Dear Thomas Sorry about the delay of my reply. I had an unexpected long field work in the last months. But in the last two weeks, I was working on FME package and finally I reached good results. Your team had done a very nice work on this package, bring really flexible functions. One of the interest points of the package are the several options of methods for fitting the equations (minimization algorithms). In fact, in all my tests, the “Pseudo-random Search Optimisation Algorithm of Price” reached equivalent results to Levenberg-Marquardt algorithm, but releasing us of search good starting values (and the dangers of local minimums).
Thank you very much for your help. Fred Takahashi PhD student Universidade de Brasilia - Brazil 2009/5/4 <r-sig-ecology-requ...@r-project.org>: > Send R-sig-ecology mailing list submissions to > r-sig-ecol...@r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > or, via email, send a message with subject or body 'help' to > r-sig-ecology-requ...@r-project.org > > You can reach the person managing the list at > r-sig-ecology-ow...@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of R-sig-ecology digest..." > > > Today's Topics: > > 1. Re: Simultaneous estimation of nonlinear models (Thomas Petzoldt) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 04 May 2009 09:58:34 +0200 > From: Thomas Petzoldt <thomas.petzo...@tu-dresden.de> > Subject: Re: [R-sig-eco] Simultaneous estimation of nonlinear models > To: Fred Takahashi <fredt...@gmail.com> > Cc: r-sig-ecology@r-project.org > Message-ID: <49fea02a.5070...@tu-dresden.de> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Hi Fred, > > the new development package "FME" (Flexible Modelling Environment) > contains (among others) functions to support fitting nonlinear models. > It is focused on numerically solved differential equation models in > ecology and related sciences, but it works also for other models. > > The package was not yet uploaded on CRAN but can be installed from the > R-Forge development server: > > > install.packages("FME", repos="http://r-forge.r-project.org";) > > Note that the latest binary version requires to have R version 2.9.0 (or > newer). > > Look at the first example ("Fitted with analytical solution") for > function "modFit" or read chapter "Fitting the model to data" of the > package vignette: > > http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/*checkout*/pkg/FME/inst/doc/FME.pdf?root=fme > > Hope it helps > > Thomas Petzoldt > > Fred Takahashi wrote: > > Hello > > > > I work with plant ecophysiology and use R for about 5 years. Now I > > need to fit nonlinear data of response of photosynthetic rate to CO2 > > concentration according well know mechanistic models. Basically, > > there are one equation for the first part of the curve, and in the > > second part, another equation (different factors limiting > > photosynthesis). But some recent research pointed out that is better > > to fit the data simultaneously to that two equations, than arbitrarily > > cut the data in the half (simultaneous estimation, also know as > > segmented regression). That is possible if the algorithm, like > > Levenberg-Marquardt, minimizes some function of two equations, > > informed in the conditional syntax (ex. If (eq1>eq2) then eq1 else > > eq2). > > > > Dubois et al. (2007) showed the procedure using SAS. The key point of > > that is to inform the equations in the conditional syntax like: > > ? > > if rubisco < RuBP then A = rubisco; > > else A = RuBP; > > ... > > or the equivalent: > > ... > > A = min(rubisco, RuBP); > > ... > > ? > > when ?rubisco? and ?RuBP? are objects representing the two equations. > > > > Also in Dubois et al. (2007), there are the entire syntax in SAS: > > ? > > proc sort data=ACI; > > by factor1 factor2 days; > > run; > > ods output ParameterEstimates=estimates; > > proc NLIN data=ACI method=Marquardt outest=status noitprint; > > by factor1 factor2 days; > > rubisco= ((Vcmax*(Ci-Gstar))/(Ci+(Kc*(1+(O/Ko))))); > > RuBP= ((J*(Ci-Gstar))/((4*Ci)+(8*Gstar))); > > control O=210; *fixes the value of O; > > bounds -3<Rd<50; > > parameters Vcmax= 5 to 330 by 25 > > J= 15 to 505 by 35 > > Rd= 1E-8 to 10.1 by .5; > > model A=min(rubisco,RuBP)-Rd; > > output out=ACiOUT parms=Vcmax J Rd predicted=Ahat student=student; > > run; > > ods listing; > > data temporary; > > set status; > > where(_TYPE_ ne'GRID' and _TYPE_ ne'COVB'); > > run; > > data estimates; > > merge estimates temporary(keep=factor1 factor2 days _status_ _iter_); > > by factor1 factor2 days; > > run; > > ? > > > > I try to do that in R in several ways, using the function nls, without > > success. Does someone have a clue? > > > > Thank you for your help! > > > > Regards > > Fred Takahashi > > > > PhD student > > Universidade de Brasilia ? Brazil > > > > > > > > > > Reference: > > Dubois, Fiscus, Booker, Flowers and Reid (2007) Optimizing the > > statistical estimation of the parameters of the Farquhar?von > > Caemmerer?Berry model of photosynthesis. New Phytologist 176: 402?414 > > > > _______________________________________________ > > R-sig-ecology mailing list > > R-sig-ecology@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > > -- > Thomas Petzoldt > Technische Universitaet Dresden > Institut fuer Hydrobiologie thomas.petzo...@tu-dresden.de > 01062 Dresden http://tu-dresden.de/hydrobiologie/ > GERMANY > > http://tu-dresden.de/Members/thomas.petzoldt > > > > ------------------------------ > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > End of R-sig-ecology Digest, Vol 14, Issue 3 > ******************************************** > _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
