outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

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>.

Version: 1.1.3
Depends: R (≥ 3.5.0)
Imports: utils, methods, stats, grDevices, Rcpp, ape, ggplot2, magrittr, visNetwork
LinkingTo: Rcpp
Suggests: coda, microbenchmark, testthat, knitr, rmarkdown, igraph, epicontacts, adegenet
Published: 2022-05-23
DOI: 10.32614/CRAN.package.outbreaker2
Author: Thibaut Jombart [aut], Finlay Campbell [aut, cre], Rich Fitzjohn [aut], Gerry Tonkin-Hill [ctb], Kristjan Eldjarn [ctb], Alexis Robert [ctb]
Maintainer: Finlay Campbell <finlaycampbell93 at gmail.com>
License: MIT + file LICENSE
NeedsCompilation: yes
SystemRequirements: C++11
Citation: outbreaker2 citation info
Materials: README NEWS
In views: Epidemiology
CRAN checks: outbreaker2 results


Reference manual: outbreaker2.pdf
Vignettes: outbreaker2: Rcpp API
Using custom priors, likelihood, or movements in outbreaker2
Introduction to outbreaker2
outbreaker2: package overview


Package source: outbreaker2_1.1.3.tar.gz
Windows binaries: r-devel: outbreaker2_1.1.3.zip, r-release: outbreaker2_1.1.3.zip, r-oldrel: outbreaker2_1.1.3.zip
macOS binaries: r-release (arm64): outbreaker2_1.1.3.tgz, r-oldrel (arm64): outbreaker2_1.1.3.tgz, r-release (x86_64): outbreaker2_1.1.3.tgz, r-oldrel (x86_64): outbreaker2_1.1.3.tgz
Old sources: outbreaker2 archive

Reverse dependencies:

Reverse imports: o2geosocial


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