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

Functions

bayou Man page
bayou2OUwie Man page
bayou.lik Man page
bayou.mcmc Man page
bayou-package Man page
cdpois Man page
combine.chains Man page
dataSim Man page
dhalfcauchy Man page
dloc Man page
dsb Man page
gelman.R Man page
identifyBranches Man page
load.bayou Man page
Lposterior Man page
make.powerposteriorFn Man page
make.prior Man page
make.refFn Man page
makeTransparent Man page
OU.lik Man page
OUphenogram Man page
OU.repar Man page
OUwie2bayou Man page
overparameterize.startingPoint Man page
parmap.W Man page
pars2simmap Man page
phalfcauchy Man page
phenogram.density Man page
plot.bayouMCMC Man page
plotBayoupars Man page
plotRegimes Man page
plotSimmap.mcmc Man page
plot.ssMCMC Man page
print.bayouFit Man page
print.priorFn Man page
print.refFn Man page
print.ssMCMC Man page
priorSim Man page
pull.pars Man page
QG.alpha Man page
QG.sig2 Man page
qhalfcauchy Man page
rdpois Man page
regime.plot Man page
rhalfcauchy Man page
rloc Man page
rsb Man page
set.burnin Man page
simmap.W Man page
steppingstone Man page
summary.bayouMCMC Man page

Files

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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All documentation is copyright its authors; we didn't write any of that.