Learn R Programming

bayou (version 2.1.1)

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

53

Version

2.1.1

License

GPL (>= 2)

Maintainer

Josef Uyeda

Last Published

October 9th, 2018

Functions in bayou (2.1.1)

OUwie2bayou

Converts OUwie data into bayou format
combine.chains

Combine mcmc chains
makeTransparent

Make a color transparent (Taken from an answer on StackOverflow by Nick Sabbe)
dataSim

Simulates data from bayou models
model.OU

Bayou Models
plotBranchHeatMap

A function to plot a heatmap of reconstructed parameter values on the branches of the tree
Lposterior

Return a posterior of shift locations
dloc

Probability density function for the location of the shift along the branch
OU.lik

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

Half cauchy distribution taken from the R package LaplacesDemon (Hall, 2012).
make.powerposteriorFn

Makes a power posterior function in bayou
make.prior

Make a prior function for bayou
plotOUtreesim

A function to visualize a multi-optimum OU process evolving on a phylogeny
plotRegimes

Function to plot the regimes from a simmap tree
priorSim

Simulates parameters from bayou models
pull.pars

Utility function for retrieving parameters from an MCMC chain
plotShiftSummaries

A function to plot a list produced by shiftSummaries
regime.plot

Adds visualization of regimes to a plot
set.burnin

Set the burnin proportion for bayouMCMC objects
QG.sig2

Calculates the sigma^2 parameter from a QG model
bayou-deprecated

Deprecated functions in package bayou.
bayou.lik

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

Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
parmap.W

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

Revision of bayou.mcmc that only makes the mcmc loop function, rather than running it itself.
OU.repar

Calculates the alpha and sigma^2 from a parameter list with supplied phylogenetic half-life and stationary variance
pars2simmap

Convert a bayou parameter list into a simmap formatted phylogeny
OUphenogram

Experimental phenogram plotting function for set of model of model parameters
plotSimmap.mcmc

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

Function for checking parameter lists, prior and models are consistent and error-free
print.bayouFit

S3 method for printing bayouFit objects
bayou2OUwie

Converts bayou data into OUwie format
cdpois

Conditional Poisson distribution
identifyBranches

Identify shifts on branches of a phylogenetic tree
print.refFn

S3 method for printing refFn objects
dsb

Probability density functions for bayou
make.refFn

Make a reference function in bayou
makeBayouModel

This function makes a bayou model object that can be used for customized allometric regression models.
plot.ssMCMC

S3 method for plotting ssMCMC objects
plotBayoupars

Plot parameter list as a simmap tree
load.bayou

Loads a bayou object
print.ssMCMC

S3 method for printing ssMCMC objects
shiftSummaries

A function for summarizing the state of a model after a shift
phenogram.density

Plot a pheongram with the posterior density for optima values
simmap.W

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

Stepping stone estimation of the marginal likelihood for a bayou model
plot.bayouMCMC

S3 method for plotting bayouMCMC objects
gelman.R

Calculate Gelman's R statistic
print.bayouMCMC

S3 method for printing bayouMCMC objects
summary.bayouMCMC

S3 method for summarizing bayouMCMC objects
print.priorFn

S3 method for printing priorFn objects
QG.alpha

Calculates the alpha parameter from a QG model