Implement the SEIR-V model from the epidemics R package

[sdwfrost]

See https://github.com/epiverse-trace/epidemics

[sdwfrost]

An R version of the code (without vaccination) is here. The blocker at the moment is that the following code for an SEIR model gives the wrong wiring diagram.

using AlgebraicPetri,AlgebraicPetri.TypedPetri
using Catlab, Catlab.CategoricalAlgebra, Catlab.Programs
using Catlab.WiringDiagrams, Catlab.Graphics
using AlgebraicDynamics.UWDDynam


epi_transitions = LabelledPetriNet(
  [:Pop],
  :infection=>((:Pop, :Pop)=>(:Pop, :Pop)),
  :progression=>(:Pop=>:Pop),
  :recovery=>(:Pop=>:Pop)
)

seir_uwd = @relation () where (S::Pop, E::Pop, I::Pop, R::Pop) begin
    infection(S, I, E, I)
    progression(E, I)
    recovery(I, R)
end
seir_acst = oapply_typed(epi_transitions, seir_uwd, [:β, :δ, :γ])
seir_lpn = dom(seir_acst)
Graph(seir_lpn)

[slwu89]

@sdwfrost the upstream bugs may have been fixed, see the result below from your code (replacing Graph(seir_lpn) with to_graphviz(seir_lpn) to conform to Catlab's standard graphics interface)