Description Details References
The fastbeta package
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 S_{0} 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 S_{0}.
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)Ñ_{0} − β(t)SI − μ(t)SThey 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.
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