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TsiR: An R package for time-series Susceptible-Infected-Recovered models of epidemics.

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.

SUBMITTER: Becker AD

PROVIDER: S-EPMC5619791 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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tsiR: An R package for time-series Susceptible-Infected-Recovered models of epidemics.

Becker Alexander D AD Grenfell Bryan T BT

PloS one 20170928 9

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 ...[more]

PMID: 28957408

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