Introduction

NEXTNetR (Next-reaction-based Epidemics eXtended to Temporal Networks) is an R package for the efficient simulation of epidemics on complex networks (including weighted and temporal networks) with arbitrary transmission and recovery time distributions. NEXTNetR is an R wrapper around the C++ library NEXTNet.

Installation

The latest development version of NEXTNetR can be installed directly from Github by executing the following in R:

install.packages("remotes")
remotes::install_github("oist/NEXTNetR")

Alternatively, the latest release can be downloaded here and installed with R CMD INSTALL NEXTNetR-v<version>-pkg.tar.gz.

Synopsis

The following minimal example simulated an epidemic on an Erdős–Rényi network with lognormally distributed transmission time

sim <- simulation(
    erdos_renyi_network(1e5, 5),
    lognormal_time(6, 30, 0.1))
simulation_addinfections(sim, 1, 0.0)
r <- simulation_run(sim, stop=list(total_infected=300e3))
plot(r$time, r$infected, type='l')

See Getting Started for stey-by-step instructions on how to use NEXTNetR.

Supported Features

NEXTNetR offers a range of common types of artifical networks such as erdos_renyi(), see help(network_types) for a full list. adjacencylist_network() and adjacencylist_weightednetwork() allow arbitrary unweighted and weighted networks to be used for simulations. Transmission and recovery times can likewise be arbitrary probability distributions, see help(time_distributions).

NEXTNetR also allows simulations on temporal networks, i.e. networks which change over time, possibly in response to epidemic events. Amongst the temporal networks currently supported by NEXTNetR are empirical_contact_temporalnetwork() and activity_driven_temporalnetwork(), see help(network_types) for a full list.