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

[Berend Hasselman]

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.

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
>> 
>> ______________________________________________
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>> http://www.R-project.org/posting-guide.html
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>> 
> 
> 
> 
> -- 
> 
> ===================================
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> Email: jannetta at henning.org
> ===================================
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