impute.incid: Optimiziation routine for incidence imputation

In tobadia/R0: Estimation of R0 and Real-Time Reproduction Number from Epidemics

Optimiziation routine for incidence imputation

Description

When first records of incidence are unavailable, tries to impute censored cases to rebuild a longer epidemic vector.

Usage

impute.incid(CD.optim.vect, CD.epid, CD.R0, CD.GT)

Arguments

CD.optim.vect	Vector of two elements (⁠c(multiplicative factor, log(highest imputed data))⁠) to be optimized.
CD.epid	Original epidemic vector, output of check.incid().
CD.R0	Assumed R0 value for the original epidemic vector.
CD.GT	Generation time distribution to be used for computations.

Details

This function is not intended for stand-alone use. It optimizes the values of vect, based upon minimization of deviation between actual epidemics data and observed generation time. The optimized function is censored.deviation(), which returns the deviation used for minimization. Stand-alone use can be conducted, however this assumes data are all of the correct format.

Value

A vector with both imputed incidence and source available data.

Author(s)

Pierre-Yves Boelle, Thomas Obadia

tobadia/R0 documentation built on Sept. 24, 2023, 5:16 p.m.