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Rule number 1: Read the help for the function you are using.
You must supply starting values for the fit --- which the code you gave
doesn't do.
Rule number 2: Don't use nls()! Endless grief results.
Instead try:
foo <- function(par,x,y){
Const <- par[1]
B <- par[2]
A <- par[3]
sum((y-(Const+B*(x^A)))^2)
}
fit <- optim(c
(1,2.5,0.2),foo,x=area,y=richness,method="BFGS",control=list
(maxit=1000))
plot(area,richness)
ccc <- fit$par
curve(ccc[1]+ccc[2]*(x^ccc[3]),from=0,to=2000,add=TRUE,col="red") #
Fit doesn't look too bad.
HTH.
cheers,
Rolf Turner
On 3/12/2007, at 8:08 AM, Milton Cezar Ribeiro wrote:
> Dear all,
> I am still fighting against my "power model".
> I tryed several times to use nls() but I can?t run it.
> I am sending my variables and also the model which I would like to
> fit.
> As you can see, this "power model" is not the best model to be
fit,
> but I really need also to fit it.
>
> The model which I would like to fit is Richness = B*(Area^A)
>
> richness<-c
> (44,36,31,39,38,26,37,33,34,48,25,22,44,5,9,13,17,15,21,10,16,22,13,20
> ,9,15,14,21,23,23,32,29,20,
> 26,31,4,20,25,24,32,23,33,34,23,28,30,10,29,40,10,8,12,13,14,56,47,44,
> 37,27,17,32,31,26,23,31,34,
> 37,32,26,37,28,38,35,27,34,35,32,27,22,23,13,28,13,22,45,33,46,37,21,2
> 8,38,21,18,21,18,24,18,23,22,
> 38,40,52,31,38,15,21)
> area<-c
> (26.22,20.45,128.68,117.24,19.61,295.21,31.83,30.36,13.57,60.47,205.30
> ,40.21,
> 7.99,1.18,5.40,13.37,4.51,36.61,7.56,10.30,7.29,9.54,6.93,12.60,
> 2.43,18.89,15.03,14.49,28.46,36.03,38.52,45.16,58.27,67.13,92.33,1.17,
> 29.52,84.38,87.57,109.08,72.28,66.15,142.27,76.41,105.76,73.47,1.71,30
> 5.75,
> 325.78,3.71,6.48,19.26,3.69,6.27,1689.67,95.23,13.47,8.60,96.00,436.97
> ,
> 472.78,441.01,467.24,1169.11,1309.10,1905.16,135.92,438.25,526.68,88.8
> 8,31.43,21.22,
> 640.88,14.09,28.91,103.38,178.99,120.76,161.15,137.38,158.31,179.36,21
> 4.36,187.05,
> 140.92,258.42,85.86,47.70,44.09,18.04,127.84,1694.32,34.27,75.19,54.39
> ,79.88,
> 63.84,82.24,88.23,202.66,148.93,641.76,20.45,145.31,27.52,30.70)
> plot(richness~area)
>
> I tryed to fit the following model:
>
> m1<-nls(richness ~ Const+B*(area^A))
>
> Thanks a lot,
> miltinho
> Brazil.
>
>
>
> para armazenamento!
>
> [[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.
