TSIR: An R package for time-series susceptible-infected-recovered models of epidemics

Alexander D. Becker, Bryan T. Grenfell

Research output: Contribution to journalArticle

5 Scopus citations

Abstract

tsiR is an open source software package implemented in the R programming language designed to analyze infectious disease time-series data. The software extends a well-studied and widely-applied algorithm, the time-series Susceptible-Infected-Recovered (TSIR) model, to infer parameters from incidence data, such as contact seasonality, and to forward simulate the underlying mechanistic model. The tsiR package aggregates a number of different fitting features previously described in the literature in a user-friendly way, providing support for their broader adoption in infectious disease research. Also included in tsiR are a number of diagnostic tools to assess the fit of the TSIR model. This package should be useful for researchers analyzing incidence data for fully-immunizing infectious diseases.

Original languageEnglish (US)
Article numbere0185528
JournalPloS one
Volume12
Issue number9
DOIs
StatePublished - Sep 2017

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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