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utils.jl
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function Dict_initializer(parameter_names::Union{Nothing,Vector{Symbol}})
isnothing(parameter_names) ? nothing : Dict(parameter_names .=> missing)
end
function vec_to_dict(v::AbstractArray, ll::AbstractVector)::AbstractDict
d = Dict()
for i in eachindex(ll)
d[ll[i]] = v[i]
end
return d
end
function logit(p)
log.( p ./ (1 .- p) )
end
function inverse_logit(x)
exp.(x) ./ (1 .+ exp.(x))
end
function set_up(max_age=111,province="BC",starting_year=2001,time_horizon=19,n=100,population_growth_type="LG")
if province=="BC" || province=="CA"
agent = Agent(false,0,starting_year,1,true,0,false,0,0,nothing,[0,0],[zeros(4),zeros(4)],0,false,false)
birth = Birth(nothing,nothing)
@set! birth.estimate = filter([:year, :province, :projection_scenario] => (x, y, z) -> x >= starting_year && y == province && (z == population_growth_type || z == "past"), master_birth_estimate)
relative(x) = x/birth.estimate.N[1]
@set! birth.estimate = transform(birth.estimate,:N => relative)
@set! birth.initial_population = filter([:year, :province, :projection_scenario] => (x, y, z) -> x == starting_year && y == province && (z == population_growth_type || z == "past"), master_population_initial_distribution)
death = Death(Dict_initializer([:β0,:β1,:β2]),nothing)
@set! death.parameters[:β0] =0;
@set! death.parameters[:β1] =0;
@set! death.parameters[:β2] =0;
@set! death.life_table = groupby(select(unstack(
select(
select(
filter([:year, :province] => (x, y) -> x >= starting_year && y == province, master_life_table),
Not(:se)),
Not(:province)),
:sex,:prob_death),:F,:M,:year),:year)
emigration = Emigration(nothing, nothing,nothing)
@set! emigration.table = groupby(select(
select(
filter([:year, :province, :proj_scenario] => (x, y,z) -> x > starting_year && y == province && z==population_growth_type, master_emigration_table),
Not(:province)),
Not(:proj_scenario)),:year)
immigration = Immigration(nothing, nothing, nothing,nothing,nothing)
@set! immigration.table = groupby(select(
select(
filter([:year, :province, :proj_scenario] => (x, y,z) -> x > starting_year && y == province && z==population_growth_type, master_immigration_table),
Not(:province)),
Not(:proj_scenario)),:year)
incidence = Incidence(Dict_initializer([:β0_μ,:β0_σ]),
Dict_initializer([:β0,:βsex,:βyear,:βage,:βsexyear,:βsexage,:βfam_hist,:βabx_exp,:βcorrection]),
Dict_initializer([:β0,:βsex,:βyear,:βage,:βsexyear,:βsexage,:βyearage,:βsexyearage,:βfam_hist,:βabx_exp,:βcorrection]),
nothing,nothing,nothing)
@set! incidence.hyperparameters[:β0_μ] = 0;
@set! incidence.hyperparameters[:β0_σ] = 0.00000001;
@set! incidence.parameters[:β0] = 34.63398846;
@set! incidence.parameters[:βsex] = -9.52017810;
@set! incidence.parameters[:βyear] = -0.01967344;
@set! incidence.parameters[:βage] = [-6.64423331,7.73720625,-5.63121394,3.90920803,-1.39497027];
@set! incidence.parameters[:βsexyear] = 0.00461397;
@set! incidence.parameters[:βsexage] = [-4.45607619,4.70483885,-2.61760564,0.79555703,0.95476291];
@set! incidence.parameters[:βfam_hist] = [log(1.13),0.3619942]
@set! incidence.parameters[:βabx_exp] = [1.711+0.115, -0.2920745,0.053];
@set! incidence.parameters[:βcorrection] = groupby(select(filter([:type] => (x) -> x == "inc" ,master_occurrence_correction),Not([:type])),[:year,:sex,:age]);
@set! incidence.parameters_prev[:β0] = -2.28093577;
@set! incidence.parameters_prev[:βsex] = -0.10755806;
@set! incidence.parameters_prev[:βyear] = [2.83586405,-1.18097542];
@set! incidence.parameters_prev[:βage] = [1.79932480805632, -2.17989374225804, 3.64152189395539, -2.91796538427475, 1.43423653685647];
@set! incidence.parameters_prev[:βsexyear] = [1.29279956487906, 0.036861276364171];
@set! incidence.parameters_prev[:βsexage] = [-7.69209530818354, 2.68306716462003, 0.865308192929771, -0.656000992252807, -0.0270826201453694];
@set! incidence.parameters_prev[:βyearage] = [50.610032709273, 6.51236955045884, -39.4569160874519, 3.69176099747937, 15.9637932343298, -4.79271775804693, -7.14281869955998, 4.18656498490802, -4.88274672641455, -3.3603262281752];
@set! incidence.parameters_prev[:βsexyearage] = [-3.19896302105009, 7.24422362459046, -25.7979736592919, 0.253623898303176, 11.3848773603672, -2.57625491419054, 7.61284030050534, 4.17111534541718, -15.2128066205219, 3.70514542334455];
@set! incidence.parameters_prev[:βfam_hist] = [log(1.13),(log(1.13)+log(2.4))/2-log(1.13)];
