Learn R Programming
⚠️There's a newer version (2.3.1) of this package.Take me there.

bayou (version 1.1.0)

Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Description

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

Copy Link

Version

Install

install.packages('bayou')

Monthly Downloads

24

Version

1.1.0

License

GPL (>= 2)

Maintainer

Josef Uyeda

Last Published

October 25th, 2015

Functions in bayou (1.1.0)

OU.repar

Calculates the alpha and sigma^2 from a parameter list with supplied phylogenetic half-life and stationary variance
phenogram.density

Plot a pheongram with the posterior density for optima values
set.burnin

Set the burnin proportion for bayouMCMC objects
plot.ssMCMC

S3 method for plotting ssMCMC objects
print.ssMCMC

S3 method for printing ssMCMC objects
makeTransparent

Make a color transparent (Taken from an answer on StackOverflow by Nick Sabbe)
bayou.lik

Function for calculating likelihood of an OU model in bayou using the threepoint algorithm
cdpois

Conditional Poisson distribution
OUphenogram

Experimental phenogram plotting function for set of model of model parameters
bayou2OUwie

Converts bayou data into OUwie format
priorSim

Simulates parameters from bayou models
pull.pars

Utility function for retrieving parameters from an MCMC chain
dsb

Probability density functions for bayou
plotRegimes

Function to plot the regimes from a simmap tree
bayou-package

bayou-package
dloc

Probability density function for the location of the shift along the branch
identifyBranches

Identify shifts on branches of a phylogenetic tree
gelman.R

Calculate Gelman's R statistic
OUwie2bayou

Converts OUwie data into bayou format
simmap.W

Calculate the weight matrix of a set of regimes on a phylogeny
load.bayou

Loads a bayou object
pars2simmap

Convert a bayou parameter list into a simmap formatted phylogeny
summary.bayouMCMC

S3 method for summarizing bayouMCMC objects
bayou.mcmc

Bayesian sampling of multi-optima OU models
plotSimmap.mcmc

Plot a phylogenetic tree with posterior probabilities from a bayouMCMC chain (function adapted from phytools' plotSimmap)
dhalfcauchy

Half cauchy distribution taken from the R package LaplacesDemon (Hall, 2012).
combine.chains

Combine mcmc chains
print.refFn

S3 method for printing refFn objects
parmap.W

Calculate the weight matrix of a set of regimes on a phylogeny
plotBayoupars

Plot parameter list as a simmap tree
make.prior

Make a prior function for bayou
dataSim

Simulates data from bayou models
make.refFn

Make a reference function in bayou
print.bayouFit

S3 method for printing bayouFit objects
QG.sig2

Calculates the sigma^2 parameter from a QG model
steppingstone

Stepping stone estimation of the marginal likelihood for a bayou model
make.powerposteriorFn

Makes a power posterior function in bayou
QG.alpha

Calculates the alpha parameter from a QG model
OU.lik

Function for calculating likelihood of an OU model in bayou using pruning algorithm or matrix inversion
overparameterize.startingPoint

Generate an overparameterized starting point for the MCMC
regime.plot

Adds visualization of regimes to a plot
Lposterior

Return a posterior of shift locations
plot.bayouMCMC

S3 method for plotting bayouMCMC objects
print.priorFn

S3 method for printing priorFn objects