Description Usage Arguments Details Functions
We parameterize the model SEIR in terms of initial doubling time, incubation period, and recovery time. The model equations are given in terms of rates, α, β, and γ. Also of interest is the basic reproduction parameter R_0.
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parms |
Named vector of model parameters |
alpha |
SEIR alpha parameter |
beta |
SEIR beta parameter |
gamma |
SEIR gamma parameter |
Recovery rate and progression rate are just the reciprocals of their respective periods:
α = 1/A_0
γ = 1/D_0
Beta is calculated from α, γ, and t_d as
β = γ + \ln 2 \frac{(α+γ)}{α t_d}
R_0 is calculated from β and γ. Note that in the absence of mortality during the exposed period, R_0 is independent of α.
R_0 = \frac{β}{γ}
calcalpha
: Calculate progression rate α from model parameters
calcbeta_approx
: Calculate transmissibility β from model parameters.
This is the approximate version, using the Taylor series expansion.
calcgamma
: Calculate recovery rate γ from model parameters.
calcbeta
: Calculate beta, given model input parameters
This is the exact version, solving the nonlinear equation for beta.
calcreff
: Calculate effective reproduction number R_e from model parameters.
calclplus
: Calculate the growth rate (lplus) given alpha, beta, gamma coefficients
calct0
: Calculate the doubling time (t0), given alpha, beta, gamma coefficients
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