A Forward Agent-Based Transmission Chain Simulator

The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. bioRxiv 2020.03.03.973107). 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.


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Reference manual

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install.packages("nosoi")

1.0.3 by Sebastian Lequime, 20 days ago


https://github.com/slequime/nosoi


Browse source code at https://github.com/cran/nosoi


Authors: Sebastian Lequime [aut, cre] , Paul Bastide [aut] , Simon Dellicour [aut] , Philippe Lemey [aut] , Guy Baele [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports stats, methods, raster

Depends on data.table

Suggests testthat, knitr, rmarkdown, igraph, tidyverse, ggplot2, ggnetwork, intergraph, viridis, gifski, png, gganimate, ape, tidytree, treeio, ggtree, magrittr, dplyr


See at CRAN