On Jul 4, 2013, at 19:11 , Berend Hasselman wrote: > > On 04-07-2013, at 18:42, Jannetta Steyn <janne...@henning.org> wrote: > >> Hi Ben and others >> >> I don't quite know how to explain the "doesn't work" in more detail without >> any visual aid. > > You said that R got into an indefinite loop, whatever that maybe. > >> When you run the two scripts it is easy to see the >> difference. MatLab produces a line on x= -55. This is what I expect - a >> more or less straight line. R on the other hand the result drops from -55 >> (the initial value) to -80 and then goes up to -71.37092. >> >> The two scripts have exactly the same equations. > > > I don't think so. > In the R script you have > > init = c(v_axon_AB=-55,mNa_axon_AB=1,hNa_axon_AB=0,mK_axon_AB=1) > > That is not the same as in your Matlab script. To make them the same you > should replace the line with > > init = c(v_axon_AB=-55,mNa_axon_AB=0,hNa_axon_AB=1,mK_axon_AB=0) > > Using this line gives quite different results. But not the same as Matlab. > > It seems that you ought to carefully check all your equations. > I don't know enough about Matlab/Octave syntax to determine if the results of > the two systems are identical.
Also, the line iLeak_axon_AB <- gLeak_axon_AB*(v_axon_AB-ELeak_axon_AB) differs from the Matlab code. Changing it gave me all-NA results, though. And the with() construct assumes that init and parms are named vectors; parms is not, so the values are taken from the global environment. It is not clear whether that makes a difference. > > Berend > >> I have even named the >> variables the same in the two scripts and copied the equations across to >> make sure I haven't made any typos. >> >> Can one attach images to posts? I'll try. The flatline image is the plot >> from MatLab and the other is the plot from R. >> >> Thanks >> Jannetta >> >> >> On 4 July 2013 16:52, Ben Bolker <bbol...@gmail.com> wrote: >> >>> Berend Hasselman <bhh <at> xs4all.nl> writes: >>> >>>> >>>> >>>> On 04-07-2013, at 17:15, Jannetta Steyn <jannetta <at> henning.org> >>> wrote: >>>> >>>>> Hi folks >>>>> >>>>> I have implemented a model of a neuron using Hodgkin Huxley equations >>> in >>>>> both R and MatLab. My preference is to work with R but R is not giving >>> me >>>>> the correct results. I also can't use ode45 as it just seems to go >>> into an >>>>> indefinite loop. However, the MatLab implementation work fine with >>>>> the same >>>>> equations, parameters and initial values and ode45. Below is my R and >>>>> MatLab implementations. >>>>> >>>> >>>> No problem in running your R file. Have plot. >>>> (Mac mini Core2Duo 2.66Ghz running R 3.0.1 Patched >>>> (2013-06-19 r62992) on Mac OS X 10.8.4: 16.5 seconds.) >>>> >>>> Trying to run your Matlab file in Octave. >>>> No success yet because of unavailable ode45. >>> >>> I'm impressed that you (BH) went to the trouble of checking >>> on this vague "doesn't work" question. If you want to go farther >>> I think you can get ode45 for octave by installing the odepkg >>> package: >>> >>> http://octave.sourceforge.net/odepkg/index.html >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >> >> >> >> -- >> >> =================================== >> Web site: http://www.jannetta.com >> Email: janne...@henning.org >> =================================== >> <Rplot01.png><MatPlot01.png>______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd....@cbs.dk Priv: pda...@gmail.com ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.