fastbeta: The 'fastbeta' package

In davidearn/fastbeta: Fast Estimation of Time-Varying Transmission Rates

Description

The fastbeta package

Details

fastbeta implements the FC, S, and SI methods for estimating time-varying transmission rates β(t) from time series data:

• estimate_beta_FC()

• estimate_beta_S()

• estimate_beta_SI()

The SI method is substantially more accurate and robust than the FC and S methods, and should be preferred in practice.

fastbeta additionally implements peak-to-peak iteration (PTPI), a method for estimating the initial number of susceptibles S₀ from time series data:

• ptpi()

• get_peak_times()

PTPI can be used in conjunction with the FC, S, and SI methods, which require users to specify an estimate of S₀.

fastbeta includes functions useful for simulating incidence time series with an underlying, seasonally forced transmission rate. These may be useful in testing:

• make_par_list()

• make_data()

• compute_rrmse()

All methods are based on the SIR model with time-varying rates of birth, death, and transmission:

S′ = ν(t)Ñ₀ − β(t)SI − μ(t)S
I′ = β(t)SI − γI − μ(t)I
R′ = γI − μ(t)R

They are fully described in the referenced manuscript.

References

deJonge MS, Jagan M, Krylova O, Earn DJD. Fast estimation of time-varying transmission rates for infectious diseases.

davidearn/fastbeta documentation built on June 14, 2020, 3:11 p.m.