epigrowthfit
Maximum likelihood estimation of nonlinear mixed effects models ofepidemic growth using Template Model Builder ('TMB'). Enablesjoint estimation for collections of disease incidence time series,including time series that describe multiple epidemic waves.Supports a set of widely used phenomenological models: exponential,logistic, Richards (generalized logistic), subexponential,and Gompertz. Provides methods for interrogating model objectsand several auxiliary functions, including one for computing basicreproduction numbers from fitted values of the initial exponentialgrowth rate.Preliminary versions of this software were appliedin Ma et al. (2014) <doi:10.1007/s11538-013-9918-2> andin Earn et al. (2020) <doi:10.1073/pnas.2004904117>.
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