Merge pull request #42 from neonWhiteout/premade_models

Premade models

src/PremadeModels.jl

@@ -0,0 +1,198 @@
+module PremadeModels
+using StockFlow.Syntax
+
+
+export seir, sis, sir, svi
+
+function seir()
+    return deepcopy(seir_model)
+end
+
+function sis()
+    return deepcopy(sis_model)
+end
+
+function sir()
+    return deepcopy(sir_model)
+end
+
+function svi()
+    return deepcopy(svi_model)
+end
+
+
+
+seir_model = @stock_and_flow begin
+
+        :stocks
+        S
+        E
+        I
+        R
+
+        :parameters
+        μ
+        β
+        tlatent
+        trecovery
+        δ
+        c 
+
+
+        :dynamic_variables
+        v_prevalence = NI / NS
+        v_meanInfectiousContactsPerS = c * v_prevalence # where c doesn't matter, can just make it 1
+        v_perSIncidenceRate = β * v_meanInfectiousContactsPerS
+        v_newIncidence = S * v_perSIncidenceRate
+
+        v_birth = μ * N
+
+        v_inf = E / tlatent
+
+        v_rec = I / trecovery 
+
+
+        v_deathS = δ * S       
+        v_deathE = δ * E
+        v_deathI = δ * I
+        v_deathR = δ * R
+
+
+        :flows
+        CLOUD => f_birth(v_birth) => S
+        S => f_incid(v_newIncidence) => E
+        S => f_deathS(v_deathS) => CLOUD
+        E => f_inf(v_inf) => I
+        E => f_deathE(v_deathE) => CLOUD
+        I => f_rec(v_rec) => R
+        I => f_deathI(v_deathI) => CLOUD
+        R => f_deathR(v_deathR) => CLOUD
+
+        :sums
+        N = [S, E, I, R]
+        NI = [I]
+        NS = [S, E, I, R]
+
+end
+
+sis_model = @stock_and_flow begin
+    :stocks
+    S
+    I
+
+
+    :parameters
+    μ
+    β
+    trec # 1 / trecovery.  This corresponds to σ.
+    δ
+    c
+
+
+    :dynamic_variables
+    v_deathsX = δ * S
+    v_births = μ * N
+
+    v_prevalence = NI / NS
+    v_meanInfectiousContactsPerS = c * v_prevalence
+    v_perSIncidenceRate = β * v_meanInfectiousContactsPerS
+    v_newIncidence = S * v_perSIncidenceRate
+
+    v_newRecovery = I * trec
+    v_deathsI = I * δ
+
+    :flows
+
+    S => f_deathsX(v_deathsX) => CLOUD
+    CLOUD => f_births(v_births) => S
+    S => f_newInfectious(v_newIncidence) => I
+    I => f_newRecovery(v_newRecovery) => S
+
+    I => f_deathsI(v_deathsI) => CLOUD
+
+    :sums
+    N = [S, I]
+    NI = [I]
+    NS = [S, I]
+
+end
+
+
+sir_model = @stock_and_flow begin
+    :stocks
+    S
+    I
+    R
+
+    :parameters
+    c
+    β
+    rRec
+
+    :dynamic_variables
+    v_prevalence = NI / NS
+    v_meanInfectiousContactsPerS = c * v_prevalence
+    v_perSIncidenceRate = β * v_meanInfectiousContactsPerS
+    v_newInfections = S * v_perSIncidenceRate
+    v_newRecovery = I * rRec
+
+    :flows
+    S => f_inf(v_newInfections) => I
+    I => f_rec(v_newRecovery) => R
+
+    :sums
+    N = [S, I, R]
+    NI = [I]
+    NS = [S,I,R]
+
+
+end
+
+
+
+svi_model = @stock_and_flow begin
+
+    :stocks
+    S
+    V
+    I
+
+    :parameters
+    rvaccine
+    δ
+    evaccine
+    c
+    β
+
+    :dynamic_variables
+    v_vacc = S * rvaccine 
+    v_deathV = δ * V
+
+    v_prevalence = NI / NS
+    v_meanInfectiousContactsPerS = c * v_prevalence
+    v_perSIncidenceRate = β * v_meanInfectiousContactsPerS
+    v_vaccineInfectionRate = V / evaccine # same thing as multiplying by complement
+    v_perSIncidenceVaccinated = v_vaccineInfectionRate * v_perSIncidenceRate
+
+
+    :flows
+    S => f_vacc(v_vacc) => V
+    V => f_deathV(v_deathV) => CLOUD
+    V => f_infV(v_perSIncidenceVaccinated) => I 
+
+
+    :sums
+    N = [S, V, I]
+    NI = [I]
+    NS = [S, V, I]
+
+end
+
+
+
+
+
+
+
+
+end

src/StockFlow.jl

@@ -936,4 +936,7 @@ include("SystemStructure.jl")
 include("visualization.jl")
 # The implementations in this file is specific for the Primitive schema of stock and flow diagram in the ACT paper
 include("PrimitiveStockFlowInPaper.jl")
+
+include("PremadeModels.jl")
+
 end