Package index • superspreading

Offspring distributions

Poisson-lognormal

PDF and CDF functions for the Poisson-lognormal compound distribution

dpoislnorm(): Density of the Poisson-lognormal compound distribution

ppoislnorm(): Cumulative distribution function of the Poisson-lognormal compound distribution

Poisson-Weibull

PDF and CDF functions for the Poisson-Weibull compound distribution

dpoisweibull(): Density of the Poisson-Weibull compound distribution

ppoisweibull(): Cumulative distribution function of the Poisson-Weibull compound distribution

Probability of epidemic, extinction, containment or emergence

Probability of a disease causing an epidemic, going extinct, being contained, or emerging

probability_contain(): Probability that an outbreak will be contained

probability_emergence(): Calculate the probability a disease will emerge and cause a sustained outbreak (\(R > 1\)) based on R and initial cases

probability_epidemic(): Calculate the probability a disease will cause an outbreak based on R, k and initial cases

probability_extinct(): Calculate the probability a branching process will go extinct based on R, k and initial cases

Proportion of transmission

proportion_transmission(): Estimate what proportion of cases cause a certain proportion of transmission

proportion_cluster_size(): Estimate what proportion of new cases originated within a transmission event of a given size

Reproduction number in heterogeneous network

calc_network_R(): Calculate the reproduction number (\(R\)) for a (heterogeneous) network

Helper functions

ic_tbl(): Helper function to create a model comparison table

Constants

FINITE_INF NSIM: Constants used in superspreading