bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Version 1.1.0

Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck models to phylogenetic comparative data using Bayesian reversible-jump methods.

AuthorJosef C. Uyeda, Jon Eastman and Luke Harmon
Date of publication2015-10-25 08:55:52
MaintainerJosef C. Uyeda <josef.uyeda@gmail.com>
LicenseGPL (>= 2)
Version1.1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("bayou")

Getting started

Package overview

Popular man pages

bayou2OUwie: Converts bayou data into OUwie format
bayou-package: bayou-package
cdpois: Conditional Poisson distribution
dataSim: Simulates data from bayou models
makeTransparent: Make a color transparent (Taken from an answer on...
plotSimmap.mcmc: Plot a phylogenetic tree with posterior probabilities from a...
summary.bayouMCMC: S3 method for summarizing bayouMCMC objects
See all...

All man pages Function index File listing

Man pages

bayou2OUwie: Converts bayou data into OUwie format
bayou.lik: Function for calculating likelihood of an OU model in bayou...
bayou.mcmc: Bayesian sampling of multi-optima OU models
bayou-package: bayou-package
cdpois: Conditional Poisson distribution
combine.chains: Combine mcmc chains
dataSim: Simulates data from bayou models
dhalfcauchy: Half cauchy distribution taken from the R package...
dloc: Probability density function for the location of the shift...
dsb: Probability density functions for bayou
gelman.R: Calculate Gelman's R statistic
identifyBranches: Identify shifts on branches of a phylogenetic tree
load.bayou: Loads a bayou object
Lposterior: Return a posterior of shift locations
make.powerposteriorFn: Makes a power posterior function in bayou
make.prior: Make a prior function for bayou
make.refFn: Make a reference function in bayou
makeTransparent: Make a color transparent (Taken from an answer on...
OU.lik: Function for calculating likelihood of an OU model in bayou...
OUphenogram: Experimental phenogram plotting function for set of model of...
OU.repar: Calculates the alpha and sigma^2 from a parameter list with...
OUwie2bayou: Converts OUwie data into bayou format
overparameterize.startingPoint: Generate an overparameterized starting point for the MCMC
parmap.W: Calculate the weight matrix of a set of regimes on a...
pars2simmap: Convert a bayou parameter list into a simmap formatted...
phenogram.density: Plot a pheongram with the posterior density for optima values
plot.bayouMCMC: S3 method for plotting bayouMCMC objects
plotBayoupars: Plot parameter list as a simmap tree
plotRegimes: Function to plot the regimes from a simmap tree
plotSimmap.mcmc: Plot a phylogenetic tree with posterior probabilities from a...
plot.ssMCMC: S3 method for plotting ssMCMC objects
print.bayouFit: S3 method for printing bayouFit objects
print.priorFn: S3 method for printing priorFn objects
print.refFn: S3 method for printing refFn objects
print.ssMCMC: S3 method for printing ssMCMC objects
priorSim: Simulates parameters from bayou models
pull.pars: Utility function for retrieving parameters from an MCMC chain
QG.alpha: Calculates the alpha parameter from a QG model
QG.sig2: Calculates the sigma^2 parameter from a QG model
regime.plot: Adds visualization of regimes to a plot
set.burnin: Set the burnin proportion for bayouMCMC objects
simmap.W: Calculate the weight matrix of a set of regimes on a...
steppingstone: Stepping stone estimation of the marginal likelihood for a...
summary.bayouMCMC: S3 method for summarizing bayouMCMC objects

