[R] Error with nls

[1-27206531-0-90000491]

On Wed, 27 Mar 2002, Shawn Hornsby wrote:

> Dear Kind,
> 
> I would like to let you know up front that I am not a mathematician nor do I
> want to insult you or your intelligence. I am a humble person of simple
> education and means and I am offering a suggestion, you may have already
> resolved this issue. Here are my suggestions:
> 
> In the expression, db5 = - (k50+k56)*b5 + k56*b6 + c*g(t) + h, I notice that
> function g(t) is not explicitly defined as an expression. I do see you make
> reference to it in, assuming that g(t) has the functional form: b4i +
> (b40-b4i)*exp(-k4*t), maybe this is the expression and I am overlooking it.
> While, I continued to examine the function g(t), I saw no explicit
> definition of variables b40, b4i, k4, and t. They are shown to be part of
> the equation but they are not explicitly defined with values.

In the origin, it was a compartment model with 6 compartments. Data was
available for every compartment. But of scientific interest are specially
the last 2 compartments, #5 and #6. The function g(t) is the approach to
fill compartment  5 via a forcing function. The parameters b4i and b40 and
k4 results from a fit of compartment 4. In my model of compartment 5 and 6
the parameters b40, b4i and k4 are like time constant covariables. 

> 
> Again, I am hoping my observation spark an idea that would lead you to your
> resolve.
> 
> If there is someone in the R-Project that has already helped Kind, I would
> like to thank you.
> 
> Regards,
> Shawn
> 
> -----Original Message-----
> From: owner-r-help at stat.math.ethz.ch
> [mailto:owner-r-help at stat.math.ethz.ch]On Behalf Of
> 1-27206531-0-90000491
> Sent: Wednesday, March 27, 2002 4:48 AM
> To: r-help at stat.math.ethz.ch
> Subject: [R] Error with nls
> 
> 
>  Dear R-group members,
> 
>  I use:
> 
>  platform i386-pc-mingw32
>  arch     x86
>  os       Win32
>  system   x86, Win32
>  status
>  major    1
>  minor    4.1
>  year     2002
>  month    01
>  day      30
>  language R
> 
>  I try to fit a 2 compartment model. The compartments are open, connected
>  to each other and are filled via constant input and a time depended
>  function as well. Data describes increasing of Apo B after dialysis. Aim
>  of the analysis is to test the hypothesis whether the data could described
>  by two simple disconnected one compartment modes ore the "saturated
>  model" holds? The first order differential equation for the saturated
>  model:
> 
>  db5 = - (k50+k56)*b5 + k56*b6 + c*g(t) + h
>  db6 = + k65*b5 - (k60+k65)*b6 + d
> 
>  db5, db6 are the first derivatives, b5, b6 are the functions to be
>  fitted. The remaining parameters are unknown and should follow from the
>  fit.
> 
>  assuming that g(t) has the functional form: b4i + (b40-b4i)*exp(-k4*t)
> 
>  (after calculations of 2 papers of A4) follows the solution:
> 
>  L5L6 <- function(b40, b4i, k4, t, p50, p56, p60, p65, pc, ph, pd, pb50,
>  pb60) {
> 
>  	k50 <- exp(p50)
>  	k56 <- exp(p56)
>  	k60 <- exp(p60)
>  	k65 <- exp(p65)
>  	c   <- exp(pc)
>  	h   <- exp(ph)
>  	d   <- exp(pd)
>  	b50 <- exp(pb50)
>  	b60 <- exp(pb60)
>  	a <- (k50+k56)
>  	b <- k65
>  	e <- k56
>  	f <- (k60+k65)
>  	z1 <- (-(a+f)/2 - sqrt((a+f)^2/4 - a*f + b*e))
>  	z2 <- (-(a+f)/2 + sqrt((a+f)^2/4 - a*f + b*e))
>  	K  <- ((z1+a)/(z2-z1))
>  	B1 <- (b/(z2-z1)*b60 - K*b50)
>  	A1 <- (b50-B1)
>  	X1 <- (b*d/(z2-z1)-K*(c*b4i+h))
>  	X2 <- (K*c*(b4i-b40))
>  	X3 <- (c*b4i + h - X1)
>  	X4 <- (c*(b40-b4i)- X2)
>  	C1E <- (X3/(-z1)*(1-exp(z1*t)) +
>  X4/(-(k4+z1))*(exp(-k4*t)-exp(z1*t)))
>  	C2E <- (X1/(-z2)*(1-exp(z2*t)) +
>  X2/(-(k4+z2))*(exp(-k4*t)-exp(z2*t)))
>  	b5 <- (A1*exp(z1*t) + B1*exp(z2*t) + C1E + C2E)
>  	b6 <- ((z1+a)/b * A1*exp(z1*t) + (z2+a)/b * B1*exp(z2*t) +
>  (z1+a)/b * C1E + (z2+a)/b * C2E)
>  	y <- f5*b5 + f6*b6
>  	return(y)
>  }
> 
>  I am in the lucky circumstances having starting values, because a nlr-fit
>  succeeds, the graphical presentation of the fits looks quite nice. The nlr
>  function is part of Lindsey's library(gnlm), but now I would like to apply
>  Pinheiro and Bates library(nlme) and I have got an error:
> 
> > m2 <- nls(y ~ L5L6(b40, b4i, k4, t, p50, p56, p60, p65, pc, ph, pd,
> > pb50, pb60),
> > + data=help, start=c(p50=0.008678954, p56=-0.595153967,
> > + p60=-4.602990518, p65=-0.625732096,
> > + pc=-0.128657978, ph=0.708033556, pd=1.140357461, pb50=1.311141424,
> > + pb60=1.270852258))
> > Error in numericDeriv(form[[3]], names(ind), env) :
> >         Missing value or an Infinity produced when evaluating the model
> >
>  If somebody feel that he can help me, I could send him my R- code and
>  data file as well.
> 
>  Kind regards,
> 
>  Dominik
> 
> 
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> 


Greetings,

Dominik

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