Dear R gurus, As part of finding initial values for a much more complicated fit I want to fit a function of the form y ~ a + bx + cx^d to fairly "noisy" data and have hit some problems.
To demonstrate the specific R-related problem, here is an idealised data set, smaller and better fitting than reality: # idealised data set aDF <- data.frame( x= c(1.80, 9.27, 6.48, 2.61, 9.86, 5.93, 6.76, 5.52, 6.06, 8.62), y= c(24.77, 2775.07, 895.15, 60.73, 3373.57, 677.82, 1021.92, 542.84, 725.25, 2200.04)) And here are some starting values, far better than I'd have in reality # good starting values startL <- list(Ca=4, Cb=3, Cc=3, Cd=3) In these idealised circumstances nls converges using the default algorithm. # nls, default algorithm nls(y ~ Ca + Cb*x + Cc*x^Cd, data=aDF, start=startL) Unfortunately, in reality it often fails to converge. This model is linear in a, b and c so I've used the plinear algorithm. # nls, plinear algorithm, explicit RHS nls(y ~ cbind(Ca=1,Cb=x, Cc=x^Cd), data=aDF, start=startL["Cd"], algorithm="plinear") This converges much more often but sometimes crashes with the error message "Error in numericDeriv(form[[3]], names(ind), env) : Missing value or an infinity produced when evaluating the model" I deduce that it is failing in the numerical differentiation of x^Cd (but don't know why), so I thought I'd avoid the numerical differentiation by putting the RHS in a function to which I could (later) add a 'gradient' attribute # function to provide RHS bFunc <- function(x, Ca, Cb, Cc, Cd) cbind(Ca=1,Cb=x, Cc=x^Cd) # nls, plinear algorithm, RHS from function nls(y ~ bFunc(x, Ca, Cb, Cc, Cd), data=aDF, start=startL["Cd"], algorithm="plinear") However, this gives me "Error in nls(y ~ bFunc(x, Ca, Cb, Cc, Cd), data = aDF, start = startL["Cd"], : parameters without starting value in 'data': Ca, Cb, Cc" Can anyone tell me a) why putting the RHS into a function "broke" the plinear algorithm b) if there's a better approach to my problem Thanks in advance, Keith Jewell ----------------- I'm using V2.7.2... > sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices datasets tcltk utils methods base other attached packages: [1] xlsReadWrite_1.3.2 svSocket_0.9-5 TinnR_1.0.2 R2HTML_1.59 Hmisc_3.4-3 loaded via a namespace (and not attached): [1] cluster_1.11.11 grid_2.7.2 lattice_0.17-14 svMisc_0.9-5 VGAM_0.7-7 ... but have also tried todays V2.7.2 patched and V2.8.0alpha, both of which give the same behaviour ______________________________________________ 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.
