Package: outbreaker2
Version: 1.1.4
Date: 2025-12-16
Title: Bayesian Reconstruction of Disease Outbreaks by Combining
        Epidemiologic and Genomic Data
Authors@R: c(person("Thibaut", "Jombart",
                    email = "thibautjombart@gmail.com",
		    role = c("aut")),
	     person("Finlay", "Campbell",
	            email = "finlaycampbell93@gmail.com",
		    role = c("aut", "cre")),
	     person("Rich", "Fitzjohn",
	            email = "r.fitzjohn@imperial.ac.uk",
		    role = c("aut")),
	     person("Gerry", "Tonkin-Hill",
	            email = "gqt20@cam.ac.uk",
		    role = c("ctb")),
	     person("Kristjan", "Eldjarn",
	            email = "kristjan@eldjarn.net",
		    role = c("ctb")),
	     person("Alexis", "Robert",
	            email = "alexis.robert@lshtm.ac.uk",
		    role = c("ctb")))
Maintainer: Finlay Campbell <finlaycampbell93@gmail.com>
Description: Bayesian reconstruction of disease outbreaks using
        epidemiological and genetic information. Jombart T, Cori A,
        Didelot X, Cauchemez S, Fraser C and Ferguson N. 2014.
        <doi:10.1371/journal.pcbi.1003457>. Campbell, F, Cori A,
        Ferguson N, Jombart T. 2019.
        <doi:10.1371/journal.pcbi.1006930>.
License: MIT + file LICENSE
Suggests: coda, microbenchmark, testthat, knitr, rmarkdown, igraph,
        epicontacts, adegenet
Depends: R (>= 3.0.0)
Imports: utils, methods, stats, grDevices, Rcpp, ape, ggplot2,
        magrittr, visNetwork
LazyData: true
LinkingTo: Rcpp
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/pak/sysreqs: cmake make libuv1-dev
Repository: https://finlaycampbell.r-universe.dev
Date/Publication: 2026-03-24 12:27:44 UTC
RemoteUrl: https://github.com/finlaycampbell/outbreaker2
RemoteRef: HEAD
RemoteSha: 69f5b232024d2742fb0e0e6f8dafe83d05a5e1f9
NeedsCompilation: yes
Packaged: 2026-06-22 10:28:10 UTC; root
Author: Thibaut Jombart [aut],
  Finlay Campbell [aut, cre],
  Rich Fitzjohn [aut],
  Gerry Tonkin-Hill [ctb],
  Kristjan Eldjarn [ctb],
  Alexis Robert [ctb]