phybreak: Analysis of Outbreaks with Sequence Data

Implementation the outbreak analysis method described by Klinkenberg et al (2017) <doi:10.1371/journal.pcbi.1005495>. Simulate outbreaks, analyse datasets by creating samples from the posterior distribution with a Markov-Chain Monte Carlo sampler, and summarize the output.

Version: 0.2.0
Depends: R (≥ 3.1.0), phangorn, ape
Imports: Rcpp (≥ 0.12.1), methods, stats, stringr, utils
LinkingTo: Rcpp
Suggests: coda, phytools, OutbreakTools, testthat, knitr, rmarkdown
Published: 2017-07-30
Author: Don Klinkenberg [aut, cre]
Maintainer: Don Klinkenberg <don at xs4all.nl>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Citation: phybreak citation info
Materials: README NEWS
CRAN checks: phybreak results

Downloads:

Reference manual: phybreak.pdf
Vignettes: Introduction to phybreak package
Package source: phybreak_0.2.0.tar.gz
Windows binaries: r-devel: phybreak_0.2.0.zip, r-release: phybreak_0.2.0.zip, r-oldrel: phybreak_0.2.0.zip
OS X El Capitan binaries: r-release: phybreak_0.2.0.tgz
OS X Mavericks binaries: r-oldrel: phybreak_0.2.0.tgz
Old sources: phybreak archive

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