Merge pull request #104 from AlgebraicJulia/docs-on-readme

Update examples to use Literate

README.md

@@ -1,8 +1,9 @@
 # AlgebraicStockFlow
+
+[![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://algebraicjulia.github.io/StockFlow.jl/dev/)
 [![Tests](https://github.com/AlgebraicJulia/StockFlow.jl/actions/workflows/tests.yml/badge.svg)](https://github.com/AlgebraicJulia/StockFlow.jl/actions/workflows/tests.yml)
 <!-- TODO: Set up on codecov.io for repo [![codecov](https://codecov.io/github/AlgebraicJulia/StockFlow.jl/branch/maaster/graph/badge.svg)](https://app.codecov.io/github/AlgebraicJulia/StockFlow.jl) -->
 
-
 StockFlow.jl is a Julia library for the creation and execution of [stock and flow modeling diagrams](https://en.wikipedia.org/wiki/System_dynamics#Stock_and_flow_diagrams), designed with model composition and stratification in mind through a [categorical approach](https://arxiv.org/abs/2211.01290).
 
 Stock-flow diagrams are used to represent systems where its population can move between different states, such as tracking how many people have been infected or recovered from a disease.  By providing initial values, and values for the parameters, we can solve the differential equation which the stock-flow diagram represents, which gives us a graph for how the population varies over time.

docs/Project.toml

@@ -1,7 +1,12 @@
 [deps]
+AlgebraicRewriting = "725a01d3-f174-5bbd-84e1-b9417bad95d9"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+GraphViz = "f526b714-d49f-11e8-06ff-31ed36ee7ee0"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
+LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 StockFlow = "58c4a0e8-2944-4d18-9fa2-e17726aee9e5"
 TikzPictures = "37f6aa50-8035-52d0-81c2-5a1d08754b2d"

