Support for compartment models / matrix exponential method
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 other things. Jim
-- 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 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- 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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