[R] fitting model to resampled data

Derek Ogle
Wed, 29 Sep 2010 20:19:40 -0000

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]]
>
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