Add AlgebraicEpiMech

.github/workflows/test.yaml

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+name: Julia tests
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+permissions:
+  actions: write
+  contents: read
+
+jobs:
+  test:
+    name: Julia ${{ matrix.julia-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version: ['1.11', '1.12', '1.13']
+
+    steps:
+    - uses: actions/checkout@v7
+    - uses: julia-actions/setup-julia@v3
+      with:
+        version: ${{ matrix.julia-version }}
+        project: AlgebraicEpiMech
+    - uses: julia-actions/cache@v3
+    - uses: julia-actions/julia-buildpkg@v1
+      with:
+        project: AlgebraicEpiMech
+    - uses: julia-actions/julia-runtest@v1
+      with:
+        project: AlgebraicEpiMech

.gitignore

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+.DS_Store
+
+Manifest*

AlgebraicEpiMech/Project.toml

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+name = "AlgebraicEpiMech"
+uuid = "a6e39d6b-8b2d-49f3-aca0-f4154643f040"
+version = "0.1.0"
+authors = ["Samuel Brand <usi1@cdc.gov>"]
+
+[workspace]
+projects = ["test"]
+
+[deps]
+AlgebraicPetri = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
+Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+
+[compat]
+AlgebraicPetri = "0.10.0"
+Catlab = "0.17.2"
+DocStringExtensions = "0.9.3"
+julia = "1.11, 1.12, 1.13"

AlgebraicEpiMech/src/AlgebraicEpiMech.jl

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+module AlgebraicEpiMech
+
+using AlgebraicPetri, AlgebraicPetri.TypedPetri
+using Catlab
+using DocStringExtensions
+import Base: *
+
+# Epidemiological typing strategies and their Petri-net type systems
+export EpidemiologicalTyping, OnePopulationTyping, UninfectedInfectedTyping, type_system
+
+# Epi mechanism functions
+export add_infection!, add_disease_progression!,
+    add_uninfected_density_progression!, add_reversion_progression!
+
+# Observation chain
+# Observation by pushout (attached after composition)
+export ObservationTarget, AtEvent, AtCompartment, attach_observation
+
+export ObservationChainLayout, ObservationLayout, observation_layout
+
+# Compartmental models types
+export CompartmentalModel, SI, SEI, SIS, SIR, SEIR, SEIRS, SEIS
+
+# Multistrain model types
+export MultiStrainModel, NoCrossImmunity, CompleteCrossImmunity
+
+# Immune-history model types
+export ImmuneHistory, ImmuneHistoryMode, FullHistory, LatestInfection
+
+# Stratification types
+export Stratification, ContactStratification, AgeStratification, GeographicStratification,
+    compose_stratifications
+
+# Model functions
+export EpiMechModel, create_model_uwd, create_model, generate_transition_names
+
+# Vectorfield functions
+export flatten_symbols, vectorfield_flat
+
+# Documentation strings
+include("docstrings.jl")
+
+# Epidemiological dynamics
+include("typing.jl")
+include("mechanisms.jl")
+include("CompartmentalModel.jl")
+include("MultiStrainModel.jl")
+include("ImmuneHistory.jl")
+include("Stratification.jl")
+include("construction_helpers.jl")
+include("create_model_uwd.jl")
+include("generate_transition_names.jl")
+include("create_model.jl")
+include("vectorfield_flat.jl")
+
+# Observation attachment.
+include("ObservationTarget.jl")
+include("ObservationLayout.jl")
+
+end

