The aim of nosoi (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator. 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.

To get the current released version from CRAN:

install.packages("nosoi")

To get the latest (and possibly unstable) version, you can use the devtools package:

install.packages("devtools")
devtools::install_github(repo = "slequime/nosoi")

You can find package documentation, with reference, tutorials and examples here: http://slequime.github.io/nosoi/ (built with pkgdown).

Sebastian Lequime, Paul Bastide, Simon Dellicour, Philippe Lemey & Guy Baele (2020) nosoi: A stochastic agent-based transmission chain simulation framework in R. Methods in Ecology and Evolution 11:1002-1007 doi:10.1111/2041-210X.13422

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