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README.md

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-## Branching process outbreak simulator
-
-Quantifies risk posed by individual importers of a novel transmissible
-pathogen to a generic population, with intervention effects.
-Scenarios(s) Modeled: Novel introduction of transmissible pathogen by
-infected traveler, by accidentally infected laboratory worker, or
-similar scenario; intervention scenarios for improved detection of
-initial case and for delayed mitigation after ongoing outbreak is
-detected.
+## 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