Understand Individual-Level Variation in Infectious Disease Transmission
Calculate the reproduction number () for a (heterogeneous) network
Constants used in superspreading
Simulate transmission chains using a stochastic branching process
Optimise a function using either numerical optimisation or grid search
Density of the Poisson-lognormal compound distribution
Density of the Poisson-Weibull compound distribution
Defines the gamma functions in terms of the mean reproductive number (...
Helper function to create a model comparison table
Generates a log scaled sequence of real numbers
Cumulative distribution function of the Poisson-lognormal compound dis...
Cumulative distribution function of the Poisson-Weibull compound distr...
Probability that an outbreak will be contained
Calculate the probability a disease will emerge and cause a sustained ...
Calculate the probability a disease will cause an outbreak based on R,...
Calculate the probability a branching process will go extinct based on...
Estimate what proportion of new cases originated within a transmission...
Estimate what proportion of cases cause a certain proportion of transm...
superspreading: Understand Individual-Level Variation in Infectious Di...
Estimate and understand individual-level variation in transmission. Implements density and cumulative compound Poisson discrete distribution functions (Kremer et al. (2021) <doi:10.1038/s41598-021-93578-x>), as well as functions to calculate infectious disease outbreak statistics given epidemiological parameters on individual-level transmission; including the probability of an outbreak becoming an epidemic/extinct (Kucharski et al. (2020) <doi:10.1016/S1473-3099(20)30144-4>), or the cluster size statistics, e.g. what proportion of cases cause X\% of transmission (Lloyd-Smith et al. (2005) <doi:10.1038/nature04153>).
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