All functions
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AR2PR()
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Calculate the prevalence rate and treatment rate for a given attack-rate,
model, and set of model parameters |
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AR2PRopt()
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Helper function for finding the maximum prevelance for a given model and set
of paramaters |
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PR2AR()
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Master function for converting prevalence rates into attack-rates |
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PR2AReq()
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Finds the equilibrium attack-rates for an input vector of prevalences,
conditional on the chosen model and parameters |
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aggAR()
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Aggregates attack-rates from time step to annual |
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findAXmax()
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Finds the maximum prevalence and associated attack-rate for a given model and
set of parameters |
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findYeq()
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Calculates the equilibrium Y for a given attack-rate and model |
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fn()
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Helper objective function for finding the optimal attack-rate for a given
prevalence rate |
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fn2()
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Helper objective function for finding a pair of optimal attack-rates for a
given pair of starting prevalence rates when the model has an exposure class |
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interpRates()
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Interpolate a vector of rates to match the model time step |
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makeB()
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A function for making the matrix representation of the simple SIS model |
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makeBage()
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A function for making the matrix representation of the age of infection (AoI)
with overwriting superinfection |
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makeBdrugs()
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A function for making the matrix representation of the simple model with
drugs added |
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makeBdrugs_age()
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A function for making the matrix representation of the age of infection (AoI)
with overwriting superinfection and drugs |
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makeD()
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Generic function for making the D matrix that maps the state vector, Y, to
prevalence |
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makeV()
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Generic function for making the W matrix associated an input B function and
set of parameters |
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makeW()
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Generic function for making the W matrix associated an input B function and
set of parameters |
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optimA()
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A function for finding the optimal attack-rate for a given prevalence rate |
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plotAR2PR()
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Make plots showing the relationship between AR and PR for a number of different Tx levels |
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simAR()
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Generic forward simulation function that can accomdate models with and
without exposure classes |