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merged ParametricModels.jl and PiecewiseInference.jl
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,182 @@ | ||
| import Base | ||
| function Base.merge(ca::ComponentArray{T}, ca2::ComponentArray{T2}) where {T, T2} | ||
| ax = getaxes(ca) | ||
| ax2 = getaxes(ca2) | ||
| vks = valkeys(ax[1]) | ||
| vks2 = valkeys(ax2[1]) | ||
| _p = Vector{T}() | ||
| for vk in vks | ||
| @assert !(getproperty(ca2, vk) isa ComponentVector) "Only non-nested `ComponentArray`s are supported by `merge`." | ||
| if vk in vks2 | ||
| _vec = vec(getproperty(ca2, vk)) # ca2[vk] | ||
| _p = vcat(_p, _vec) | ||
| else | ||
| _vec = vec(getproperty(ca, vk)) # ca1[vk] | ||
| _p = vcat(_p, _vec) | ||
| end | ||
| end | ||
| # for vk in vks2 | ||
| # if vk not in vks | ||
| # _vec = vec(getproperty(ca2, vk)) # ca1[vk] | ||
| # _p = vcat(_p, _vec) | ||
| # ax = merge(ax, ) | ||
| # end | ||
| # end | ||
| ComponentArray(_p, ax) | ||
| end | ||
|
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||
| Base.merge(::Nothing, ca2::ComponentArray{T2}) where {T2} = ca2 | ||
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| # This piece is inspired from https://github.com/jonniedie/ComponentArrays.jl/pull/217 | ||
| # import ComponentArrays: promote_type, getval, Val, indexmap | ||
| # @generated function valkeys(ax::AbstractAxis) | ||
| # idxmap = indexmap(ax) | ||
| # k = Val.(keys(idxmap)) | ||
| # return :($k) | ||
| # end | ||
| # valkeys(ca::ComponentVector) = valkeys(getaxes(ca)[1]) | ||
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| # function merge(cvec1::ComponentVector{T1}, cvec2::ComponentVector{T2}) where {T1, T2} | ||
| # typed_dict = ComponentVector{promote_type(T1, T2)}(cvec1) | ||
| # for key in valkeys(cvec2) | ||
| # keyname = getval(key) | ||
| # val = cvec2[key] | ||
| # typed_dict = eval(:( ComponentArray($typed_dict, $keyname = $val) )) | ||
| # end | ||
| # typed_dict | ||
| # end | ||
|
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| abstract type AbstractModel end | ||
| name(m::AbstractModel) = string(nameof(typeof(m))) | ||
| Base.show(io::IO, cm::AbstractModel) = println(io, "`Model` ", name(cm)) | ||
|
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||
| """ | ||
| $(SIGNATURES) | ||
| Returns the `ODEProblem` associated with to `m`. | ||
| """ | ||
| function get_prob(m::AbstractModel, u0, tspan, p) | ||
| prob = ODEProblem(m, u0, tspan, p) | ||
| return prob | ||
| end | ||
|
|
||
| """ | ||
| $(SIGNATURES) | ||
| Simulate model `m` and returns an `ODESolution`. | ||
| When provided, keyword arguments overwrite default solving options | ||
| in m. | ||
| """ | ||
| function simulate(m::AbstractModel; u0 = nothing, tspan=nothing, p = nothing, alg = nothing, kwargs...) | ||
| isnothing(u0) ? u0 = get_u0(m) : nothing | ||
| isnothing(tspan) ? tspan = get_tspan(m) : nothing | ||
| if isnothing(p) | ||
| p = get_p(m) | ||
| else | ||
| # p can be a sub tuple of the full parameter tuple | ||
| p0 = get_p(m) | ||
| p = merge(p0, p) | ||
| end | ||
| isnothing(alg) ? alg = get_alg(m) : nothing | ||
| prob = get_prob(m, u0, tspan, p) | ||
| # kwargs erases get_kwargs(m) | ||
| sol = solve(prob, alg; get_kwargs(m)..., kwargs...) | ||
| return sol | ||
| end | ||
|
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| struct ModelParams{P,T,U0,A,K} | ||
| p::P # model parameters; we require dictionary or named tuples or componentarrays | ||
| tspan::T # time span | ||
| u0::U0 # initial conditions | ||
| alg::A # alg for ODEsolve | ||
| kwargs::K # kwargs given to solve fn, e.g., saveat | ||
| end | ||
|
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||
| import SciMLBase.remake | ||
| function remake(mp::ModelParams; | ||
| p = mp.p, | ||
| tspan = mp.tspan, | ||
| u0 = mp.u0, | ||
| alg = mp.alg, | ||
| kwargs = mp.kwargs) | ||
| ModelParams(p, tspan, u0, alg, kwargs) | ||
| end | ||
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| # # for the remake fn | ||
| # function ModelParams(;p, | ||
| # p_bij::PST, | ||
| # re, | ||
| # tspan, | ||
| # u0, | ||
| # u0_bij, | ||
| # alg, | ||
| # dims, | ||
| # plength, | ||
| # kwargs) where PST <: Bijector | ||
| # ModelParams(p, | ||
| # p_bij, | ||
| # re, | ||
| # tspan, | ||
| # u0, | ||
| # u0_bij, | ||
| # alg, | ||
| # dims, | ||
| # plength, | ||
| # kwargs) | ||
| # end | ||
|
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| # model parameters | ||
| """ | ||
| $(SIGNATURES) | ||
| Structure containing the details for the numerical simulation of a model. | ||
| # Arguments | ||
| - `tspan`: time span of the simulation | ||
| - `u0`: initial condition of the simulation | ||
| - `alg`: numerical solver | ||
| - `kwargs`: extra keyword args provided to the `solve` function. | ||
| # Optional | ||
| - `p`: default parameter values | ||
| # Example | ||
| mp = ModelParams() | ||
| """ | ||
| function ModelParams(; p = nothing, tspan = nothing, u0 = nothing, alg = nothing, kwargs...) | ||
| ModelParams(p, | ||
| tspan, | ||
| u0, | ||
| alg, | ||
| kwargs) | ||
| end | ||
| ModelParams(p, tspan, u0, alg) = ModelParams(p, tspan, u0, alg, ()) | ||
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| get_mp(m::AbstractModel) = m.mp | ||
| get_p(m::AbstractModel) = m.mp.p | ||
| get_u0(m::AbstractModel) = m.mp.u0 | ||
| get_alg(m::AbstractModel) = m.mp.alg | ||
| get_tspan(m::AbstractModel) = m.mp.tspan | ||
| get_kwargs(m::AbstractModel) = m.mp.kwargs | ||
| """ | ||
| $SIGNATURES | ||
| Returns the dimension of the state variable | ||
| """ | ||
| get_dims(m::AbstractModel) = length(get_u0(m)) | ||
|
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| """ | ||
| $SIGNATURES | ||
| Generates the skeleton of the model, a `struct` containing details of the numerical implementation. | ||
| """ | ||
| macro model(name) | ||
| expr = quote | ||
| struct $name{MP<:ModelParams} <: AbstractModel | ||
| mp::MP | ||
| end | ||
|
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||
| $(esc(name))(;mp) = $(esc(name))(mp) | ||
| end | ||
| return expr | ||
| end |
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