From a7b5d768836c4ed2b52dd1404e90fd73892d8c36 Mon Sep 17 00:00:00 2001
From: Moein Khalighi <56591583+moeinkh88@users.noreply.github.com>
Date: Fri, 16 Dec 2022 10:13:21 +0200
Subject: [PATCH] Delete SEIPAHRF_Wuhan.jl

---
 .../SEIPAHRF_Wuhan.jl                         | 113 ------------------
 1 file changed, 113 deletions(-)
 delete mode 100644 examples/Applications/Epidemiological analysis of Covid-19 transmission dynamics/SEIPAHRF_Wuhan.jl

diff --git a/examples/Applications/Epidemiological analysis of Covid-19 transmission dynamics/SEIPAHRF_Wuhan.jl b/examples/Applications/Epidemiological analysis of Covid-19 transmission dynamics/SEIPAHRF_Wuhan.jl
deleted file mode 100644
index 6e4c989..0000000
--- a/examples/Applications/Epidemiological analysis of Covid-19 transmission dynamics/SEIPAHRF_Wuhan.jl	
+++ /dev/null
@@ -1,113 +0,0 @@
-# ref:
-# https://doi.org/10.1016/j.chaos.2020.109846
-# https://doi.org/10.1016/j.chaos.2021.110652
-# https://doi.org/10.3390/axioms10030135
-
-using Optim, StatsBase
-using FdeSolver
-using Plots
-using SpecialFunctions
-using CSV
-using DataFrames
-using Dates
-
-# Data of Wuhan
-C=Float64.([6, 12, 19, 25, 31, 38, 44, 60, 80, 131, 131,259, 467, 688, 776,
- 1776, 1460, 1739, 1984, 2101,2590, 2827, 3233, 3892, 3697, 3151,
- 3387, 2653, 2984, 2473, 2022,1820, 1998, 1506, 1278, 2051, 1772,
- 1891, 399, 894, 397, 650, 415,518, 412, 439, 441, 435, 579, 206,
- 130, 120, 143, 146, 102, 46, 45,20, 31, 26, 11, 18, 27, 29, 39, 39])
-D=[0, 0, 0, 0, 0, 0, 0, 0, 4, 4, 4, 8, 15, 15, 25, 26, 26, 38, 43, 46,
- 45, 57, 64, 66, 73, 73, 86, 89, 97, 108, 97, 254, 121, 121, 142, 106,
- 106, 98, 115, 118, 109, 97, 150, 71, 52, 29, 44, 37, 35, 42, 31, 38,
- 31, 30, 28, 27, 23, 17, 22, 11, 7, 14, 10, 14, 13, 13]
-## System definition
-
-# Define SIR model.
-function SIR(t, u, p)
-    # Model parameters.
-	β=2.55
-	l=1.56
-	β′=7.65
-	κ=0.25
-	ρ₁=0.58
-	ρ₂=0.001
-	γₐ=0.94
-	γᵢ=0.27
-	γᵣ=0.5
-	δᵢ=1/23
-	δₚ=1/23
-	δₕ=1/23
-
-	p=N
-
-    # Current state.
-    S, E, I, P, A, H, R, F = u
-
-# ODE
-    dS = - β * I * S/N - l * β * H * S/N - β′* P * S/N
-    dE = β * I * S/N + l * β * H * S/N + β′ *P* S/N - κ * E
-    dI = κ * ρ₁ * E - (γₐ + γᵢ )*I - δᵢ * I
-    dP = κ* ρ₂ * E - (γₐ + γᵢ)*P - δₚ * P
-    dA = κ *(1 - ρ₁ - ρ₂ )* E
-	dH = γₐ *(I + P ) - γᵣ *H - δₕ *H
-	dR = γᵢ * (I + P ) + γᵣ* H
-	dF = δᵢ * I + δₚ* P + δₕ *H
-    return [dS, dE, dI, dP, dA, dH, dR, dF]
-end
-
-#initial conditions
-N=11000000/250
-par=N
-S0=N-6; E0=0; I0=1; P0=5; A0=0; H0=0; R0=0; F0=0
-X0=[S0, E0, I0, P0, A0, H0, R0, F0]
-tspan=[1,66]
-t1, x1 = FDEsolver(SIR, tspan, X0, ones(8), par, h = .1)
-plot(t1,x1)
-
-XX=sum(x1[1:10:end,[3,4,6]], dims=2)
-plot(t1[1:10:end],XX)
-scatter!(C)
-
-function loss(μ)
-	if size(X0,2) != Int64(ceil(maximum(μ)))
-		indx=findall(x-> x>1, μ)
-		μ[indx]=ones(length(indx))
-	end
-	_, x = FDEsolver(SIR, tspan, X0, μ, par, h = .1)
-    appX=vec(sum(x[1:10:end,[3,4,6]], dims=2))
-    rmsd(C, appX; normalize=:true)
-    # sqrt(sum(abs2, appX .- data1))
-end
-
-p_lo=.5*ones(8)
-p_up=ones(8)
-pvec=.9*ones(8)
-Result=optimize(loss,p_lo,p_up,pvec,Fminbox(LBFGS()),
-# Result=optimize(loss,p_lo,p_up,pvec,SAMIN(rt=.99),
-			Optim.Options(outer_iterations = 10,
-						  iterations=10000,
-						  show_trace=true,
-						  show_every=1))
-pp=vcat(Optim.minimizer(Result))
-pp[3]=1;pp[7]=1
-tf, xf = FDEsolver(SIR, tspan, X0, pp, par, h = .1)
-
-Xf=sum(xf[1:10:end,[3,4,6]], dims=2)
-plot(t1[1:10:end],Xf)
-plot!(t1[1:10:end],XX)
-scatter!(C)
-
-Err1=rmsd(C, vec(XX); normalize=:true)
-Errf=rmsd(C, vec(Xf); normalize=:true)
-#
-# julia> pp
-# 8-element Vector{Float64}:
-#  0.9590130843157745
-#  0.9103147682079581
-#  0.9999999977774652
-#  0.5000000007931332
-#  0.7499999564104551
-#  0.999999995960407
-#  0.7499999564104551
-#  0.7499999564104551