coefs: Caclulate model coefficients from parameters

In rplzzz/CovMitigation: COVID-19 infection model for Virginia

Description

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.

Usage

calcalpha(parms)

calcbeta_approx(parms)

calcgamma(parms)

calcbeta(parms)

calcreff(parms)

calclplus(alpha, beta, gamma)

calct0(alpha, beta, gamma)

Arguments

parms	Named vector of model parameters
alpha	SEIR alpha parameter
beta	SEIR beta parameter
gamma	SEIR gamma parameter

Details

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}

Functions

• 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

rplzzz/CovMitigation documentation built on June 7, 2021, 8:48 a.m.