Wonderful, great! That solves my problem nicely (on to the next one!). Thanks a lot,
Keith Jewell "Katharine Mullen" <[EMAIL PROTECTED]> wrote in message news:[EMAIL PROTECTED] > a) you should put values for Ca, Cb, Cc directly into the data list as > data=list(Ca=1, .... > > b) you can simplify the call to > > # 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)) > > bFunc <- function(x, Cd) cbind(Ca=1,Cb=x, Cc=x^Cd) > > # nls, plinear algorithm, RHS from function > nls(y ~ bFunc(x, Cd), data=list(x=aDF$x, y=aDF$y), > start=list(Cd=3), algorithm="plinear") > > On Thu, 2 Oct 2008, Keith Jewell wrote: > >> 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. >> > > ______________________________________________ > 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-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.
