[R] A Hodgkin Huxley Model

[David Winsemius]

On Feb 10, 2013, at 8:09 AM, Ben Bolker wrote:

> Jannetta Steyn <jannetta <at> henning.org> writes:
>
>>
>> Hi All
>>
>> It has been suggested to me that the folks in this list might be  
>> able to
>> help me out of my misery.
>>
>> As part of my learning curve to building a rather detailed model of  
>> a small
>> neurone complex I am implementing some existing models in R.
>>
>> For the moment I want to implement the Izhikevich model as  
>> described in his
>> 2003 paper. The equations are as follows:
>>
>> v' = 0.04v^2 + 5v + 140 - u - I
>> u' = a(bv - u)
>> if v=30 then v<-c else u<-u+d
>>
>> I don't know how to implement the if condition in my R code. I'm  
>> using
>> deSolve. Here is my code so far.
>>
>> library(deSolve);
>> Izhikevich <- function(time, init, parms) {
>>  with(as.list(c(init, parms)),{
>>    dv <- (0.04*v^2)+(5*v)+140-u+I;
>>    du <- a*(b*v-u);
>>    if (v>=30) v<-c else v<-u+d;
>>    list( c(dv, du))
>>  })}
>> parms=c( a=0.02, b=0.2, c=-65, d=8,I=10);
>> times=seq(from=1, to=1000, by=1);
>> init=c(v=-65, u=0.2);
>>
>> out<-ode(y=init, times=times, func=Izhikevich, parms=parms)
>> plot(out)
>>
>> Can someone perhaps help me out?
>>
>> Regards
>> Jannetta
>>
>
> I'm not sure what "if v=30 then v<-c else u<-u+d" means. The first  
> clause
> is OK: I can imagine you want to implement a resetting event where
> when v crosses 30, it gets reset to c: to do this part, see ?events in
> the deSolve package (you are looking for "roots" in particular), and
> the examples in ?lsodar.  The "else" clause doesn't make much sense to
> me, as v will essentially *always* (except at particular, non-generic
> time points) be not-equal to 30 ... it would probably make sense to me
> if I went back to read the original paper, but that's too much work
> ...
>

I was interested enough to already have done that work. The else  
clause is incorrect:

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> (By the way, the semicolons at the ends of lines are unnecessary;
> they're harmless, but usually the mark of a recovering MATLAB
> user ...)
>
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David Winsemius, MD
Alameda, CA, USA