Merge pull request #1 from Song921012/dev

SIRbasis

Author: Song921012

Project.toml

@@ -3,6 +3,10 @@ uuid = "2bd2a319-f9c6-417c-a4f9-7b097fc62840"
 authors = ["Pengfei Song"]
 version = "0.1.0"
 
+[deps]
+DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+
 [compat]
 julia = "1.6"
 

README.md

@@ -7,3 +7,4 @@
 [![Build Status](https://ci.appveyor.com/api/projects/status/github/Song921012/MathepiaModels.jl?svg=true)](https://ci.appveyor.com/project/Song921012/MathepiaModels-jl)
 [![Coverage](https://codecov.io/gh/Song921012/MathepiaModels.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/Song921012/MathepiaModels.jl)
 [![Coverage](https://coveralls.io/repos/github/Song921012/MathepiaModels.jl/badge.svg?branch=main)](https://coveralls.io/github/Song921012/MathepiaModels.jl?branch=main)
+[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)

src/MathepiaModels.jl

@@ -1,5 +1,9 @@
 module MathepiaModels
+using DifferentialEquations
+using Plots
 
-# Write your package code here.
+include("Models/odecompartmentsmodel.jl")
+
+export SIRbasic
 
 end

src/Models/odecompartmentsmodel.jl

@@ -0,0 +1,23 @@
+@doc raw"""
+    SIR(du,u,p,t)
+
+Define classic SIR(suspected-infected-recovered) model. 
+
+Parameters: (birth rate, natural death rate, disaese induced death rate, population, infection rate, recovery rate)
+
+``$$
+\begin{aligned}
+& \frac{\rm{d}S}{\rm{dt}} = \Lambda -\beta S I/N - d S,\\
+&\frac{\rm{d}I}{\rm{dt}} = \beta  S I/N - \gamma I - d I - \alpha I,\\
+&\frac{\rm{d}R}{\rm{dt}} = \gamma I - d R,\\
+\end{aligned}
+$$``
+"""
+function SIRbasic(du, u, p,t)
+    Λ,d,α,N,β,γ = p
+    pop = (Λ>0&d>0) ? Λ/d : N
+    S, I, R = u
+    du[1] = Λ - β*S*I/pop - d*S
+    du[2] =  β*S*I/pop - γ * I - d*I -α * I
+    du[3] = γ * I - d * R
+end

src/solve.jl

@@ -0,0 +1,6 @@
+function solve end
+
+function solve(model::SIR)
+    function SIR_model(t,u,du)
+        
+end

src/type.jl

@@ -0,0 +1,7 @@
+abstract type AbstractEpiModel end
+
+mutable struct SIR <: AbstractEpiModel
+    tspan::Tuple
+    parameter:: NamedTuple
+    saveat
+end

test/runtests.jl

@@ -1,6 +1,16 @@
 using MathepiaModels
+using DifferentialEquations
+using Plots
 using Test
-
+const DE = DifferentialEquations
 @testset "MathepiaModels.jl" begin
-    # Write your tests here.
+    u_0 = [1000, 0.1, 0]
+    p_data = (Λ = 0, d = 0, α = 0, N = 1000, β = 0.2, γ = 0.1)
+    tspan_data = (0.0, 100.0)
+    prob_data = DE.ODEProblem(SIRbasic, u_0, tspan_data, p_data)
+    data_solve = DE.solve(prob_data, Tsit5(), abstol = 1e-12, reltol = 1e-12, saveat = 0.1)
+    data_withoutnois = Array(data_solve)
+    data = data_withoutnois #+ Float32(2e-1)*randn(eltype(data_withoutnois), size(data_withoutnois))
+    Plots.scatter(data_solve.t, data[1, :], label = "Train S")
+    Plots.scatter!(data_solve.t, data[2, :], label = "Train I")
 end