[R] R and MatLab implementations of the same model differs

[peter dalgaard]

On Jul 4, 2013, at 19:11 , Berend Hasselman wrote:

> 
> On 04-07-2013, at 18:42, Jannetta Steyn <jannetta at 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 <bbolker at 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 at 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: jannetta at henning.org
>> ===================================
>> <Rplot01.png><MatPlot01.png>______________________________________________
>> R-help at 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 at 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.mes at cbs.dk  Priv: PDalgd at gmail.com