Man pages for bayou
Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

bayou2OUwieConverts bayou data into OUwie format
bayou.checkModelFunction for checking parameter lists, prior and models are...
bayou-deprecatedDeprecated functions in package bayou.
bayou.likFunction for calculating likelihood of an OU model in bayou...
bayou.makeMCMCRevision of bayou.mcmc that only makes the mcmc loop...
bayou-packageBayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
cdpoisConditional Poisson distribution
combine.chainsCombine mcmc chains
dataSimSimulates data from bayou models
dhalfcauchyHalf cauchy distribution taken from the R package...
dlocProbability density function for the location of the shift...
dsbProbability density functions for bayou
gelman.RCalculate Gelman's R statistic
identifyBranchesIdentify shifts on branches of a phylogenetic tree
load.bayouLoads a bayou object
LposteriorReturn a posterior of shift locations
makeBayouModelThis function makes a bayou model object that can be used for...
make.powerposteriorFnMakes a power posterior function in bayou
make.priorMake a prior function for bayou
make.refFnMake a reference function in bayou
makeTransparentMake a color transparent (Taken from an answer on...
model.OUBayou Models
OU.likFunction for calculating likelihood of an OU model in bayou...
OUphenogramExperimental phenogram plotting function for set of model of...
OU.reparCalculates the alpha and sigma^2 from a parameter list with...
OUwie2bayouConverts OUwie data into bayou format
parmap.WCalculate the weight matrix of a set of regimes on a...
pars2simmapConvert a bayou parameter list into a simmap formatted...
phenogram.densityPlot a pheongram with the posterior density for optima values
plot.bayouMCMCS3 method for plotting bayouMCMC objects
plotBayouparsPlot parameter list as a simmap tree
plotBranchHeatMapA function to plot a heatmap of reconstructed parameter...
plotOUtreesimA function to visualize a multi-optimum OU process evolving...
plotRegimesFunction to plot the regimes from a simmap tree
plotShiftSummariesA function to plot a list produced by 'shiftSummaries'
plotSimmap.mcmcPlot a phylogenetic tree with posterior probabilities from a...
plot.ssMCMCS3 method for plotting ssMCMC objects
print.bayouFitS3 method for printing bayouFit objects
print.bayouMCMCS3 method for printing bayouMCMC objects
print.priorFnS3 method for printing priorFn objects
print.refFnS3 method for printing refFn objects
print.ssMCMCS3 method for printing ssMCMC objects
priorSimSimulates parameters from bayou models
pull.parsUtility function for retrieving parameters from an MCMC chain
QG.alphaCalculates the alpha parameter from a QG model
QG.sig2Calculates the sigma^2 parameter from a QG model
regime.plotAdds visualization of regimes to a plot
set.burninSet the burnin proportion for bayouMCMC objects
shiftSummariesA function for summarizing the state of a model after a shift
simmap.WCalculate the weight matrix of a set of regimes on a...
steppingstoneStepping stone estimation of the marginal likelihood for a...
summary.bayouMCMCS3 method for summarizing bayouMCMC objects
bayou documentation built on Oct. 9, 2018, 5:04 p.m.