On 04-07-2013, at 19:56, peter dalgaard <pda...@gmail.com> wrote: > > 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. >
Same NA results here. Making parms a named vector makes no difference but is is certainly necessary to do that. In that case there is probably an inconsistency in the file simulate.m near the end: The last non empty line before the line out = … reads iLeak_axon = gLeak_axon_AB.*(v_axon_AB-ELeak_axon_AB); and this doesn't agree with the line iLeak_axon = ELeak_axon_AB*(v_axon_AB-ELeak_axon_AB); in the function xdot. Final question for the OP: if the model is supposed to be dynamic, isn't it suspicious that Matlab gives a constant result? Berend > >> >> 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.
