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

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Bayesian reconstruction of disease outbreaks using epidemiological and genetic information.

Author
Thibaut Jombart <thibautjombart@gmail.com>, Anne Cori, Joel Hellewell
Date of publication
2015-12-07 23:13:36
Maintainer
Thibaut Jombart <thibautjombart@gmail.com>
License
GPL (>= 2)
Version
1.1-7
URLs

View on CRAN

Man pages

get.mu
Derive mutation rate estimation from outbreak's outputs
outbreaker
Outbreaker: disease outbreak reconstruction using genetic...
outbreaker.package
outbreaker: disease outbreak reconstruction using...
plot
Plot outbreaker's results
repro
Derive reproduction numbers from outbreak's outputs
selectChains
Select 'good' runs from independent MCMC chains
simOutbreak
Simulation of pathogen genotypes during disease outbreaks
simulated-outbreak-dataset
Toy outbreak dataset used to illustrate outbreaker
tTree
Simple transmission tree from outreaber's output

Files in this package

outbreaker
outbreaker/inst
outbreaker/inst/CITATION
outbreaker/configure.ac
outbreaker/src
outbreaker/src/distances.h
outbreaker/src/common.h
outbreaker/src/distances.c
outbreaker/src/mcmc.h
outbreaker/src/moves.c
outbreaker/src/structures.h
outbreaker/src/outbreaker.c
outbreaker/src/matvec.c
outbreaker/src/structures.c
outbreaker/src/prior.c
outbreaker/src/prior.h
outbreaker/src/moves.h
outbreaker/src/Makevars.in
outbreaker/src/init.h
outbreaker/src/likelihood.c
outbreaker/src/genclasses.h
outbreaker/src/matvec.h
outbreaker/src/Makevars.win
outbreaker/src/init.c
outbreaker/src/likelihood.h
outbreaker/src/genclasses.c
outbreaker/src/mcmc.c
outbreaker/NAMESPACE
outbreaker/data
outbreaker/data/fakeOutbreak.RData
outbreaker/R
outbreaker/R/selectChains.R
outbreaker/R/mutationRates.R
outbreaker/R/simOutbreak.R
outbreaker/R/plot.R
outbreaker/R/reproRate.R
outbreaker/R/data.R
outbreaker/R/tTree.R
outbreaker/R/package.R
outbreaker/R/interface.R
outbreaker/R/zzz.R
outbreaker/README.md
outbreaker/MD5
outbreaker/DESCRIPTION
outbreaker/configure
outbreaker/ChangeLog
outbreaker/man
outbreaker/man/simulated-outbreak-dataset.Rd
outbreaker/man/selectChains.Rd
outbreaker/man/outbreaker.package.Rd
outbreaker/man/outbreaker.Rd
outbreaker/man/tTree.Rd
outbreaker/man/simOutbreak.Rd
outbreaker/man/plot.Rd
outbreaker/man/repro.Rd
outbreaker/man/get.mu.Rd