An Implementation of the TSIR Model

An implementation of the time-series Susceptible-Infected-Recovered (TSIR) model using a number of different fitting options for infectious disease time series data. The manuscript based on this package can be found here < https://doi:10.1371/0185528>. The method implemented here is described by Finkenstadt and Grenfell (2000) .

Build Status

Information regarding this package and a short tutorial can be found here:

If you've found the package useful in your research, I ask that you cite the above PLOS ONE paper.

This package can be installed via CRAN. Updates to the package post the PLOS ONE paper will follow below as they occur.

Update V.0.4.0 : Lyapunov Analysis 08/20/2018

The tsiR package has been updated to include Global and Local Lyapunov Exponents. You can learn more and find examples of how to use this function for the London data by typing ?TSIR_LE ?TSIR_LLE and ?plotLLE in the R console. This updateis now on CRAN.


Reference manual

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0.4.2 by Alexander D. Becker, a year ago

Browse source code at

Authors: Alexander D. Becker [aut, cre] , Sinead E. Morris [ctb] , Ottar N. Bjornstad [ctb]

Documentation:   PDF Manual  

GPL-3 license

Imports ggplot2, kernlab, reshape2, grid

See at CRAN