Package: bayou 2.3.0

Josef C. Uyeda

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.

Authors:Josef C. Uyeda, Jon Eastman and Luke Harmon

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bayou.pdf |bayou.html✨
bayou/json (API)

# Install 'bayou' in R:
install.packages('bayou', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/uyedaj/bayou/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

On CRAN:

43 exports 21 stars 2.09 score 63 dependencies 62 scripts 48 downloads

Last updated 2 months agofrom:b57d7eaff3. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKAug 27 2024
R-4.5-win-x86_64OKAug 27 2024
R-4.5-linux-x86_64OKAug 27 2024
R-4.4-win-x86_64OKAug 27 2024
R-4.4-mac-x86_64OKAug 27 2024
R-4.4-mac-aarch64OKAug 27 2024
R-4.3-win-x86_64OKAug 27 2024
R-4.3-mac-x86_64OKAug 27 2024
R-4.3-mac-aarch64OKAug 27 2024

Exports:bayou.checkModelbayou.likbayou.makeMCMCbayou.mcmcbayou2OUwiecdpoiscombine.chainsdataSimdhalfcauchydlocdsbgelman.RidentifyBranchesload.bayouLposteriormake.powerposteriorFnmake.priormake.refFnmakeBayouModelmakeTransparentOU.likOUphenogramOUwie2bayouparmap.Wpars2simmapphalfcauchyphenogram.densityplotBayouparsplotBranchHeatMapplotOUtreesimplotRegimesplotShiftSummariesplotSimmap.mcmcpriorSimpull.parsqhalfcauchyrdpoisrhalfcauchyrlocrsbset.burninshiftSummariessimmapW

Dependencies:apeassertthatcliclusterGenerationcodacodetoolscolorspacecombinatcpp11denstripDEoptimdeSolvedigestdoParallelexpmfansifarverfastmatchfitdistrplusforeachgeigergenericsggplot2ggseqlogogluegtableigraphisobanditeratorslabelinglatticelifecyclemagrittrmapsMASSMatrixmgcvmnormtmunsellmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspillarpkgconfigquadprogR6RColorBrewerRcppRcppArmadillorlangscalesscatterplot3dsubplexsurvivaltibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogeniesbayou-package bayou
Function for checking parameter lists, prior and models are consistent and error-freebayou.checkModel
Function for calculating likelihood of an OU model in bayou using the threepoint algorithmbayou.lik
Revision of bayou.mcmc that only makes the mcmc loop function, rather than running it itself.bayou.makeMCMC
Converts bayou data into OUwie formatbayou2OUwie
Conditional Poisson distributioncdpois rdpois
Combine mcmc chainscombine.chains
Simulates data from bayou modelsdataSim
Half cauchy distribution taken from the R package LaplacesDemon (Hall, 2012).dhalfcauchy phalfcauchy qhalfcauchy rhalfcauchy
Probability density function for the location of the shift along the branchdloc rloc
Probability density functions for bayoudsb rsb
Calculate Gelman's R statisticgelman.R
Identify shifts on branches of a phylogenetic treeidentifyBranches
Loads a bayou objectload.bayou
Return a posterior of shift locationsLposterior
Makes a power posterior function in bayoumake.powerposteriorFn
Make a prior function for bayoumake.prior
Make a reference function in bayoumake.refFn
This function makes a bayou model object that can be used for customized allometric regression models.makeBayouModel
Make a color transparent (Taken from an answer on StackOverflow by Nick Sabbe)makeTransparent
Bayou Modelsmodel.OU
Function for calculating likelihood of an OU model in bayou using pruning algorithm or matrix inversionOU.lik
Calculates the alpha and sigma^2 from a parameter list with supplied phylogenetic half-life and stationary varianceOU.repar
Experimental phenogram plotting function for set of model of model parametersOUphenogram
Converts OUwie data into bayou formatOUwie2bayou
Calculate the weight matrix of a set of regimes on a phylogenyparmap.W
Convert a bayou parameter list into a simmap formatted phylogenypars2simmap
Plot a pheongram with the posterior density for optima valuesphenogram.density
S3 method for plotting bayouMCMC objectsplot.bayouMCMC
S3 method for plotting ssMCMC objectsplot.ssMCMC
Plot parameter list as a simmap treeplotBayoupars
A function to plot a heatmap of reconstructed parameter values on the branches of the treeplotBranchHeatMap
A function to visualize a multi-optimum OU process evolving on a phylogenyplotOUtreesim
Function to plot the regimes from a simmap treeplotRegimes
A function to plot a list produced by 'shiftSummaries'plotShiftSummaries
Plot a phylogenetic tree with posterior probabilities from a bayouMCMC chain (function adapted from phytools' plotSimmap)plotSimmap.mcmc
S3 method for printing bayouFit objectsprint.bayouFit
S3 method for printing bayouMCMC objectsprint.bayouMCMC
S3 method for printing priorFn objectsprint.priorFn
S3 method for printing refFn objectsprint.refFn
S3 method for printing ssMCMC objectsprint.ssMCMC
Simulates parameters from bayou modelspriorSim
Utility function for retrieving parameters from an MCMC chainpull.pars
Calculates the alpha parameter from a QG modelQG.alpha
Calculates the sigma^2 parameter from a QG modelQG.sig2
Adds visualization of regimes to a plotregime.plot
Set the burnin proportion for bayouMCMC objectsset.burnin
A function for summarizing the state of a model after a shiftshiftSummaries
Calculate the weight matrix of a set of regimes on a phylogenysimmapW
S3 method for summarizing bayouMCMC objectssummary.bayouMCMC