Grokbase Groups R r-help March 2002
FAQ
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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r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._

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  • Shawn Hornsby at Mar 27, 2002 at 3:56 pm
    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.

    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


    -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.
    -.-
    r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
    Send "info", "help", or "[un]subscribe"
    (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch
    _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._.
    _._

    -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
    r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
    Send "info", "help", or "[un]subscribe"
    (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch
    _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
  • 1-27206531-0-90000491 at Mar 28, 2002 at 6:27 pm

    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


    -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.
    -.-
    r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
    Send "info", "help", or "[un]subscribe"
    (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch
    _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._.
    _._

    Greetings,

    Dominik

    -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
    r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
    Send "info", "help", or "[un]subscribe"
    (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch
    _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
  • Shawn Hornsby at Mar 29, 2002 at 2:37 pm
    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


    -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. -.
    -.-
    r-help mailing list -- Read
    http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
    Send "info", "help", or "[un]subscribe"
    (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch
    _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._.
    _._

    Greetings,

    Dominik


    -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
    r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
    Send "info", "help", or "[un]subscribe"
    (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch
    _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
  • Douglas Bates at Mar 27, 2002 at 4:46 pm

    1-27206531-0-90000491 <domi@sun11.ukl.uni-freiburg.de> writes:

    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
    Thank you for providing that information.
    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.
    It is likely that the iterative algorithm is progressing to values of
    the parameters that don't make sense physically. I suggest that you
    add trace = TRUE to your call to nls. This will provide a record of the
    parameter values, the residual sum of squares, and the convergence
    criterion throughout the iterations.

    -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
    r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
    Send "info", "help", or "[un]subscribe"
    (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch
    _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
  • 1-27206531-0-90000491 at Mar 28, 2002 at 6:40 pm
    Thank for the advice.

    I repeated the call of nls with option: trace=TRUE:
    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),
    + trace=TRUE)
    4189.237 : 0.008678954 -0.595153967 -4.602990518 -0.625732096
    -0.128657978 0.708033556 1.140357461 1.311141424 1.270852258
    Error in numericDeriv(form[[3]], names(ind), env) :
    Missing value or an Infinity produced when evaluating the model

    Excuse me, but I did not know, how I should interpretate it, or what
    consequences I have to do.

    Kind regards,

    Dominik
    On 27 Mar 2002, Douglas Bates wrote:

    1-27206531-0-90000491 <domi@sun11.ukl.uni-freiburg.de> writes:
    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
    Thank you for providing that information.
    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.
    It is likely that the iterative algorithm is progressing to values of
    the parameters that don't make sense physically. I suggest that you
    add trace = TRUE to your call to nls. This will provide a record of the
    parameter values, the residual sum of squares, and the convergence
    criterion throughout the iterations.

    -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
    r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
    Send "info", "help", or "[un]subscribe"
    (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch
    _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
    -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
    r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
    Send "info", "help", or "[un]subscribe"
    (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch
    _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._

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