{ "_id": "6ad0b963b0a1b4b4099d7622", "Type": "Package", "Package": "bayou", "Title": "Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies", "Version": "2.3.2", "Date": "2026-02-04", "Authors@R": "c(\nperson(\"Josef C.\", \"Uyeda\", ,\"juyeda@vt.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-4624-9680\")),\nperson(\"Jon\", \"Eastman\", role = \"ctb\"),\nperson(\"Luke\", \"Harmon\", , \"lukeh@uidaho.edu\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4985-5750\")),\nperson(\"Abhishek\", \"Hari\", , \"abhihari010@vt.edu\", role = \"ctb\")\n)", "Maintainer": "Josef C. Uyeda ", "Description": "Fits and simulates multi-optima Ornstein-Uhlenbeck models\nto phylogenetic comparative data using Bayesian reversible-jump\nmethods. See Uyeda and Harmon (2014)\n.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libglpk-dev make libxml2-dev", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2026-02-11 18:08:46 UTC", "RemoteUrl": "https://github.com/uyedaj/bayou", "RemoteRef": "HEAD", "RemoteSha": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-15 11:22:20 UTC", "User": "root" }, "Author": "Josef C. Uyeda [aut, cre] (ORCID:\n),\nJon Eastman [ctb],\nLuke Harmon [ctb] (ORCID: ),\nAbhishek Hari [ctb]", "_user": "phylotastic", "_type": "src", "_file": "bayou_2.3.2.tar.gz", "_fileid": "https://r2.ropensci.org/e5fb69047b25e76cd2e3edd5b2933ffea7a95338fa816db2c2fb032b2c628ad5", "_filesize": 287814, "_sha256": "e5fb69047b25e76cd2e3edd5b2933ffea7a95338fa816db2c2fb032b2c628ad5", "_expires": "2027-01-23T11:30:41.000Z", "_created": "2026-10-15T11:22:20.000Z", "_published": "2026-10-15T11:30:43.452Z", "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116395030041, "time": 146, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11968553968" }, { "job": 116395030104, "time": 169, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11967464965" }, { "job": 116395030004, "time": 132, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11967444943" }, { "job": 116395030052, "time": 144, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11967589690" }, { "job": 116395030182, "time": 103, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11968529140" }, { "job": 116395029957, "time": 368, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11968264889" }, { "job": 116395030388, "time": 175, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11968189566" }, { "job": 116395029982, "time": 278, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11968239841" }, { "job": 116393491043, "time": 227, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11967773882" }, { "job": 116395029917, "time": 121, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11967789313" }, { "job": 116395030151, "time": 237, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11968765367" }, { "job": 116395029998, "time": 197, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11967964565" }, { "job": 116395030336, "time": 135, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11968139036" }, { "job": 116395030187, "time": 261, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11968860279" }, { "job": 116395030214, "time": 122, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11967784318" } ], "_upstream": "https://github.com/uyedaj/bayou", "_commit": { "id": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "author": "Josef Uyeda ", "committer": "GitHub ", "message": "Update R-CMD-check.yaml\n\nCheck with LTO support", "time": 1770833326 }, "_maintainer": { "name": "Josef C. Uyeda", "email": "juyeda@vt.edu", "login": "uyedaj", "description": "", "uuid": 2087512, "orcid": "0000-0003-4624-9680" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "ape", "version": ">= 3.0-6", "role": "Depends" }, { "package": "coda", "role": "Depends" }, { "package": "geiger", "version": ">= 2.0", "role": "Depends" }, { "package": "phytools", "role": "Depends" }, { "package": "R", "version": ">= 2.15.