R_eff_poisson: Obtain an effective R when conditionning on extinction and...

In reconhub/branchr: R Estimation from Cluster Sizes

Description

For any Rl>1, we can find an Rs<1 guaranteeing that conditional on extinction, outbreak properties starting from Rs or Rl are exactly the same. We call this Rs an effective R. The funtion compute the effetive R as well as alpha (see alpha_poisson) and the probability of extinction (see proba_ext)

Usage

R_eff_poisson(R)

Arguments

R	is the reproduction number, i.e. the average number of secondary cases due to a single case. This can be any positive number. if R is a vector, then the length of R must be 'n' (see below).

Value

The function returns a list including:

• R_eff: the effective reproduction number. Note that if R<1, then R_eff=R.

• alpha given the reproduction number and assuming a Poisson offspring distribution. Note that if R<1, then alpha=0.

• proba_ext: the probability of extinction given alpha. Note that if R<1, then proba_ext=1.

#'

Author(s)

Pierre Nouvellet ([e-mail])

Examples

x <- R_eff_poisson(.5)
x
x <- R_eff_poisson(1.5)
x

reconhub/branchr documentation built on May 27, 2019, 4:01 a.m.