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On Sun, Dec 02, 2007 at 11:08:01AM -0800, Milton Cezar Ribeiro wrote:> Dear all, > I am still fighting against my "power model". > I tryed several times to use nls() but I can??t run it. > I am sending my variables and also the model which I would like to fit. > As you can see, this "power model" is not the best model to be fit, but I really need also to fit it. > > The model which I would like to fit is Richness = B*(Area^A) > > richness<-c(44,36,31,39,38,26,37,33,34,48,25,22,44,5,9,13,17,15,21,10,16,22,13,20,9,15,14,21,23,23,32,29,20, > 26,31,4,20,25,24,32,23,33,34,23,28,30,10,29,40,10,8,12,13,14,56,47,44,37,27,17,32,31,26,23,31,34, > 37,32,26,37,28,38,35,27,34,35,32,27,22,23,13,28,13,22,45,33,46,37,21,28,38,21,18,21,18,24,18,23,22, > 38,40,52,31,38,15,21) > area<-c(26.22,20.45,128.68,117.24,19.61,295.21,31.83,30.36,13.57,60.47,205.30,40.21, > 7.99,1.18,5.40,13.37,4.51,36.61,7.56,10.30,7.29,9.54,6.93,12.60, > 2.43,18.89,15.03,14.49,28.46,36.03,38.52,45.16,58.27,67.13,92.33,1.17, > 29.52,84.38,87.57,109.08,72.28,66.15,142.27,76.41,105.76,73.47,1.71,305.75, > 325.78,3.71,6.48,19.26,3.69,6.27,1689.67,95.23,13.47,8.60,96.00,436.97, > 472.78,441.01,467.24,1169.11,1309.10,1905.16,135.92,438.25,526.68,88.88,31.43,21.22, > 640.88,14.09,28.91,103.38,178.99,120.76,161.15,137.38,158.31,179.36,214.36,187.05, > 140.92,258.42,85.86,47.70,44.09,18.04,127.84,1694.32,34.27,75.19,54.39,79.88, > 63.84,82.24,88.23,202.66,148.93,641.76,20.45,145.31,27.52,30.70) > plot(richness~area) > > I tryed to fit the following model: > > m1<-nls(richness ~ Const+B*(area^A)) > > Thanks a lot, > miltinho > Brazil. >for easier notation, let y=richness, x=area, C=const in the following. then nls(y~B*x^A + C, start = c(A=3.2, B=0.002, C=0)) converges alright. where's the problem (apart from this being not a very good model for the data)? the critical point is to provide some reasonable estimate of the parameters as starting values. to get reasonable start values, I'd use: y = B*x^A + C --> log(y-C) = log(B) + A*log(x) --> ly = b + a*lx, estimate C from the x -> 0 asymptotic value (approx. 0) and use lm(ly~lx) which yields a and b estimates which you could use in `nls'. and, contrary to other assessments you've received, I definitely would prefer `nls' for least squares fitting instead of using `optim' or other general minimization routines. hth joerg
Is that really the model we want? When we have problems sometimes its just a sign that the model is not very good in the first place. plot(richness ~ area) shows most of the points crowded the left and just a few points out to the right. This does not seem like a very good pattern for model fitting. plot(richness ~ log(area)) plot(log(richness) ~ log(area)) both look nicer. On Dec 2, 2007 2:08 PM, Milton Cezar Ribeiro <milton_ruser at yahoo.com.br> wrote:> Dear all, > I am still fighting against my "power model". > I tryed several times to use nls() but I can?t run it. > I am sending my variables and also the model which I would like to fit. > As you can see, this "power model" is not the best model to be fit, but I really need also to fit it. > > The model which I would like to fit is Richness = B*(Area^A) > > richness<-c(44,36,31,39,38,26,37,33,34,48,25,22,44,5,9,13,17,15,21,10,16,22,13,20,9,15,14,21,23,23,32,29,20, > 26,31,4,20,25,24,32,23,33,34,23,28,30,10,29,40,10,8,12,13,14,56,47,44,37,27,17,32,31,26,23,31,34, > 37,32,26,37,28,38,35,27,34,35,32,27,22,23,13,28,13,22,45,33,46,37,21,28,38,21,18,21,18,24,18,23,22, > 38,40,52,31,38,15,21) > area<-c(26.22,20.45,128.68,117.24,19.61,295.21,31.83,30.36,13.57,60.47,205.30,40.21, > 7.99,1.18,5.40,13.37,4.51,36.61,7.56,10.30,7.29,9.54,6.93,12.60, > 2.43,18.89,15.03,14.49,28.46,36.03,38.52,45.16,58.27,67.13,92.33,1.17, > 29.52,84.38,87.57,109.08,72.28,66.15,142.27,76.41,105.76,73.47,1.71,305.75, > 325.78,3.71,6.48,19.26,3.69,6.27,1689.67,95.23,13.47,8.60,96.00,436.97, > 472.78,441.01,467.24,1169.11,1309.10,1905.16,135.92,438.25,526.68,88.88,31.43,21.22, > 640.88,14.09,28.91,103.38,178.99,120.76,161.15,137.38,158.31,179.36,214.36,187.05, > 140.92,258.42,85.86,47.70,44.09,18.04,127.84,1694.32,34.27,75.19,54.39,79.88, > 63.84,82.24,88.23,202.66,148.93,641.76,20.45,145.31,27.52,30.70) > plot(richness~area) > > I tryed to fit the following model: > > m1<-nls(richness ~ Const+B*(area^A)) > > Thanks a lot, > miltinho > Brazil. > > > > para armazenamento! > > [[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. > >