[R] Error with nls
Shawn Hornsby
shawnhornsby at netzero.net
Fri Mar 29 15:37:02 CET 2002
Dear Dominik,
It has been in my experience that with global variables sometimes it has to
be defined and initialized within the local module before the variables can
use to manipulate data from another source.
Something else came to mind with function g(t), there are times when the
space causes the operation to be read incorrectly, and it see it as, do "g"
then do "t" and not, do function g(t).
When combining modules sometimes you may have to check each module manually
to make sure that it's algorithm routine is functioning correctly. I have
been told some time ago by a wise person, do the mathematical operation
manually then, use a calculator, then, use a spreadsheet and finally enter
it into you code. Here is where you will have additional references to check
you result(s). Give it a try and let me know how you made out...
Regards,
Shawn
-----Original Message-----
From: 1-27206531-0-90000491 [mailto:domi at sun11.ukl.uni-freiburg.de]
Sent: Thursday, March 28, 2002 1:27 PM
To: Shawn Hornsby
Cc: r-help at stat.math.ethz.ch
Subject: RE: [R] Error with nls
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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