AlgebraicEpiMech/src/CompartmentalModel.jl

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+"""
+Abstract base type for all epidemiological-mechanical models in the AlgebraicEpiMech framework.
+
+All concrete epidemiological-mechanical model types should be subtypes of `EpiMechModel`.
+This abstract type serves as the root of the type hierarchy for models that combine
+epidemiological dynamics with mechanical or algebraic structures.
+
+# Extended help
+
+Subtypes of `EpiMechModel` should implement the necessary interface methods for their
+specific model formulation.
+
+# See also
+- Related concrete model types (define as needed)
+"""
+abstract type EpiMechModel end
+
+"""
+Abstract base type for compartmental epidemiological models.
+
+Compartmental models define the specific disease dynamics and transitions
+between epidemiological states (e.g., S→I→R) as undirected wiring diagrams.
+"""
+abstract type CompartmentalModel <: EpiMechModel end
+
+function _validate_stage_count(name::Symbol, count::Int)
+    count >= 1 || throw(ArgumentError("$name must be at least 1"))
+    return count
+end
+
+# Base compartmental models - concrete structs for clean dispatch
+
+"""
+Susceptible-Infected (SI) compartmental model.
+
+The SI model includes:
+- Susceptible (S): Individuals who can become infected
+- Infected (I): Individuals who are infectious
+
+Transitions:
+- S + I → I + I (infection/transmission)
+
+The SI model represents endemic diseases with no recovery.
+"""
+struct SI <: CompartmentalModel
+    number_I_stages::Int
+    number_of_states::Int
+
+    function SI(; number_I_stages::Int = 1)
+        _validate_stage_count(:number_I_stages, number_I_stages)
+        return new(number_I_stages, 1 + number_I_stages)
+    end
+end
+
+"""
+Susceptible-Exposed-Infected (SEI) compartmental model.
+
+The SEI model extends SI with an exposed compartment:
+- Susceptible (S): Individuals who can become infected
+- Exposed (E): Individuals who are infected but not yet infectious
+- Infected (I): Individuals who are infectious
+
+Transitions:
+- S + I → E + I (exposure/transmission)
+- E → I (progression to infectious)
+
+The SEI model represents diseases with an incubation period but no recovery.
+"""
+struct SEI <: CompartmentalModel
+    number_E_stages::Int
+    number_I_stages::Int
+    number_of_states::Int
+
+    function SEI(; number_E_stages::Int = 1, number_I_stages::Int = 1)
+        _validate_stage_count(:number_E_stages, number_E_stages)
+        _validate_stage_count(:number_I_stages, number_I_stages)
+        return new(number_E_stages, number_I_stages, 1 + number_E_stages + number_I_stages)
+    end
+end
+
+# Extended compartmental models - built by extending base models
+
+"""
+Susceptible-Infected-Recovered (SIR) compartmental model.
+
+The SIR model extends SI with recovery:
+- Susceptible (S): Individuals who can become infected
+- Infected (I): Individuals who are infectious
+- Recovered (R): Individuals who have recovered and gained immunity
+
+Transitions:
+- S + I → I + I (infection/transmission) [from SI]
+- I → R (recovery) [extension]
+
+Built by extending SI model with recovery transition.
+"""
+struct SIR <: CompartmentalModel
+    number_I_stages::Int
+    number_of_states::Int
+
+    function SIR(; number_I_stages::Int = 1)
+        _validate_stage_count(:number_I_stages, number_I_stages)
+        return new(number_I_stages, 2 + number_I_stages)
+    end
+end
+
+"""
+Susceptible-Exposed-Infected-Recovered (SEIR) compartmental model.
+
+The SEIR model extends SEI with recovery:
+- Susceptible (S): Individuals who can become infected
+- Exposed (E): Individuals who are infected but not yet infectious
+- Infected (I): Individuals who are infectious
+- Recovered (R): Individuals who have recovered and gained immunity
+
+Transitions:
+- S + I → E + I (exposure/transmission) [from SEI]
+- E → I (progression to infectious) [from SEI]
+- I → R (recovery) [extension]
+
+Built by extending SEI model with recovery transition.
+"""
+struct SEIR <: CompartmentalModel
+    number_E_stages::Int
+    number_I_stages::Int
+    number_of_states::Int
+
+    function SEIR(; number_E_stages::Int = 1, number_I_stages::Int = 1)
+        _validate_stage_count(:number_E_stages, number_E_stages)
+        _validate_stage_count(:number_I_stages, number_I_stages)
+        return new(number_E_stages, number_I_stages, 2 + number_E_stages + number_I_stages)
+    end
+end
+
+"""
+Susceptible-Infected-Susceptible (SIS) compartmental model.
+
+The SIS model extends SI with waning immunity (reversion):
+- Susceptible (S): Individuals who can become infected
+- Infected (I): Individuals who are infectious
+
+Transitions:
+- S + I → I + I (infection/transmission) [from SI]
+- I → S (waning immunity/reversion) [extension]
+
+The SIS model represents diseases with no lasting immunity.
+"""
+struct SIS <: CompartmentalModel
+    number_I_stages::Int
+    number_of_states::Int
+
+    function SIS(; number_I_stages::Int = 1)
+        _validate_stage_count(:number_I_stages, number_I_stages)
+        return new(number_I_stages, 1 + number_I_stages)
+    end
+end
+
+"""
+Susceptible-Exposed-Infected-Susceptible (SEIS) compartmental model.
+
+The SEIS model extends SEI with waning immunity (reversion):
+- Susceptible (S): Individuals who can become infected
+- Exposed (E): Individuals who are infected but not yet infectious
+- Infected (I): Individuals who are infectious
+
+Transitions:
+- S + I → E + I (exposure/transmission) [from SEI]
+- E → I (progression to infectious) [from SEI]
+- I → S (waning immunity/reversion) [extension]
+
+The SEIS model represents diseases with incubation period but no lasting immunity.
+"""
+struct SEIS <: CompartmentalModel
+    number_E_stages::Int
+    number_I_stages::Int
+    number_of_states::Int
+
+    function SEIS(; number_E_stages::Int = 1, number_I_stages::Int = 1)
+        _validate_stage_count(:number_E_stages, number_E_stages)
+        _validate_stage_count(:number_I_stages, number_I_stages)
+        return new(number_E_stages, number_I_stages, 1 + number_E_stages + number_I_stages)
+    end
+end
+
+"""
+Susceptible-Exposed-Infected-Recovered-Susceptible (SEIRS) compartmental model.
+
+The SEIRS model extends SEIR with waning immunity:
+- Susceptible (S): Individuals who can become infected
+- Exposed (E): Individuals who are infected but not yet infectious
+- Infected (I): Individuals who are infectious
+- Recovered (R): Individuals who have recovered but may lose immunity
+
+Transitions:
+- S + I → E + I (exposure/transmission) [from SEIR]
+- E → I (progression to infectious) [from SEIR]
+- I → R (recovery) [from SEIR]
+- R → S (waning immunity) [extension]
+
+Built by extending SEIR model with waning transition.
+"""
+struct SEIRS <: CompartmentalModel
+    number_E_stages::Int
+    number_I_stages::Int
+    number_of_states::Int
+
+    function SEIRS(; number_E_stages::Int = 1, number_I_stages::Int = 1)
+        _validate_stage_count(:number_E_stages, number_E_stages)
+        _validate_stage_count(:number_I_stages, number_I_stages)
+        return new(number_E_stages, number_I_stages, 2 + number_E_stages + number_I_stages)
+    end
+end