Functions

C_threepoint Source code
C_transf_branch_lengths Source code
C_weightmatrix Source code
D.from.theta Source code
Lposterior Man page Source code
OU.asr Source code
OU.lik Man page Source code Source code
OU.repar Man page Source code
OUphenogram Man page Source code
OUwie2bayou Man page Source code
QG.alpha Man page Source code
QG.sig2 Man page Source code
addshift2map Source code
adjustTheta Source code
allnodes.W Source code
bayou Man page
bayou-package Man page
bayou.lik Man page Source code
bayou.mcmc Man page Source code
bayou2OUwie Man page Source code
buildControl Source code
cache.descendants Source code
cache.tree Source code
cache.y.nodes Source code
cdpois Man page Source code
combine.chains Man page Source code
computelnr Source code
dataSim Man page Source code
dhalfcauchy Man page Source code
discard.burnin Source code
dloc Man page Source code
dsb Man page Source code
fastbm.lik Source code
fix.root.bm Source code
gelman.R Man page Source code
get.ancestor.of.node Source code
get.ancestors.of.node Source code
heights.cache Source code Source code
identifyBranches Man page Source code
load.bayou Man page Source code
make.powerposteriorFn Man page Source code
make.prior Man page Source code
make.refFn Man page Source code
makeTransparent Man page Source code
mrca Source code
multiplierProposal Source code
optima.ages Source code
ou.cache.fast Source code
ouMatrix Source code
overparameterize.startingPoint Man page Source code
parmap.W Man page Source code Source code
pars2map Source code
pars2simmap Man page Source code
phalfcauchy Man page Source code
phenogram.density Man page Source code
plot.bayouMCMC Man page Source code
plot.ssMCMC Man page Source code
plotBayoupars Man page Source code
plotRegimes Man page Source code
plotSimmap.mcmc Man page Source code
posterior.Q Source code
prepare.bm.univariate Source code
prepare.ou.univariate Source code
print.bayouFit Man page Source code
print.priorFn Man page Source code
print.refFn Man page Source code
print.ssMCMC Man page Source code
priorSim Man page Source code
proposalFn Source code
pruningwise.branching.times Source code
pruningwise.distFromRoot Source code
pull.pars Man page Source code
pull.rsample Source code
qhalfcauchy Man page Source code
rdpois Man page Source code
regime.plot Man page Source code
repars Source code
rhalfcauchy Man page Source code
rloc Man page Source code
rsb Man page Source code
sample Source code
set.burnin Man page Source code
set.defaults Source code
simmap.W Man page Source code Source code
slide Source code
slidespace Source code
splitmerge Source code
steppingstone Man page Source code
steppingstone.mcmc Source code
store.bayou Source code
summary.bayouMCMC Man page Source code
toSimmap Source code
tune.D Source code
updateControl Source code
vcv.asrOU Source code
whichorder Source code

Files

inst
inst/tests
inst/tests/test-likelihood.r
inst/tests/test-prior.r
inst/tests/test-weight_matrix.r
inst/tests/test-data_load.r
src
src/weightmatrix.cpp
src/branches.cpp
src/Makevars.win
src/RcppExports.cpp
src/threepoint.cpp
NAMESPACE
R
R/conversion-utilities.R
R/bayou-mcmc.R
R/bayou-utilities.R
R/bayou-mcmc-utilities.R
R/bayou-plotting.R
R/bayou-package.R
R/RcppExports.R
R/bayou-moves.R
R/bayou-steppingstone.R
R/bayou-likelihood.R
R/bayou-prior.R
R/probability.R
R/bayou-weight_matrix.R
R/bayou-simulation.r
MD5
DESCRIPTION
man
man/load.bayou.Rd
man/regime.plot.Rd
man/OUwie2bayou.Rd
man/make.refFn.Rd
man/dataSim.Rd
man/summary.bayouMCMC.Rd
man/plot.ssMCMC.Rd
man/OU.lik.Rd
man/pull.pars.Rd
man/Lposterior.Rd
man/bayou.mcmc.Rd
man/make.prior.Rd
man/identifyBranches.Rd
man/make.powerposteriorFn.Rd
man/cdpois.Rd
man/overparameterize.startingPoint.Rd
man/print.ssMCMC.Rd
man/plot.bayouMCMC.Rd
man/simmap.W.Rd
man/bayou2OUwie.Rd
man/steppingstone.Rd
man/dsb.Rd
man/combine.chains.Rd
man/priorSim.Rd
man/plotSimmap.mcmc.Rd
man/phenogram.density.Rd
man/OUphenogram.Rd
man/plotRegimes.Rd
man/QG.sig2.Rd
man/plotBayoupars.Rd
man/print.bayouFit.Rd
man/gelman.R.Rd
man/QG.alpha.Rd
man/dloc.Rd
man/bayou.lik.Rd
man/makeTransparent.Rd
man/set.burnin.Rd
man/dhalfcauchy.Rd
man/print.priorFn.Rd
man/print.refFn.Rd
man/pars2simmap.Rd
man/OU.repar.Rd
man/bayou-package.Rd
man/parmap.W.Rd
bayou documentation built on May 19, 2017, 1:18 p.m.

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