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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

bayou_2.3.0.tar.gz
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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'))

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

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

On CRAN:

openblas cpp

4.60 score 22 stars 60 scripts 51 downloads 43 exports 45 dependencies

Last updated 6 months agofrom:b57d7eaff3. Checks:OK: 9. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 25 2024
R-4.5-win-x86_64	OK	Nov 25 2024
R-4.5-linux-x86_64	OK	Nov 25 2024
R-4.4-win-x86_64	OK	Nov 25 2024
R-4.4-mac-x86_64	OK	Nov 25 2024
R-4.4-mac-aarch64	OK	Nov 25 2024
R-4.3-win-x86_64	OK	Nov 25 2024
R-4.3-mac-x86_64	OK	Nov 25 2024
R-4.3-mac-aarch64	OK	Nov 25 2024

Exports:bayou.checkModel bayou.lik bayou.makeMCMC bayou.mcmc bayou2OUwie cdpois combine.chains dataSim dhalfcauchy dloc dsb gelman.R identifyBranches load.bayou Lposterior make.powerposteriorFn make.prior make.refFn makeBayouModel makeTransparent OU.lik OUphenogram OUwie2bayou parmap.W pars2simmap phalfcauchy phenogram.density plotBayoupars plotBranchHeatMap plotOUtreesim plotRegimes plotShiftSummaries plotSimmap.mcmc priorSim pull.pars qhalfcauchy rdpois rhalfcauchy rloc rsb set.burnin shiftSummaries simmapW

Dependencies:ape assertthat cli clusterGeneration coda codetools colorspace combinat cpp11 denstrip DEoptim deSolve digest doParallel expm fitdistrplus foreach geiger generics glue igraph iterators lattice lifecycle magrittr maps MASS Matrix mnormt mvtnorm ncbit nlme numDeriv optimParallel phangorn phytools pkgconfig quadprog Rcpp RcppArmadillo rlang scatterplot3d subplex survival vctrs

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies	bayou-package bayou
Function for checking parameter lists, prior and models are consistent and error-free	bayou.checkModel
Function for calculating likelihood of an OU model in bayou using the threepoint algorithm	bayou.lik
Revision of bayou.mcmc that only makes the mcmc loop function, rather than running it itself.	bayou.makeMCMC
Converts bayou data into OUwie format	bayou2OUwie
Conditional Poisson distribution	cdpois rdpois
Combine mcmc chains	combine.chains
Simulates data from bayou models	dataSim
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 branch	dloc rloc
Probability density functions for bayou	dsb rsb
Calculate Gelman's R statistic	gelman.R
Identify shifts on branches of a phylogenetic tree	identifyBranches
Loads a bayou object	load.bayou
Return a posterior of shift locations	Lposterior
Makes a power posterior function in bayou	make.powerposteriorFn
Make a prior function for bayou	make.prior
Make a reference function in bayou	make.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 Models	model.OU
Function for calculating likelihood of an OU model in bayou using pruning algorithm or matrix inversion	OU.lik
Calculates the alpha and sigma^2 from a parameter list with supplied phylogenetic half-life and stationary variance	OU.repar
Experimental phenogram plotting function for set of model of model parameters	OUphenogram
Converts OUwie data into bayou format	OUwie2bayou
Calculate the weight matrix of a set of regimes on a phylogeny	parmap.W
Convert a bayou parameter list into a simmap formatted phylogeny	pars2simmap
Plot a pheongram with the posterior density for optima values	phenogram.density
S3 method for plotting bayouMCMC objects	plot.bayouMCMC
S3 method for plotting ssMCMC objects	plot.ssMCMC
Plot parameter list as a simmap tree	plotBayoupars
A function to plot a heatmap of reconstructed parameter values on the branches of the tree	plotBranchHeatMap
A function to visualize a multi-optimum OU process evolving on a phylogeny	plotOUtreesim
Function to plot the regimes from a simmap tree	plotRegimes
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 objects	print.bayouFit
S3 method for printing bayouMCMC objects	print.bayouMCMC
S3 method for printing priorFn objects	print.priorFn
S3 method for printing refFn objects	print.refFn
S3 method for printing ssMCMC objects	print.ssMCMC
Simulates parameters from bayou models	priorSim
Utility function for retrieving parameters from an MCMC chain	pull.pars
Calculates the alpha parameter from a QG model	QG.alpha
Calculates the sigma^2 parameter from a QG model	QG.sig2
Adds visualization of regimes to a plot	regime.plot
Set the burnin proportion for bayouMCMC objects	set.burnin
A function for summarizing the state of a model after a shift	shiftSummaries
Calculate the weight matrix of a set of regimes on a phylogeny	simmapW
S3 method for summarizing bayouMCMC objects	summary.bayouMCMC