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "assertthat", "role": "Imports" }, { "package": "denstrip", "role": "Imports" }, { "package": "fitdistrplus", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "mnormt", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.10.3", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "doParallel", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "uyedaj", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-07", "n": 6 } ], "_tags": [], "_stars": 25, "_contributors": [ { "user": "uyedaj", "count": 131, "uuid": 2087512 }, { "user": "macroevolab", "count": 30, "uuid": 43342043 }, { "user": "abhihari10", "count": 7, "uuid": 187028447 }, { "user": "caetanods", "count": 2, "uuid": 3672680 }, { "user": "jeroen", "count": 1, "uuid": 216319 } ], "_userbio": { "uuid": 1652822, "type": "organization", "name": "phylotastic", "followers": 5 }, "_downloads": { "count": 449, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bayou" }, "_devurl": "https://github.com/uyedaj/bayou", "_searchresults": 76, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/bayou.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/uyedaj/bayou", "_realowner": "uyedaj", "_cranurl": true, "_releases": [ { "version": "1.0", "date": "2014-07-18" }, { "version": "1.0.1", "date": "2014-07-31" }, { "version": "1.1.0", "date": "2015-10-25" }, { "version": "2.1", "date": "2018-06-07" }, { "version": "2.1.1", "date": "2018-10-09" }, { "version": "2.3.1", "date": "2025-06-10" }, { "version": "2.3.2", "date": "2026-02-16" } ], "_exports": [ "bayou.checkModel", "bayou.lik", "bayou.makeMCMC", "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" ], "_help": [ { "page": "bayou-package", "title": "Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies", "topics": [ "bayou-package", "bayou" ] }, { "page": "bayou.checkModel", "title": "Function for checking parameter lists, prior and models are consistent and error-free", "topics": [ "bayou.checkModel" ] }, { "page": "bayou.lik", "title": "Function for calculating likelihood of an OU model in bayou using the threepoint algorithm", "topics": [ "bayou.lik" ] }, { "page": "bayou.makeMCMC", "title": "Builds a bayouMCMCFn object that can run MCMC and stepping stone analyses.", "topics": [ "bayou.makeMCMC" ] }, { "page": "bayou2OUwie", "title": "Converts bayou data into OUwie format", "topics": [ "bayou2OUwie" ] }, { "page": "cdpois", "title": "Conditional Poisson distribution", "topics": [ "cdpois", "rdpois" ] }, { "page": "combine.chains", "title": "Combine mcmc chains", "topics": [ "combine.chains" ] }, { "page": "dataSim", "title": "Simulates data from bayou models", "topics": [ "dataSim" ] }, { "page": "dhalfcauchy", "title": "Half cauchy distribution taken from the R package LaplacesDemon (Hall, 2012).", "topics": [ "dhalfcauchy", "phalfcauchy", "qhalfcauchy", "rhalfcauchy" ] }, { "page": "dloc", "title": "Probability density function for the location of the shift along the branch", "topics": [ "dloc", "rloc" ] }, { "page": "dsb", "title": "Probability density functions for bayou", "topics": [ "dsb", "rsb" ] }, { "page": "gelman.R", "title": "Calculate Gelman's R statistic", "topics": [ "gelman.R" ] }, { "page": "identifyBranches", "title": "Identify shifts on branches of a phylogenetic tree", "topics": [ "identifyBranches" ] }, { "page": "load.bayou", "title": "Loads a bayou object", "topics": [ "load.bayou" ] }, { "page": "Lposterior", "title": "Return a posterior of shift locations", "topics": [ "Lposterior" ] }, { "page": "make.powerposteriorFn", "title": "Makes a power posterior function in bayou", "topics": [ "make.powerposteriorFn" ] }, { "page": "make.prior", "title": "Make a prior function for bayou", "topics": [ "make.prior" ] }, { "page": "make.refFn", "title": "Make a reference function in bayou", "topics": [ "make.refFn" ] }, { "page": "makeBayouModel", "title": "This function makes a bayou model object that can be used for customized allometric regression models.", "topics": [ "makeBayouModel" ] }, { "page": "makeTransparent", "title": "Make a color transparent (Taken from an answer on StackOverflow by Nick Sabbe)", "topics": [ "makeTransparent" ] }, { "page": "model.OU", "title": "Bayou Models", "topics": [ "model.OU" ] }, { "page": "OU.lik", "title": "Function for calculating likelihood of an OU model in bayou using pruning algorithm or matrix