parameters.jl

@enum HEALTH SUSC = 1 LAT = 2 SYMP = 3 ASYMP = 4 REC = 5 UNDEF = 0


@with_kw type InfluenzaParameters @deftype Int64

    sim_time = 150
    grid_size_human = 1000
    initial_infected = 1
    

    ProbAsympMin::Float64 = 0.3
    ProbAsympMax::Float64 = 0.7
    reduction_factor::Float64 = 0.5

    Latent_period_Max = 2
    Latent_period_Min = 1
    max_infectious_period = 15

    Prob_transmission::Float64 = 0.079
    log_normal_mean::Float64 = 1.0
    log_normal_shape::Float64 = 0.4356
    
    #precaution_factorS::Float64 = 0.8
    #precaution_factorV::Float64 = 0.2

    #NumberOfContactsMin = 3
    #NumberOfContactsMax = 12

    GeneralCoverage::Int64 = 1
    VaccineEfficacy::Float64 = 0.2
    
    mutation_rate::Float64 = 0.00416
    matrix_strain_lines = 30
    number_of_states = 20
    sequence_size = 566
    initial_p0::Float64 = 0.0
    initial_p::Float64 = 0.0
    initial_p2::Float64 = 0.0
    initial_p3::Float64 = 0.0
    start_different = 0
end


## age distribution discrete for humans
function distribution_age()  
   
    ProbBirthAge = Vector{Float64}(17)
    SumProbBirthAge = Vector{Float64}(17)
    AgeMin = Vector{Int64}(17)
    AgeMax = Vector{Int64}(17)


    ProbBirthAge[1] = 0.0532142275
    ProbBirthAge[2] = 0.0545793774
    ProbBirthAge[3] = 0.0523384586
    ProbBirthAge[4] = 0.0560316901
    ProbBirthAge[5] = 0.0674724602
    ProbBirthAge[6] = 0.0701439068
    ProbBirthAge[7] = 0.0695785615
    ProbBirthAge[8] = 0.0682851526
    ProbBirthAge[9] = 0.064437731
    ProbBirthAge[10] = 0.0655332187
    ProbBirthAge[11] = 0.0719434263
    ProbBirthAge[12] = 0.0731115814
    ProbBirthAge[13] = 0.064701399
    ProbBirthAge[14] = 0.0544144521
    ProbBirthAge[15] = 0.0421691092
    ProbBirthAge[16] = 0.0293566227
    ProbBirthAge[17] = 0.0426886252


    SumProbBirthAge = cumsum(ProbBirthAge)
 
    AgeMin[1] = 0;
    AgeMax[1] = 4;

    AgeMin[2] = 5;
    AgeMax[2] = 9;

    AgeMin[3] = 10;
    AgeMax[3] = 14;

    AgeMin[4] = 15;
    AgeMax[4] = 19;

    AgeMin[5] = 20;
    AgeMax[5] = 24;

    AgeMin[6] = 25;
    AgeMax[6] = 29;

    AgeMin[7] = 30;
    AgeMax[7] = 34;

    AgeMin[8] = 35;
    AgeMax[8] = 39;

    AgeMin[9] = 40;
    AgeMax[9] = 44;

    AgeMin[10] = 45;
    AgeMax[10] = 49;

    AgeMin[11] = 50;
    AgeMax[11] = 54;

    AgeMin[12] = 55;
    AgeMax[12] = 59;

    AgeMin[13] = 60;
    AgeMax[13] = 64;

    AgeMin[14] = 65;
    AgeMax[14] = 69;

    AgeMin[15] = 70;
    AgeMax[15] = 74;

    AgeMin[16] = 75;
    AgeMax[16] = 79;

    AgeMin[17] = 80;
    AgeMax[17] = 100;

    return SumProbBirthAge,AgeMin,AgeMax
end

function ReductionPerGroup()
    Reduction = Vector{Float64}(15)

    Reduction[1] = 0.5883212623051612
    Reduction[2] =  0.6057753194036136
    Reduction[3] =  0.6223362260154172
    Reduction[4] =  0.6433283687160004
    Reduction[5] =  0.6619723535662496
    Reduction[6] =  0.6789357497894256
    Reduction[7] =  0.6966433712730415
    Reduction[8] =  0.6646629167123203
    Reduction[9] =  0.6142525576610639
    Reduction[10] =  0.5625963990585514
    Reduction[11] =  0.5116166856783396
    Reduction[12] =  0.46292829585154177
    Reduction[13] =  0.41219197569675525
    Reduction[14] =  0.35636586929717184
    Reduction[15] =  0.2335717105984882

    Reduction = Reduction/0.8

    return Reduction
end