phybreak: Analysis of Outbreaks with Sequence Data

Share:

Implementation the outbreak analysis method described by Klinkenberg et al (2016) <doi:10.1101/069195>. Simulate outbreaks, analyse datasets by creating samples from the posterior distribution with a Markov-Chain Monte Carlo sampler, and summarize the output.

Author
Don Klinkenberg [aut, cre]
Date of publication
2016-09-01 01:39:46
Maintainer
Don Klinkenberg <don@xs4all.nl>
License
GPL (>= 2)
Version
0.1.1

View on CRAN

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.

Files in this package

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