Niklaus: 1. First, you mat not need to use nls at all, although I am not familiar with the "port" algorithm, so I could very well be wrong about this. Generally speaking, one uses time series methods (e.g. fourier analysis) to fit periodic sine waves, so you may wish to check out CRAN's TimeSeries task view to see whether there is something there that fits your constrained fit situation.
2. If you DO need to fit a nonlinear function the short answer to your questions is maybe/maybe not; obviously, Hans's suggestions may help you get a better starting point but it still usea the same sensitive algorithm, which is some version of gradient descent iirc. The optimx package contains a varied collection of optimizers, some of which may well be more robust than that of nls2. Check out that package and the Optimization task view for background, references, and alternatives (such as derivative-free optimizers) Cheers, Bert On Tue, Dec 13, 2011 at 7:53 AM, Hans W Borchers <hwborch...@googlemail.com> wrote: > Niklaus Fankhauser <niklaus.fankhauser <at> cell.biol.ethz.ch> writes: > >> I'm using nls to fit periodic gene-expression data to sine waves. I need >> to set the upper and lower boundaries, because I do not want any >> negative phase and amplitude solutions. This means that I have to use >> the "port" algorithm. The problem is, that depending on what start value >> I choose for phase, the fit works for some cases, but not for others. >> In the example below, the fit works using phase=pi, but not using >> phase=0. But there are many examples which fit just fine using 0. >> >> Is there a comparable alternative to nls that is not so extremely >> influenced by the start values? >> > > Use package `nls2' to first search on a grid, and then apply `nls' again > to identify the globally best point: > > # Data for example fit > afreq <- 1 / (24 / 2 / pi) > tpoints <- c(0,0,0,2,2,2,4,4,4,6,6,6,8,8,8,12,12,12, > 14,14,14,16,16,16,18,18,18,20,20,20,24,24,24) > gene_expression <- > c(1.551383, 1.671742, 1.549499, 1.694480, 1.632436, 1.471568, 1.623381, > 1.579361, 1.809394, 1.753223, 1.685918, 1.754968, 1.963069, 1.820690, > 1.985159, 2.205064, 2.160308, 2.120189, 2.194758, 2.165993, 2.189981, > 2.098671, 2.122207, 2.012621, 1.963610, 1.884184, 1.955160, 1.801175, > 1.829686, 1.773260, 1.588768, 1.563774, 1.559192) > shift=mean(gene_expression) # y-axis (expression) shift > > # Grid search > library("nls2") > frml <- gene_expression ~ sin(tpoints * afreq + phase) * amp + shift > startdf <- data.frame(phase=c(0, 2*pi), amp = c(0, 2)) > nls2(frml, algorithm = "grid-search", start = startdf, > control = list(maxiter=200)) > > # Perfect fit > startvals <- list(phase = 4.4880, amp = 0.2857) > sine_nls <- nls(frml, start=startvals) > # phase amp > # 4.3964 0.2931 > # residual sum-of-squares: 0.1378 > > Maybe this can be done in one step. > Hans Werner > > ______________________________________________ > 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 Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm ______________________________________________ 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.