rbrothers: rbrothers: multiple change-point recombination detection
Version 0.0-1

rbrothers is a phylogenetic recombination detection package. Starting with aligned DNA sequences, rbrothers uses the Bayesian multiple change-point model implemented in the JAVA package DualBrothers to create posterior tree probability plots. rbrothers automates the production of a reasonable set of candidate trees and provides trace plots and autocorrelation plots that allow the user to monitor the convergence and mixing of the Markov chain Monte Carlo algorithm.

AuthorVladimir Minin, Jan Irvahn
Date of publication2015-07-31 19:02:46
MaintainerJan Irvahn <ji26@uw.edu>
LicenseGPL-3
Version0.0-1
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rbrothers", repos="http://R-Forge.R-project.org")

Popular man pages

breakpointCI: 95% breakpoint credible interval
dualbrothers: Recombination Analysis via DualBrothers
extractbasename: extract the basename from an rbrothers object
plot.db: Plot a dualbrothers object
readdb: import a dualbrothers object
summary.db: Summary of a dualbrothers object
topologyprofile: TopologyProfile
See all...

All man pages Function index File listing

Man pages

breakpointCI: 95% breakpoint credible interval
db: db
db.default: db.default
dualbrothers: Recombination Analysis via DualBrothers
epprofile: EPProfile
extractbasename: extract the basename from an rbrothers object
findbreakpoints: FindBreakPoints
plot.db: Plot a dualbrothers object
plotkappa: Plot Posterior values of Kappa for a DualBrothers object
plotmcmc: MCMC trace plot of log likelihoods
plotmu: Plot Posterior values of Mu for a DualBrothers object
plottree.db: Plots the most likely phylogenetic trees
readdb: import a dualbrothers object
summary.db: Summary of a dualbrothers object
topologyprofile: TopologyProfile

Functions

breakpointCI Man page Source code
db Man page
db.default Man page
dualbrothers Man page
epprofile Man page
extractbasename Man page Source code
findbreakpoints Man page
findmax Source code
onLoad Source code
plot.db Man page
plotkappa Man page Source code
plotmcmc Man page Source code
plotmu Man page Source code
plottree.db Man page
readdb Man page
summary.db Man page
topologyprofile Man page

Files

DESCRIPTION
NAMESPACE
R
R/breakpointCI.R
R/db.R
R/db.default.R
R/dualbrothers.R
R/epprofile.R
R/extractbasename.R
R/findbreakpoints.R
R/findmax.R
R/onLoad.R
R/plot.db.R
R/plotkappa.r
R/plotmcmc.r
R/plotmu.r
R/plottree.db.R
R/readdb.R
R/summary.db.R
R/topologyprofile.R
build
build/vignette.rds
demo
demo/00Index
demo/fimH_example.r
demo/salmonella_example.R
inst
inst/doc
inst/doc/rbrothers_tutorial.R
inst/doc/rbrothers_tutorial.Rnw
inst/doc/rbrothers_tutorial.pdf
inst/extdata
inst/extdata/KAL153
inst/extdata/KAL153/KAL153.cmdfile
inst/extdata/KAL153/KAL153.phy
inst/extdata/Primate
inst/extdata/Primate/primate.cmdfile
inst/extdata/Primate/primate.phy
inst/extdata/RW024
inst/extdata/RW024/RW024.cmdfile
inst/extdata/RW024/RW024.phy
inst/extdata/Salmonella
inst/extdata/Salmonella/Salmonella_fimA8.phy
inst/extdata/Salmonella/Salmonella_fimH8.phy
inst/extdata/UA0116
inst/extdata/UA0116/UA0116.cmdfile
inst/extdata/UA0116/UA0116.phy
inst/extdata/fimH
inst/extdata/fimH/fimH8.phy
inst/extdata/smalltrees
inst/extdata/smalltrees/five-input.tre
inst/extdata/smalltrees/four-input.tre
inst/extdata/smalltrees/six-input.tre
inst/extdata/smalltrees/three-input.tre
inst/java
inst/java/DualBrothers.jar
inst/java/colt.jar
man
man/breakpointCI.Rd
man/db.Rd
man/db.default.Rd
man/dualbrothers.Rd
man/epprofile.Rd
man/extractbasename.Rd
man/findbreakpoints.Rd
man/plot.db.Rd
man/plotkappa.Rd
man/plotmcmc.Rd
man/plotmu.Rd
man/plottree.db.Rd
man/readdb.Rd
man/summary.db.Rd
man/topologyprofile.Rd
vignettes
vignettes/rbrothers_tutorial.Rnw
rbrothers documentation built on May 21, 2017, 12:17 a.m.