Dear Alasdair,
There is all sorts of oddness with the ODE API, which appears to be in a
bit of flux at the moment, so I haven't filed any issues. For example,
ode23 really should only accept a span, but will accept a vector of any
length. It would make sense to use types to enforce this; perhaps using
(F::Function, tfinal::{T}, y0::AbstractVector{T})
for a final time
(F::Function, tspan::(T,T), y0::AbstractVector{T})
for a span
(F::Function, tvec::AbstractVector{T}, y0::AbstractVector{T})
for pre-specified times, and so on.
Also, ode23 will accept an Array{Float64,1} for initial values, but ode4,
which I'm currently using as it allows a fixed set of times to be specified
out of the box (needed as I'm fitting an ODE model to data) accepts a
column vector Array{Float64,2}.
Best
Simon
On Tuesday, January 7, 2014 11:04:18 AM UTC, Alasdair McAndrew wrote:
>
> Actually, I've looked at
> https://github.com/JuliaLang/ODE.jl/blob/master/test/test_ode.jl and
> attempted:
>
> t,x =
> ode.ode45((t,x)->[-beta*x[1]*x[2],beta*x[1]*x[2]-gamma*x[2],gamma*x[2]],[0,14],[760.,3.,0.]);
>
> where x[1], x[2] and x[3] are S, I, R respectively, and the parameters
> beta and gamma were defined earlier. This seems to work well. I suppose
> there's a way of using S, I, R instead of x[1], x[2], x[3] here...
>
> Sundials may well be the perfect solution, but I couldn't get it to work,
> and the documentation is daunting, to say the least!
>
> On Tuesday, January 7, 2014 9:58:54 PM UTC+11, Ivar Nesje wrote:
>>
>> This seems likely to be caused by changes in Julia. The fix will probably
>> involve a bug report to https://github.com/JuliaLang/ODE.jl and some
>> code reading and testing. If you see that the commit count on that
>> repository is 11 it is quite possible that it does not receive the care ODE
>> solvers deserve in a language like Julia.
>>
>> I am not sure, but Sundials.jl <https://github.com/JuliaLang/Sundials.jl>
>> might
>> be an option, but when I tried it last time it was no automatic script for
>> compiling and installing the dependencies.
>>
>>
>>
>> kl. 11:23:33 UTC+1 tirsdag 7. januar 2014 skrev Alasdair McAndrew
>> følgende:
>>>
>>> I have copied the SIR model here:
>>> http://phylodynamics.blogspot.co.uk/2013/07/differential-equation-modeling-with.htmlwhich
>>> works fine with ode23. But ode45, which would seem to have the same
>>> syntax, throws an error:
>>>
>>> julia> sol = ode.ode45((t,x)->SIR(t,x,p),t,inits);
>>> ERROR: InexactError()
>>> in setindex! at array.jl:471
>>> in oderkf at /opt/julia/usr/share/julia/site/v0.3/ODE/src/ODE.jl:217
>>> in ode45_dp at /opt/julia/usr/share/julia/site/v0.3/ODE/src/ODE.jl:277
>>>
>>> Does anybody know what's going on here, and how I can overcome it? In
>>> other words, how do I use ode45? Thanks!
>>>
>>>
>>>
