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

Documentation:

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

Downloads:

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

Linking:

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