Optimiziation routine for incidence imputation
When first records of incidence are unavailable, tries to impute censored cases to rebuild longer epidemic vector
impute.incid(CD.optim.vect, CD.epid, CD.R0, CD.GT)
Vector of two elements (multiplicative factor, log(highest imputed data) to be optimized
Original epidemic vector, output of check.incid()
Assumed R0 value for the original epidemic vector
Generation time distribution to be used for computations
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.
A vector with both imputed incidence and source available data.
Pierre-Yves Boelle, Thomas Obadia
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