getR0

Output of a nosoi simulation (object of class <code><a rd-options="" href="/link/nosoiSim?package=nosoi&version=1.0.0" data-mini-rdoc="nosoi::nosoiSim">nosoiSim</a></code>).

nosoi.output

Gets an estimate of secondary cases (what R0 usually tries to estimate) and its distribution from the output of a <code>nosoiSim</code> simulation. The actual calculation is based on inactive hosts at the end of the simulation to avoid bias introduced by hosts that have not finished their transmission potential.

The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. in prep). It is named after the daimones of plague, sickness and disease that escaped Pandora's jar in the Greek mythology. 'nosoi' is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.

Sebastian Lequime

nosoi

A Forward Agent-Based Transmission Chain Simulator

Paul Bastide

Simon Dellicour

Philippe Lemey

Guy Baele

getR0 function

Output of a nosoi simulation (object of class <code><a rd-options='' href='nosoiSim'>nosoiSim</a></code>).

getR0: Gets R0 from a `nosoi` simulation

Description

Usage

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See Also