[R] How can I fitting this function from values.
Frede Aakmann Tøgersen
FredeA.Togersen at agrsci.dk
Tue Nov 13 08:54:21 CET 2007
R is case sensitive ;-) so in your list of start values you must have B=3 and not b=3. Perhaps you have an object named b of a different length than your data somewhere giving rise to your error message.
Also brute force wont work as Joerg point out. We have
A*1/(1+t/B)*1/sqrt(1+t/C) = D/(B+t)/sqrt(C+t),
where D = A*B*sqrt(C).
We notice that we need B > -t and C > -t.
Now one can use the "port" algorithme of nls() with constraints on parameters:
foo <- function(t,ccc){
D <- ccc[1]
B <- ccc[2]
C <- ccc[3]
D/(B+t)/sqrt(C+t)
}
ttt <- seq(1,10,length=100)
yyy <- foo(ttt,c(5*3*sqrt(2),3,2))
set.seed(42)
dat.test <- data.frame(t=ttt,y=yyy+rnorm(100,0,.1))
fit.test <- nls(y~D/(B+t)/sqrt(C+t),data=dat.test,
start=c(D=5*3*sqrt(2),B=3,C=2),
lower=c(-Inf,-1,-1),alg="port")
# -Inf could be 0, -1 could be -min(dat.test$t)
with(dat.test,plot(t,y))
with(dat.test,lines(t,foo(t,c(21.21,3,2)),col="green")) # Looks cool.
lines(ttt,fitted(fit.test),col="red")
Best regards
Frede Aakmann Tøgersen
Scientist
UNIVERSITY OF AARHUS
Faculty of Agricultural Sciences
Dept. of Genetics and Biotechnology
Blichers Allé 20, P.O. BOX 50
DK-8830 Tjele
Phone: +45 8999 1900
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E-mail: FredeA.Togersen at agrsci.dk
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> -----Oprindelig meddelelse-----
> Fra: r-help-bounces at r-project.org
> [mailto:r-help-bounces at r-project.org] På vegne af Rolf Turner
> Sendt: 12. november 2007 21:16
> Til: Horacio Castellini
> Cc: r-help at r-project.org
> Emne: Re: [R] How can I fitting this function from values.
>
>
> On 13/11/2007, at 8:27 AM, Horacio Castellini wrote:
>
> > Hi all, I'd like fit this function:
> >
> > G(t)=A*1/(1+t/B)*1/sqrt(1+t/C)
> >
> > where A, B and C are fitting constants that one like search. I have
> > got a fcs<-(t,G(t)) value table in a data frame.
> >
> > Any one can help me? Tahnks Horacio.
>
>
> I ***thought*** that nls would solve your problem in a trice.
> But I tried a toy example before replying to you, and it messed up
> mightily:
>
> foo <- function(t,ccc){
> ccc[1]*1/(1+t/ccc[2])*1/sqrt(1+1/ccc[3])
> }
> ttt <- seq(1,10,length=100)
> yyy <- foo(ttt,c(5,3,2))
> set.seed(42)
> dat.test <- data.frame(t=ttt,y=yyy+rnorm(100,0,0.1))
> with(dat.test,plot(t,y))
> with(dat.test,lines(t,foo(t,c(5,3,2)))) # Looks cool.
> fit.test <- nls(y~A*1/(1+t/B)*1/sqrt(1+t/C),start=list
> (A=5,b=3,C=2),data=dat.test)
> # Gives error; no idea what the implications are.
>
> The error message:
>
> Error in `[[<-.data.frame`(`*tmp*`, var, value =
> c(0.70934153524875, 0.761288405463172, :
> replacement has 65 rows, data has 100 In addition: Warning message:
> In t/B : longer object length is not a multiple of shorter
> object length
>
> I don't think I have *ever* had a good experience with nls();
> it is always pretty flaky.
> (Well, maybe it worked for me once ..., can't remember for sure. :-) )
>
> cheers,
>
> Rolf Turner
>
>
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