R help - Apr 2001 - Support for compartment models / matrix exponential method

I try to fit reaction kinetic data to a given hypothetical model
consisting of 3 ODEs. After some reading in Bates/Watts and the literature
cited there (e.g. Jennrich/Bright) I looked in R for functions that support
the use of the matrix exponential method. Until now I used for a similar
(but simpler) problem the nls package and fitted against the the parameterized
solution function. But this works only for simple kinetics.

The algorithms in the nls package (e.g. SSfol) work on "closed forms"
of the
solution function, too.

My question is: Are there examples or functions in R that show the usage of
the matrix exponential method or do I have to build the steps from primitive
functions myself, e.g. following the recipe in Jennrich/Bright (or is there 
even a superior method for this kind of tasks that I am not aware of)?


============================================================================Thomas
Hoffmann, Institut fuer Halbleiter- und Mikrosystemtechnik, TU Dresden
E-mail: hoffmann at ehmgs2.et.tu-dresden.de
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Thomas Hoffmann <hoffmann at ehmgs2.et.tu-dresden.de> writes:
> I try to fit reaction kinetic data to a given hypothetical model
> consisting of 3 ODEs. After some reading in Bates/Watts and the literature
> cited there (e.g. Jennrich/Bright) I looked in R for functions that support
> the use of the matrix exponential method. Until now I used for a similar
> (but simpler) problem the nls package and fitted against the the
parameterized
> solution function. But this works only for simple kinetics.
> 
> The algorithms in the nls package (e.g. SSfol) work on "closed
forms" of the
> solution function, too.
> 
> My question is: Are there examples or functions in R that show the usage of
> the matrix exponential method or do I have to build the steps from
primitive
> functions myself, e.g. following the recipe in Jennrich/Bright (or is there
> even a superior method for this kind of tasks that I am not aware of)?
There's a strong temptation to lift the expm function off of Octave... 

Yes, we need it, for compartment models and also continuous-time
Markov chain models.

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907
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