Calculate Outbreak Probabilities for a Branching Process Model

The goal of branchingprocess is to quantify outbreak risk posed by individual importers of a transmissible pathogen. Input parameters of negative binomial offspring distributions for the number of transmissions from each infected individual and initial number of infected. Calculate probabilities of final outbreak size and generations of transmission. A full description and derivation of the mathematical results implemented in these functions can be found in the following manuscripts:

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

Work to create this software tool was made possible by cooperative agreement CDC-RFA-FT-23-0069 from the CDC’s Center for Forecasting and Outbreak Analytics.

Installation

You can install the development version of branchingprocess from GitHub with:

devtools::install_github("EpiForeSITE/branchingprocess")

You can install branchingprocess from CRAN with:

install.packages("branchingprocess")