Sl/dependent machines

[slwu89]

@slibkind I'm adding a simplest possible example of the RM ODE model with an InstantaneousContinuousMachine; the composed dynamical system should be the exact same as the existing ODE model there. The oapply is running into some problems when composing however, if you have a minute can you help me take a look? The composition pattern is ok so it must be an error in how I'm setting up the InstantaneousContinuousMachine.

The dyn sys should be:
EIR = maZ
\kappa = c*X

\dot{Z} = a*\kappa*(e^{-gn} - Z) - gZ

\dot{X} = bEIR(1-X) - rX

[slwu89]

oapply works for me after changing the induced_dynamics and induced_readout methods to be less parametrically constrained, that is, where {T,I, M<:AbstractMachine{T,I}} to where {M<:AbstractMachine} in both those methods. Still encounter an error when running the ODE solver though!

[slwu89]

Update, trying out the example again after merging the latest (today) updates to the sl/dependent_machines branch. Error when calling solve:

ERROR: type Float64 has no field c
Stacktrace:
  [1] getproperty
    @ ./Base.jl:42 [inlined]
  [2] (::var"#5#6")(u::Vector{Float64}, x::LArray{Real, 1, Vector{Real}, (:a, :b, :c, :g, :n, :r, :m)}, p::Float64, t::Int64)
    @ Main ./REPL[15]:4
  [3] readout(m::AlgebraicDynamics.DWDDynam.Machine{Float64, AlgebraicDynamics.DWDDynam.InstantaneousDirectedInterface{Float64}, AlgebraicDynamics.DWDDynam.ContinuousDirectedSystem{Float64}}, u::Vector{Float64}, x::LArray{Real, 1, Vector{Real}, (:a, :b, :c, :g, :n, :r, :m)}, p::Float64, t::Int64) (repeats 2 times)
    @ AlgebraicDynamics.DWDDynam ~/Desktop/git/AlgebraicDynamics.jl/src/dwd_dynam.jl:261
  [4] (::AlgebraicDynamics.DWDDynam.var"#102#103"{Vector{Vector{Float64}}, LArray{Real, 1, Vector{Real}, (:a, :b, :c, :g, :n, :r, :m)}, Float64})(::Tuple{Int64, AlgebraicDynamics.DWDDynam.Machine{Float64, AlgebraicDynamics.DWDDynam.InstantaneousDirectedInterface{Float64}, AlgebraicDynamics.DWDDynam.ContinuousDirectedSystem{Float64}}})
    @ AlgebraicDynamics.DWDDynam ~/Desktop/git/AlgebraicDynamics.jl/src/dwd_dynam.jl:590

So the issue is here in dwd_dynam:

AlgebraicDynamics.jl/src/dwd_dynam.jl

Lines 590 to 592 in 13d5935

	get_readouts(ms::AbstractArray{M}, states, p, t) where {M <: AbstractMachine} = map(enumerate(ms)) do (i, m)
	readout(m, states[i], p, t)
	end

which calls

AlgebraicDynamics.jl/src/dwd_dynam.jl

Lines 261 to 262 in 13d5935

	readout(m::Machine{T,I,S}, u::AbstractVector, x::AbstractVector, p=nothing, t=0) where {T, I<:InstantaneousDirectedInterface{T}, S} =
	readout(m)(u,x,p,t)

Somehow the wrong args are getting passed to the readout function, such that the time is getting sent into the spot where parameters should be passed.

[slibkind]

I think the problem comes from the fact that you are composing and InstantaneousContinuousMachine with two ContinuousMachine. A good addition to PR #99 would be to explicitly enable this.

In the meantime a quick solution would be to write the mosquito and host models as instantaneous machines with trivial input/output dependency. For example, instead of

mosquito_model = ContinuousMachine{Float64}(1, 1, 1, dZdt, (u,p,t) -> u)

try

mosquito_model = InstantaneousContinuousMachine{Float64}(1, 1 ,1, dZdt, (u,x,p,t) -> u, [])

Another good addition to PR #99 would be to have a method which turns ContinuousMachines into InstantaneousContinuousMachines.

[slibkind]

Lastest commit on PR #99 adds a constructor for InstantaneousMachine from an ordinary machine. Now you should be able to write the above as:

mosquito_model = ContinuousMachine{Float64}(1, 1, 1, dZdt, (u,p,t) -> u)
instantaneous_mosquito_model = InstantaneousContinuousMachine{Float64}(mosquito_model)