[R] Support for compartment models / matrix exponential method

Peter Dalgaard BSA p.dalgaard at biostat.ku.dk
Mon Apr 16 17:40:22 CEST 2001

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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