(A = 1, F = 1), trace=T) # even this gave a max iteration error r<-nls(y ~ A*sin(2*pi*F*x), start=list(A = 1, F = .5), trace=T) I have a feeling I am approaching this incorrectly. Thank you all very much for the guidance. Jon R 2.7.0 mac os 10.5 Jon Loehrke Graduate Research Assistant Department of Fisheries Oceanography School for Marine Science and Technology University of Massachusetts 200 Mill Road, Suite 325 Fairhaven, MA 02719 jloehrke at umassd.edu T 508-910-6393 F 509-910-6396
______________________________________________ R-help at 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.
In addition to Gabor's suggestion, note the following warning from ?nls Warning Do not use nls on artificial "zero-residual" data. The nls function uses a relative-offset convergence criterion that compares the numerical imprecision at the current parameter estimates to the residual sum-of-squares. This performs well on data of the form y = f(x, theta) + eps (with var(eps) > 0). It fails to indicate convergence on data of the form y = f(x, theta) because the criterion amounts to comparing two components of the round-off error. If you wish to test nls on artificial data please add a noise component, as shown in the example below. So for instance if you try with: r<-nls(y ~ A*sin(2*pi*F*x), start=list(A = 1, F = .5), trace=T) You will get convergence. Haris Skiadas Department of Mathematics and Computer Science Hanover College
On Jun 10, 2008, at 10:25 AM, Jon Loehrke wrote:
I have been attempting to estimate the periodic contribution of an effect to some data but have not been able to fit a sine wave within R. It would be nice to start by being able to fit a sine wave with an amplitude and frequency. x<-seq(0,20,by=0.5) y<-2*sin(2*pi*.5*x) #amplitude =2, frequency=0.5 # This failed to converge r<-nls(y ~ A*sin(2*pi*F*x), start=list(A = 1, F = 1), trace=T) # even this gave a max iteration error r<-nls(y ~ A*sin(2*pi*F*x), start=list(A = 1, F = .5), trace=T) I have a feeling I am approaching this incorrectly. Thank you all very much for the guidance. Jon R 2.7.0 mac os 10.5 Jon Loehrke Graduate Research Assistant Department of Fisheries Oceanography School for Marine Science and Technology University of Massachusetts 200 Mill Road, Suite 325 Fairhaven, MA 02719 jloehrke at umassd.edu T 508-910-6393 F 509-910-6396
If you make the x-values more dense, e.g. with x<-seq(0,20,0.1) then your example works. Plotting your data might give a hint to why your example fails.... Btw: It is generally not a good idea to use F for a parameter because F usually means FALSE. Regards S?ren ________________________________ Fra: r-help-bounces at r-project.org p? vegne af Jon Loehrke Sendt: ti 10-06-2008 16:25 Til: r-help at r-project.org Emne: [R] fitting periodic 'sine wave' model I have been attempting to estimate the periodic contribution of an effect to some data but have not been able to fit a sine wave within R. It would be nice to start by being able to fit a sine wave with an amplitude and frequency. x<-seq(0,20,by=0.5) y<-2*sin(2*pi*.5*x) #amplitude =2, frequency=0.5 # This failed to converge r<-nls(y ~ A*sin(2*pi*F*x), start=list(A = 1, F = 1), trace=T) # even this gave a max iteration error r<-nls(y ~ A*sin(2*pi*F*x), start=list(A = 1, F = .5), trace=T) I have a feeling I am approaching this incorrectly. Thank you all very much for the guidance. Jon R 2.7.0 mac os 10.5 Jon Loehrke Graduate Research Assistant Department of Fisheries Oceanography School for Marine Science and Technology University of Massachusetts 200 Mill Road, Suite 325 Fairhaven, MA 02719 jloehrke at umassd.edu T 508-910-6393 F 509-910-6396 ______________________________________________ R-help at 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.