bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

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

Author
Josef C. Uyeda, Jon Eastman and Luke Harmon
Date of publication
2015-10-25 08:55:52
Maintainer
Josef C. Uyeda <josef.uyeda@gmail.com>
License
GPL (>= 2)
Version
1.1.0

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