Infectious Disease Spread Models

A stochastic SEIIaR (susceptible, exposed, infectious, infectious asymptomatic, recovered) metapopulation model that including commuting. Each location has a local infection system, while the locations are connected by people who commute each day. The model differentiates between day and night. During the day you can infect/be infected in the location where you work, while during the night you can infect/be infected in the location where you live. It is the same commuters who travel back and forth each day. At the start of a day, all commuters are sent to their work location, where they mix for 12 hours. The commuters are then sent to their respective home locations, where they mix for 12 hours. The model is loosely based upon a published model by Engebretsen (2019) .


Reference manual

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2019.8.5 by Richard White, a year ago

Browse source code at

Authors: Solveig Engebretsen [aut] , Andreas Nygård Osnes [aut] , Richard White [aut, cre]

Documentation:   PDF Manual  

GPL-3 license

Imports Rcpp, RcppProgress, data.table, fhidata, stringr, readxl, zoo

Suggests testthat, knitr, ggplot2, glue, rmarkdown

Linking to Rcpp, RcppProgress

System requirements: C++11

See at CRAN