docs/literate/Covid19_composition_model_in_paper.jl

@@ -0,0 +1,111 @@
+# # COVID-19 Composition Model
+
+using StockFlow
+
+using Catlab
+using Catlab.CategoricalAlgebra
+using LabelledArrays
+using OrdinaryDiffEq
+using Plots
+
+using Catlab.Graphics
+using Catlab.Programs
+using Catlab.WiringDiagrams
+
+display_uwd(ex) = to_graphviz(ex, box_labels=:name, junction_labels=:variable, edge_attrs=Dict(:len=>"1"));
+
+# Define functions ϕ of flows in the SEIRH model
+fNewIncidence(u,p,t)=p.β*u.S*u.I/p.N
+fNewInfectious(u,p,t)=u.E*p.ri
+fNewRecovery(u,p,t)=u.I/p.tr * (1.0-p.fH )
+fWaningImmunityR(u,p,t)=u.R/p.tw
+fHICUAdmission(u,p,t) = u.I/p.tr * p.fH * p.fICU
+fHNICUAdmission(u,p,t) = u.I/p.tr * p.fH * (1.0-p.fICU)
+fOutICU(u,p,t) = u.HICU/p.tICU
+fRecoveryH(u,p,t)= u.HNICU/p.tH
+
+# StockAndFlowp(stocks,
+#               (flow=>function, upstream=>downstream) => stocks linked)
+seirh = StockAndFlowp((:S, :E, :I, :R, :HICU, :HNICU), 
+   ((:NewIncidence=>fNewIncidence, :S=>:E) => (:S, :I), 
+    (:NewInfectious=>fNewInfectious, :E=>:I) => :E,
+    (:NewRecovery=>fNewRecovery, :I=>:R) => :I, 
+    (:WaningImmunityR=>fWaningImmunityR, :R=>:S) => :R,
+    (:HICUAdmission=>fHICUAdmission, :I=>:HICU) => :I, 
+    (:HNICUAdmission=>fHNICUAdmission, :I=>:HNICU) => :I, 
+    (:OutICU=>fOutICU, :HICU=>:HNICU) => :HICU,
+    (:RecoveryH=>fRecoveryH, :HNICU=>:R) => :HNICU))
+
+# Graph(primitive stock-flow model, direction of the diagram - the default value is "LR" from left to right; 
+# users could also use "TB" from top to bottom)
+# Graph(seirh)
+
+# Define functions ϕ of flows in the Vaccine model
+fFirstdoseVaccine(u,p,t) = u.S * p.rv
+fSeconddoseVaccine(u,p,t) = u.VP * p.rv
+fWaningImmunityVP(u,p,t) = u.VP / p.tw
+fWaningImmunityVF(u,p,t) = u.VF / p.tw
+fNewIncidenceVP(u,p,t) = p.β*u.VP*u.I*(1.0-p.eP)/p.N
+fNewIncidenceVF(u,p,t) = p.β*u.VF*u.I*(1.0-p.eF)/p.N
+
+# Stock and flow diagram of Vaccine model
+v = StockAndFlowp((:S, :E, :I, :VP, :VF), 
+   ((:FirstdoseVaccine=>fFirstdoseVaccine, :S=>:VP) => :S, 
+    (:SeconddoseVaccine=>fSeconddoseVaccine, :VP=>:VF) => :VP, 
+    (:WaningImmunityVP=>fWaningImmunityVP, :VP=>:S) => :VP,
+    (:WaningImmunityVF=>fWaningImmunityVF, :VF=>:VP) => :VF,
+    (:NewIncidenceVP=>fNewIncidenceVP, :VP=>:E) => (:VP, :I),
+    (:NewIncidenceVF=>fNewIncidenceVF, :VF=>:E) => (:VF, :I)))
+
+# Graph(v,"TB")
+
+# Define functions ϕ of flows in the Persist Asymptomaticity model
+fNewPersistentAsymptomaticity(u,p,t) = u.E * p.ria
+fNewRecoveryIA(u,p,t) = u.IA / p.tr
+
+# Stock and flow diagram of Persistent Asymptomaticity Model
+ia = StockAndFlowp((:E, :IA, :R), 
+   ((:NewPersistentAsymptomaticity=>fNewPersistentAsymptomaticity, :E=>:IA) => :E, 
+    (:NewRecoveryIA=>fNewRecoveryIA, :IA=>:R) => :IA))
+
+# Graph(ia)
+
+covid = @relation (S, E, I, R) begin
+    modelA(S,E,I,R)
+    modelB(S,E,I)
+    modelC(E,R)
+end;
+display_uwd(covid)
+
+# Open three Stock and Flow Diagrams
+openseirh = Open(seirh, [:S], [:E], [:I], [:R])
+openv = Open(v, [:S], [:E], [:I])
+openia = Open(ia, [:E], [:R])
+# Compose those three models according the UWD-algebra
+openCOVID19 = oapply(covid, [openseirh, openv, openia])
+# Generate the composed model (Stock and Flow Diagram)
+COVID19 = apex(openCOVID19)
+
+# Graph(COVID19)
+
+# Define constant parameters
+p_COVID19 = LVector(
+    β=0.8, N=38010001.0, tr=12.22, tw=2*365.0,
+    fH=0.002, fICU=0.23, tICU=6.0, tH = 12.0,
+    rv=0.01, eP=0.6, eF=0.85, ri=0.207, ria=0.138  
+)
+# Define initial values for stocks
+u0_COVID19 = LVector(
+    S=38010000.0, E=0.0, I=1.0, IA=0.0, R=0.0, HICU=0.0, HNICU=0.0, VP=0.0, VF=0.0
+)
+
+# Check the dependencies of links of all flows' functions
+# checkfls(COVID19, u0_COVID19, p_COVID19)
+
+# Solve the ODEs
+prob_COVID19 = ODEProblem(vectorfield(COVID19),u0_COVID19,(0.0,300.0),p_COVID19);
+sol_COVID19 = solve(prob_COVID19,Tsit5(),abstol=1e-8);
+plot(sol_COVID19)
+
+# Flow of ```FirstdoseVaccine```
+ϕFirstdoseVaccine = map(x->fFirstdoseVaccine(sol_COVID19.u[x],p_COVID19,sol_COVID19.t[x]),collect(1:length(sol_COVID19.t)))

docs/literate/full_fledged_schema_examples_new/CasualLoopDiagrams/convert_from_SEIR_stockFlowDiagram.jl

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+# # Convert from SEIR Stock Flow Diagram
+
+using GraphViz
+
+using StockFlow
+using StockFlow.Syntax
+
+seir = @stock_and_flow begin
+    :stocks
+    S
+    E
+    I
+    R
+
+    :parameters
+    μ
+    β
+    tlatent
+    trecovery
+    δ
+
+    :dynamic_variables
+    v_birth = μ * N
+    v_incid₁ = I / N
+    v_incid₂ = S * v_incid₁
+    v_incid₃ = β *  v_incid₂
+    v_inf = E / tlatent
+    v_rec = I / trecovery
+    v_deathS = S * δ
+    v_deathE = E * δ 
+    v_deathI = I * δ
+    v_deathR = R * δ
+
+    :flows
+    CLOUD => f_birth(v_birth) => S
+    S => f_incid(v_incid₃) => E
+    S => v_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]
+
+end
+
+GraphF(seir)
+
+seir_causalLoop = convertToCausalLoop(seir)
+
+Graph(seir_causalLoop)
+
+