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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.
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Version
2.1.1
2.1
1.1.0
1.0.1
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Install
install.packages('bayou')
Monthly Downloads
56
Version
2.1.1
License
GPL (>= 2)
Maintainer
Josef Uyeda
Last Published
October 9th, 2018
Functions in bayou (2.1.1)
Search functions
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