SIR.jl 1.2 KB
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import StaticArrays: SVector, SMatrix, @SMatrix

d=3
k=2
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dict_var = Dict("S" => 1, "I" => 2, "R" => 3)
dict_p = Dict("ki" => 1, "kr" => 2)
l_tr = ["R1","R2"]
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p = [0.0012, 0.05]
x0 = [95, 5, 0]
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t0 = 0.0
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function SIR_f!(xnplus1::Vector{Int}, tnplus1::Vector{Float64}, tr::Vector{String}, 
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           xn::Vector{Int}, tn::Float64, p::Vector{Float64})
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    a1 = p[1] * xn[1] * xn[2]
    a2 = p[2] * xn[2]
    l_a = SVector(a1, a2)
    asum = sum(l_a)
    # column-major order
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    l_nu = @SMatrix [-1 0;
                     1 -1;
                     0 1]
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    u1, u2 = rand(), rand()
    tau = - log(u1) / asum
    b_inf = 0.0
    b_sup = a1
    reaction = 0
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    for i = 1:2 
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        if b_inf < asum*u2 < b_sup
            reaction = i
            break
        end
        b_inf += l_a[i]
        b_sup += l_a[i+1]
    end
 
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    nu = @view l_nu[:,reaction] # macro for avoiding a copy
    xnplus1[1] = xn[1]+nu[1]
    xnplus1[2] = xn[2]+nu[2]
    xnplus1[3] = xn[3]+nu[3]
    tnplus1[1] = tn + tau
    tr[1] = "R$(reaction)"
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end
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is_absorbing_SIR(p::Vector{Float64}, xn::Vector{Int}) = (p[1]*xn[1]*xn[2] + p[2]*xn[2]) === 0.0
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g = ["I"]
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SIR = CTMC(d,k,dict_var,dict_p,l_tr,p,x0,t0,SIR_f!,is_absorbing_SIR; g=g)
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export SIR
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