inversion", "topics": [ "OU.lik" ] }, { "page": "OU.repar", "title": "Calculates the alpha and sigma^2 from a parameter list with supplied phylogenetic half-life and stationary variance", "topics": [ "OU.repar" ] }, { "page": "OUphenogram", "title": "Experimental phenogram plotting function for set of model of model parameters", "topics": [ "OUphenogram" ] }, { "page": "OUwie2bayou", "title": "Converts OUwie data into bayou format", "topics": [ "OUwie2bayou" ] }, { "page": "parmap.W", "title": "Calculate the weight matrix of a set of regimes on a phylogeny", "topics": [ "parmap.W" ] }, { "page": "pars2simmap", "title": "Convert a bayou parameter list into a simmap formatted phylogeny", "topics": [ "pars2simmap" ] }, { "page": "phenogram.density", "title": "Plot a pheongram with the posterior density for optima values", "topics": [ "phenogram.density" ] }, { "page": "plot.bayouMCMC", "title": "S3 method for plotting bayouMCMC objects", "topics": [ "plot.bayouMCMC" ] }, { "page": "plot.ssMCMC", "title": "S3 method for plotting ssMCMC objects", "topics": [ "plot.ssMCMC" ] }, { "page": "plotBayoupars", "title": "Plot parameter list as a simmap tree", "topics": [ "plotBayoupars" ] }, { "page": "plotBranchHeatMap", "title": "A function to plot a heatmap of reconstructed parameter values on the branches of the tree", "topics": [ "plotBranchHeatMap" ] }, { "page": "plotOUtreesim", "title": "A function to visualize a multi-optimum OU process evolving on a phylogeny", "topics": [ "plotOUtreesim" ] }, { "page": "plotRegimes", "title": "Function to plot the regimes from a simmap tree", "topics": [ "plotRegimes" ] }, { "page": "plotShiftSummaries", "title": "A function to plot a list produced by 'shiftSummaries'", "topics": [ "plotShiftSummaries" ] }, { "page": "plotSimmap.mcmc", "title": "Plot a phylogenetic tree with posterior probabilities from a bayouMCMC chain (function adapted from phytools' plotSimmap)", "topics": [ "plotSimmap.mcmc" ] }, { "page": "print.bayouFit", "title": "S3 method for printing bayouFit objects", "topics": [ "print.bayouFit" ] }, { "page": "print.bayouMCMC", "title": "S3 method for printing bayouMCMC objects", "topics": [ "print.bayouMCMC" ] }, { "page": "print.priorFn", "title": "S3 method for printing priorFn objects", "topics": [ "print.priorFn" ] }, { "page": "print.refFn", "title": "S3 method for printing refFn objects", "topics": [ "print.refFn" ] }, { "page": "print.ssMCMC", "title": "S3 method for printing ssMCMC objects", "topics": [ "print.ssMCMC" ] }, { "page": "priorSim", "title": "Simulates parameters from bayou models", "topics": [ "priorSim" ] }, { "page": "pull.pars", "title": "Utility function for retrieving parameters from an MCMC chain", "topics": [ "pull.pars" ] }, { "page": "QG.alpha", "title": "Calculates the alpha parameter from a QG model", "topics": [ "QG.alpha" ] }, { "page": "QG.sig2", "title": "Calculates the sigma^2 parameter from a QG model", "topics": [ "QG.sig2" ] }, { "page": "regime.plot", "title": "Adds visualization of regimes to a plot", "topics": [ "regime.plot" ] }, { "page": "set.burnin", "title": "Set the burnin proportion for bayouMCMC objects", "topics": [ "set.burnin" ] }, { "page": "shiftSummaries", "title": "A function for summarizing the state of a model after a shift", "topics": [ "shiftSummaries" ] }, { "page": "simmapW", "title": "Calculate the weight matrix of a set of regimes on a phylogeny", "topics": [ "simmapW" ] }, { "page": "summary.bayouMCMC", "title": "S3 method for summarizing bayouMCMC objects", "topics": [ "summary.bayouMCMC" ] } ], "_readme": "https://github.com/uyedaj/bayou/raw/HEAD/README.md", "_rundeps": [ "ape", "assertthat", "backports", "checkmate", "cli", "clusterGeneration", "coda", "codetools", "colorspace", "combinat", "cpp11", "denstrip", "DEoptim", "deSolve", "digest", "doParallel", "expm", "fitdistrplus", "foreach", "future", "future.apply", "geiger", "generics", "globals", "glue", "igraph", "iterators", "lattice", "lifecycle", "listenv", "magrittr", "maps", "MASS", "Matrix", "mnormt", "mvtnorm", "ncbit", "nlme", "numDeriv", "optimParallel", "osqp", "parallelly", "phangorn", "phytools", "pkgconfig", "progressr", "Rcpp", "RcppArmadillo", "rlang", "S7", "scatterplot3d", "subplex", "survival", "vctrs" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 