Reconstruction of Transmission Chains from Surveillance Data

Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. 2020 ).


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1.0.1 by Alexis Robert, a month ago

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Authors: Alexis Robert [aut, cre, cph] , Sebastian Funk [aut] , Adam J Kucharski [aut] , Thibaut Jombart [ctb]

Documentation:   PDF Manual  

MIT + file LICENSE license

Imports Rcpp, methods, stats, grDevices, geosphere, ggplot2, visNetwork, data.table, outbreaker2

Suggests testthat, tigris, sf, knitr, socialmixr, rmarkdown

Linking to Rcpp

See at CRAN