@set! incidence.parameters_prev[:βabx_exp] = [1.711+0.115,-0.225,0.053];
@set! incidence.parameters_prev[:βcorrection] = groupby(select(filter([:type] => (x) -> x == "prev" ,master_occurrence_correction),Not([:type])),[:year,:sex,:age]);
@set! incidence.min_year = collect(keys(incidence.parameters[:βcorrection])[1])[1]+1
@set! incidence.max_year = collect(keys(incidence.parameters[:βcorrection])[length(incidence.parameters[:βcorrection])])[1] - 1
@set! incidence.max_age = 63
reassessment = Reassessment(nothing)
@set! reassessment.table = groupby(filter([:year, :province] => (x, y) -> x >= starting_year && y == province, master_reassessment),:year)
control = Control(Dict_initializer([:β0_μ,:β0_σ]), Dict_initializer( [:β0,:βage,:βsex,:βsexage,:βsexage2,:βage2, :βDx2,:βDx3,:θ]))
@set! control.hyperparameters[:β0_μ] = 0;
@set! control.hyperparameters[:β0_σ] = 1.678728;
@set! control.parameters[:βage] = 3.5430381;
@set! control.parameters[:βage2] =-3.4980710;
@set! control.parameters[:βsexage] = -0.8161495;
@set! control.parameters[:βsexage2] = -1.1654264;
@set! control.parameters[:βsex] = 0.2347807;
@set! control.parameters[:θ] = [-0.3950; 2.754];
exacerbation = Exacerbation(Dict_initializer([:β0_μ,:β0_σ]),
Dict_initializer([:β0,:βage,:βsex,:βasthmaDx,:βprev_exac1,:βprev_exac2,:βcontrol_C,:βcontrol_PC,:βcontrol_UC,:calibration,:min_year]),
0)
@set! exacerbation.initial_rate = 0.347;
@set! exacerbation.hyperparameters[:β0_μ] = 0;
@set! exacerbation.hyperparameters[:β0_σ] = 0.0000001;
@set! exacerbation.parameters[:β0_calibration] = 0.0; # 0.056
@set! exacerbation.parameters[:βage] = 0;
@set! exacerbation.parameters[:βsex] = 0;
@set! exacerbation.parameters[:βasthmaDx] = 0;
@set! exacerbation.parameters[:βprev_exac1] = 0;
@set! exacerbation.parameters[:βprev_exac2] = 0;
@set! exacerbation.parameters[:βcontrol_C] = log(0.1880058);
@set! exacerbation.parameters[:βcontrol_PC] = log(0.3760116);
@set! exacerbation.parameters[:βcontrol_UC] = log(0.5640174);
@set! exacerbation.parameters[:βcontrol] = 0;
@set! exacerbation.parameters[:calibration] = groupby(select(filter([:province] => (x) -> x == province ,exacerbation_calibration),Not([:province])),[:year,:sex]);
@set! exacerbation.parameters[:min_year] = collect(keys(exacerbation.parameters[:calibration])[1])[1]+1
exacerbation_severity = Exacerbation_Severity(Dict_initializer([:p0_μ,:p0_σ]), Dict_initializer([:p,:βprev_hosp_ped,:βprev_hosp_adult]))
@set! exacerbation_severity.hyperparameters[:p0_μ] = [0.495, 0.195, 0.283, 0.026];
@set! exacerbation_severity.hyperparameters[:p0_σ] = 100;
@set! exacerbation_severity.parameters[:p] = ones(4)/4;
@set! exacerbation_severity.parameters[:βprev_hosp_ped] = 1.79
@set! exacerbation_severity.parameters[:βprev_hosp_adult] = 2.88
antibioticExposure = AntibioticExposure(Dict_initializer([:β0_μ,:β0_σ]),Dict_initializer([:θ,:β0,:βage,:βsex,:βcal_year,:β2005,:β2005_cal_year,:fix2000,:βfloor,:midtrends]),nothing)
@set! antibioticExposure.parameters[:θ] = 727.383;
@set! antibioticExposure.parameters[:β0] = 110.000442;
@set! antibioticExposure.parameters[:βage] = 0.0;
@set! antibioticExposure.parameters[:βsex] = 0.249033;
@set! antibioticExposure.parameters[:βcal_year] = -0.055100;
@set! antibioticExposure.parameters[:β2005] = 55.033675;
@set! antibioticExposure.parameters[:β2005_cal_year] = -0.027437;
@set! antibioticExposure.parameters[:fixyear] = nothing;
@set! antibioticExposure.parameters[:βfloor] = 50/1000;
@set! antibioticExposure.parameters[:midtrends] = abx_mid_trends;
familyHistory = FamilyHistory(nothing,Dict_initializer([:p]))
@set! familyHistory.parameters[:p] = 0.2927242;
util = Utility(Dict_initializer([:eq5d,:control,:exac]))
@set! util.parameters[:eq5d] = eq5d
# disutil
@set! util.parameters[:control] = [0.06,0.09,0.10]
# disutil: duration 1 week for mild and two weeks for the rest
@set! util.parameters[:exac] = [0.32 * 1, 0.44 * 2 , 0.50 * 2 , 0.56 * 2 ] / 52
cost = Cost(Dict_initializer([:control,:exac]))
# 1.66 is the exchange rate btw 2018 USD and 2023 CAD Sept
@set! cost.parameters[:control] = [2372, 2965, 3127]*1.66;
@set! cost.parameters[:exac] = [130,594, 2425,9900]*1.66;
sim = Simulation(max_age,province,starting_year,time_horizon,n,population_growth_type,
agent,
birth,
emigration,
immigration,
death,
incidence,
reassessment,
control,
exacerbation,
exacerbation_severity,
antibioticExposure,
familyHistory,
util,
cost,
nothing,
(;))
return sim
else
error("Province not supported")
end
end