5.57978359661681, "_indexed": false, "_nocasepkg": "bayou", "_universes": [ "phylotastic" ], "_indexurl": "https://uyedaj.r-universe.dev/bayou", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.3.2", "date": "2026-10-15T11:24:43.000Z", "distro": "resolute", "arch": "aarch64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/5a68376cff9c92d17e719c2ce65c51a37e45901102bd3e47dca4f0e78cdd69bb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.7.0", "os": "linux", "version": "2.3.2", "date": "2026-10-15T11:24:46.000Z", "distro": "resolute", "arch": "x86_64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/2b1d6b9b770ac57b05c930973ab3e9305a56da51b64f0510325e6cbda67e25dd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.6.1", "os": "linux", "version": "2.3.2", "date": "2026-10-15T11:24:26.000Z", "distro": "resolute", "arch": "aarch64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/3537f789ad20e4d1bd09bb9d3dae8535a16215f99f4d41fc09d78296f7156e44", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.6.1", "os": "linux", "version": "2.3.2", "date": "2026-10-15T11:24:37.000Z", "distro": "resolute", "arch": "x86_64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/e70fd309d349a631d19db743de107d272d0b8863c359140a205e482582c2ed6f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.5.3", "os": "mac", "version": "2.3.2", "date": "2026-10-15T11:25:29.000Z", "arch": "aarch64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/34af0cf756fbdc41e13f74cb8f45a82335695b6dae2307101d52666cab105fc3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.5.3", "os": "mac", "version": "2.3.2", "date": "2026-10-15T11:27:36.000Z", "arch": "x86_64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/646cbe8e8796cf410eeab8f56bcf6ab8da54bccdd706191846953c2fc3a9032b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.6.1", "os": "mac", "version": "2.3.2", "date": "2026-10-15T11:26:20.000Z", "arch": "aarch64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/0dbbc1364e22bd9ee45d9488db1434ac3e883a311938508c8b59a5b763f8449b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.6.1", "os": "mac", "version": "2.3.2", "date": "2026-10-15T11:26:56.000Z", "arch": "x86_64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/2ba0e924092edf89d289a3707b715aa36b8305c9237b541452c8c00fd74dc432", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.6.0", "os": "wasm", "version": "2.3.2", "date": "2026-10-15T11:24:44.000Z", "arch": "emscripten", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/1bc338b00eb4ebc44c3b95aa45333462a5b1c5b12af4add51747aa1ab2240a3e", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.7.0", "os": "win", "version": "2.3.2", "date": "2026-10-15T11:25:38.000Z", "arch": "aarch64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/5321147cd54b6f5b956c5e3bde3c5972e56d7c6dcbaa11f58b66dbf52147bcdc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.7.0", "os": "win", "version": "2.3.2", "date": "2026-10-15T11:23:58.000Z", "arch": "x86_64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/5bdaadf56b0ee58756ea55d7e838c09882ff06aca3035247c20a2d7fae53a1e8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.5.3", "os": "win", "version": "2.3.2", "date": "2026-10-15T11:23:50.000Z", "arch": "x86_64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/df54bdea15ec132720e5c10e272d38d4866a5ee0745cdc999d9500f9a70ada08", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.6.1", "os": "win", "version": "2.3.2", "date": "2026-10-15T11:26:09.000Z", "arch": "aarch64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/c7edb84049f6f9e42c2fda7e65d851259f52ad08dc09f442b14a37f5a14bdf85", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" }, { "r": "4.6.1", "os": "win", "version": "2.3.2", "date": "2026-10-15T11:23:52.000Z", "arch": "x86_64", "commit": "e8bf7f7f0c85cca83d8be4cd584cf3dd3318157d", "fileid": "https://r2.ropensci.org/968cfa08b8846d7f5402ace8c51e744f498933b5671cd9d7b1ae271f7e667b07", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726440561" } ] }