Infectious disease outbreak quantification using a branching process model with negative binomial offspring distribution

This package provides functions that quantify infectious disease outbreaks using a branching process, a stochastic process in which each individual in generation n produces a random number of individuals in generation n+1, continuing for some number of generations or until there are no individuals remaining.

The random number of next-generation individuals produced by each individual is drawn from the offspring distribution, a discrete probability distribution with non-negative range. To model infectious disease outbreaks, it is common to use a negative binomial offspring distribution, parameterized by the mean R and dispersion parameter k. This parameterization is equivalent to using mu = R and size = k in R’s “NegBinomial”, e.g. dnbinom(x, mu=R, size=k) would give the density, i.e. the probability of exactly x transmissions from one individual.

The functions in the package can be used to quantify the risk posed by individual importers of a novel transmissible pathogen to a generic population, including intervention effects. They can also be used for transmission parameter estimation, e.g. via maximum likelihood, for observed outbreak clusters, such as the basic reproduction number, a dispersion parameter quantifying variance in transmission, and a post-control reproduction number.

Many functions in the package were used in the following publications.

• Toth D, Gundlapalli A, Khader K, Pettey W, Rubin M, Adler F, Samore M (2015). Estimates of outbreak risk from new introductions of Ebola with immediate and delayed transmission control. Emerg Infect Dis, 21(8), 1402-1408. https://doi.org/10.3201/eid2108.150170.

• Toth D, Tanner W, Khader K, Gundlapalli A (2016). Estimates of the risk of large or long-lasting outbreaks of Middle East respiratory syndrome after importations outside the Arabian Peninsula. Epidemics, 16, 27-32. https://doi.org/10.1016/j.epidem.2016.04.002

Installing the package

To install the package, you can use the following code:

devtools::install_github("EpiForeSITE/branching_process")

To cite the package in publications

To cite the package in publications, please use:

## To cite package 'branchingprocess' in publications use:
## 
##   Toth D (????). _Branching Process Outbreak Simulator_. R package
##   version 0.0-9, <https://epiforesite.github.io/branching_process/>.
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     heather = {To cite branchingprocess in publications use:},
##     title = {Branching Process Outbreak Simulator},
##     author = {Damon Toth},
##     note = {R package version 0.0-9},
##     url = {https://epiforesite.github.io/branching_process/},
##   }