fastbeta: The 'fastbeta' package

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The fastbeta package


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

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 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:

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

S′ = ν(t)Ñ0β(t)SIμ(t)S
I′ = β(t)SIγIμ(t)I
R′ = γIμ(t)R

They are fully described in the referenced manuscript.


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.