Re: [R] How can I fitting this function from values.

2007-11-13 Thread Horacio Castellini 
Thanks for the help received, I will test the proposal.

 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
 Direct:  +45 8999 1878

 E-mail:  [EMAIL PROTECTED]
 Web:   http://www.agrsci.org

 This email may contain information that is confidential.
 Any use or publication of this email without written permission from Faculty 
 of Agricultural Sciences is not allowed.
 If you are not the intended recipient, please notify Faculty of Agricultural 
 Sciences immediately and delete this email.




  -Oprindelig meddelelse-
  Fra: [EMAIL PROTECTED]
  [mailto:[EMAIL PROTECTED] På vegne af Rolf Turner
  Sendt: 12. november 2007 21:16
  Til: Horacio Castellini
  Cc: r-help@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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  confid...{{dropped:9}}
 
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  http://www.R-project.org/posting-guide.html
  and provide commented, minimal, self-contained, reproducible code.
 


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Re: [R] How can I fitting this function from values.

2007-11-13 Thread Rolf Turner 

On 13/11/2007, at 8:54 PM, Frede Aakmann Tøgersen wrote:

 R is case sensitive ;-) so in your list of start values you must  
 have B=3 and not b=3.

Duhh!!! Typo.

 Perhaps you have an object named b of a different length than your  
 data somewhere giving rise to your error message.

Nope.  That's not it.

 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.

OTOH if one invokes optim() --- with method=BFGS (no constraints)
it goes like a train (given the excellent starting values, at least):

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

bar - function(par,y,t) {
 yhat - foo(t,par)
 sum((y-yhat)^2)
}

fit.test - optim(c(5,3,2),bar,method=BFGS,control=list 
(trace=6),t=dat.test$t,y=dat.test$y)

It converges virtually instantaneously and the fit looks good:

  fit.test
$par
[1] 5.096597 2.888116 2.039852

$value
[1] 1.062285

$counts
function gradient
   176

$convergence
[1] 0

$message
NULL

  yhat - foo(dat.test$t,fit.test$par)
  lines(dat.test$t,yhat,col=red)

Moral of the story:  It's better and easier and less frustrating to  
use optim()
rather than nls() wherever possible.

cheers,

Rolf Turner

 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
 Direct:  +45 8999 1878

 E-mail:  [EMAIL PROTECTED]
 Web: http://www.agrsci.org

 This email may contain information that is confidential.
 Any use or publication of this email without written permission  
 from Faculty of Agricultural Sciences is not allowed.
 If you are not the intended recipient, please notify Faculty of  
 Agricultural Sciences immediately and delete this email.




 -Oprindelig meddelelse-
 Fra: [EMAIL PROTECTED]
 [mailto:[EMAIL PROTECTED] På vegne af Rolf Turner
 Sendt: 12. november 2007 21:16
 Til: Horacio Castellini
 Cc: r-help@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


 # 
 #
 Attention:\ This e-mail message is privileged and
 confid...{{dropped:9}}

 __
 R-help@r-project.org mailing list
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 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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[R] How can I fitting this function from values.

2007-11-12 Thread Horacio Castellini 
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.

__
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.

Re: [R] How can I fitting this function from values.

2007-11-12 Thread Joerg van den Hoff 
On Mon, Nov 12, 2007 at 04:27:26PM -0300, 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.

if your data are in `df' and the columns are labeled `t' and `G'
this seems what you want (cf. `?nls'):

nls(G ~ A*1/(1+t/B)*1/sqrt(1+t/C), start =list(A=1, B=2, C=3), data = df) 

where `start' should be set to reasonable start values.

and I would think, it is better to use p1 = 1/B, p2= 1/C during the fit
(no singularities of G for certain parameter values...).

joerg

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] How can I fitting this function from values.

2007-11-12 Thread Rolf Turner 

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


##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}

__
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.

Re: [R] How can I fitting this function from values.

2007-11-12 Thread Frede Aakmann Tøgersen 
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
Direct:  +45 8999 1878

E-mail:  [EMAIL PROTECTED]
Web:   http://www.agrsci.org

This email may contain information that is confidential.
Any use or publication of this email without written permission from Faculty of 
Agricultural Sciences is not allowed.
If you are not the intended recipient, please notify Faculty of Agricultural 
Sciences immediately and delete this email.


 

 -Oprindelig meddelelse-
 Fra: [EMAIL PROTECTED] 
 [mailto:[EMAIL PROTECTED] På vegne af Rolf Turner
 Sendt: 12. november 2007 21:16
 Til: Horacio Castellini
 Cc: r-help@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
 
 
 ##
 Attention:\ This e-mail message is privileged and 
 confid...{{dropped:9}}
 
 __
 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.
 

__
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.