TimTam
Time-series Integration Method Through Approximation of Moments
Project maintained by Alexander E. Zarebski
TimTam is a software package which enables you to use either viral genomes, time series of confirmed cases or both to estimate both the reproduction number and the prevalence of infection.
Installation and Usage
TimTam is a BEAST2 package. There are detailed instructions for the installation and usage available in the wiki.
TimtamslamR is an R package which makes it easier to set up Timtam analyses. The examples in the wiki make use of this package.
Feedback, Feature Requests and Bug Reports
Feature requests and bug reports should be submitted via the project's issues page.
Citing TimTam
If you use TimTam as part of research that leads to a publication, we ask that you cite the following article:
A. E. Zarebski, L. du Plessis, K. V. Parag, and O. G. Pybus, "A computationally tractable birth-death model that combines phylogenetic and epidemiological data", PLOS Comput. Biol. 18(2): e1009805, 2022 (Link)
Phyloseminar
Bibliography
Zarebski AE, Zwaans A, Gutierrez B, du Plessis L, Pybus OG (2023) Estimating epidemic dynamics with genomic and time series data. medRxiv 2023.08.03.23293620. (Link)
Zarebski AE, du Plessis L, Parag KV, Pybus OG (2022) A computationally tractable birth-death model that combines phylogenetic and epidemiological data. PLOS Computational Biology 18(2): e1009805. (Link)