I apologize if this comes across as confusing. I will try to explain my situation as best I can. I have R bootstrapping my growth data for fish. It's resampling my database of age and length data and then produces several new datasets for me. In this case, it's resampling my data to create three new datasets of age and length data. Here is my code with my original data called growth: replicate(3, growth[sample(9,12,replace=T),], simplify = FALSE) This is working very well. Now, the problem that I am now stuck with is incorporating a growth model into the three new datasets to estimate growth parameters. Since there are now three new datasets I want to get three new estimates of the growth parameters, essentially one from each new dataset. I am using the von Bertalanffy growth model. Here is my code: par<-list(Linf=700, K=0.20, to=-0.1) #these are the starting values for parameters vb<-nls(Length~Linf*(1-exp(-K*(Age-to))), start=par, data=???) #this is the growth model with the parameters estimated with non linear least squares (nls) I tried placing my resampling function the data part of the nls function but it asks me for parameter estimates. Any advice would be greatly appreciated. Mike [[alternative HTML version deleted]]
Mike, Without completely knowing your end game with these questions and this procedure it does seem like you are "re-inventing the wheel" here. If that is true and given the nls() fit that you are using I would suggest that you look at boot.case() in the alr3 package or nlsBoot() in the nlstools package. I have used both of those functions with success when fitting the von Bertalanffy growth model to fish length-age data. Some general help for fitting von Bertalanffy growth models to fish data can be found at http://www.ncfaculty.net/dogle/fishR/gnrlex/gnrlex.html> -----Original Message----- > From: r-help-bounces at r-project.org [mailto:r-help-bounces at r- > project.org] On Behalf Of Michael Larkin > Sent: Wednesday, September 29, 2010 2:57 PM > To: r-help at r-project.org > Subject: [R] fitting model to resampled data > > I apologize if this comes across as confusing. I will try to explain > my > situation as best I can. > > > > I have R bootstrapping my growth data for fish. It's resampling my > database > of age and length data and then produces several new datasets for me. > In > this case, it's resampling my data to create three new datasets of age > and > length data. Here is my code with my original data called growth: > > > > replicate(3, growth[sample(9,12,replace=T),], simplify = FALSE) > > > > This is working very well. > > > > Now, the problem that I am now stuck with is incorporating a growth > model > into the three new datasets to estimate growth parameters. Since there > are > now three new datasets I want to get three new estimates of the growth > parameters, essentially one from each new dataset. > > > > I am using the von Bertalanffy growth model. Here is my code: > > > > par<-list(Linf=700, K=0.20, to=-0.1) > #these are the starting values for parameters > > vb<-nls(Length~Linf*(1-exp(-K*(Age-to))), start=par, data=???) > #this is > the growth model with the parameters estimated with non linear least > > squares (nls) > > > > I tried placing my resampling function the data part of the nls > function but > it asks me for parameter estimates. > > > > Any advice would be greatly appreciated. > > > > Mike > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > 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.
Try this: growthBoot <- replicate(3, growth[sample(9,12,replace=T),], simplify FALSE) lapply(growthBoot, nls, formula = Length ~ Linf * (1 - exp(-K * (Age - to))), start = par) On Wed, Sep 29, 2010 at 4:56 PM, Michael Larkin <mlarkin@rsmas.miami.edu>wrote:> I apologize if this comes across as confusing. I will try to explain my > situation as best I can. > > > > I have R bootstrapping my growth data for fish. It's resampling my > database > of age and length data and then produces several new datasets for me. In > this case, it's resampling my data to create three new datasets of age and > length data. Here is my code with my original data called growth: > > > > replicate(3, growth[sample(9,12,replace=T),], simplify = FALSE) > > > > This is working very well. > > > > Now, the problem that I am now stuck with is incorporating a growth model > into the three new datasets to estimate growth parameters. Since there are > now three new datasets I want to get three new estimates of the growth > parameters, essentially one from each new dataset. > > > > I am using the von Bertalanffy growth model. Here is my code: > > > > par<-list(Linf=700, K=0.20, to=-0.1) > #these are the starting values for parameters > > vb<-nls(Length~Linf*(1-exp(-K*(Age-to))), start=par, data=???) #this > is > the growth model with the parameters estimated with non linear least > > squares (nls) > > > > I tried placing my resampling function the data part of the nls function > but > it asks me for parameter estimates. > > > > Any advice would be greatly appreciated. > > > > Mike > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. >-- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40" S 49° 16' 22" O [[alternative HTML version deleted]]