[R] Support for compartment models / matrix exponential method
james.lindsey at luc.ac.be
Tue Apr 17 11:23:24 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.
There is mexp in my rmutil library. I use a version of it in chidden
(repeated library) for continuous time hidden Markov chains, among
> 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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