phybreak: Analysis of Outbreaks with Sequence Data
Version 0.1.1

Implementation the outbreak analysis method described by Klinkenberg et al (2016) . Simulate outbreaks, analyse datasets by creating samples from the posterior distribution with a Markov-Chain Monte Carlo sampler, and summarize the output.

AuthorDon Klinkenberg [aut, cre]
Date of publication2016-09-01 01:39:46
MaintainerDon Klinkenberg <don@xs4all.nl>
LicenseGPL (>= 2)
Version0.1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("phybreak")

Getting started

README.md

Popular man pages

burnin.phybreak: MCMC updating of a phybreak-object.
logLik.phybreak: Log-likelihood of a phybreak-object.
phylotree: Maximum clade credibility tree.
plot.phybreak: Plotting a phybreak object.
sample.phybreak: Sampling from a phybreak MCMC-chain.
sim.phybreak: Outbreak simulation.
transtree: Create a consensus transmission tree.
See all...

All man pages Function index File listing

Man pages

burnin.phybreak: MCMC updating of a phybreak-object.
get.phybreak: Accessing a phybreak object
infectorsets: Sampled infectors for each host in a phybreak-object.
logLik.phybreak: Log-likelihood of a phybreak-object.
phybreak: Create a phybreak-object from data and prior distributions.
phylotree: Maximum clade credibility tree.
plot.phybreak: Plotting a phybreak object.
sample.phybreak: Sampling from a phybreak MCMC-chain.
sim.phybreak: Outbreak simulation.
thin.phybreak: Remove posterior samples from a phybreak-object.
transtree: Create a consensus transmission tree.

Functions

Files

inst
inst/CITATION
src
src/likseq.cpp
src/CCphylo_support.cpp
src/CCphylotree.cpp
src/CCtranstree.cpp
src/mcctree.cpp
src/CCtrans_support.cpp
src/CCtrans_support.h
src/mtcctree.cpp
src/likseqenv.cpp
src/CCphylo_support.h
src/RcppExports.cpp
src/ptr.cpp
src/sctwh3.cpp
NAMESPACE
NEWS.md
R
R/phylotree.R
R/plot-phybreak.R
R/sim-phybreak.R
R/make-phyloclass.R
R/sample-phybreak.R
R/sample-minitrees.R
R/get-current.R
R/mcmc-updateparameters.R
R/phybreak-class.R
R/mcmc-updatehost-paths.R
R/RcppExports.R
R/logLik-phybreak.R
R/mcmc-environment-functions.R
R/thin_phybreak.R
R/phybreak.R
R/burnin-phybreak.R
R/infectorsets.R
R/transtree.R
README.md
MD5
DESCRIPTION
man
man/sim.phybreak.Rd
man/phylotree.Rd
man/thin.phybreak.Rd
man/logLik.phybreak.Rd
man/transtree.Rd
man/plot.phybreak.Rd
man/infectorsets.Rd
man/burnin.phybreak.Rd
man/get.phybreak.Rd
man/phybreak.Rd
man/sample.phybreak.Rd
phybreak documentation built on May 19, 2017, 9:04 p.m.

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