bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

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

View on CRAN

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

Files in this package

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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