{ "_id": "6a1f34aeb401979e7342846b", "Package": "OUwie", "Version": "3.02", "Date": "2026-04-16", "Title": "Analysis of Evolutionary Rates in an OU Framework", "Author": "Jeremy M. Beaulieu , Brian O'Meara\n", "Maintainer": "Jeremy Beaulieu ", "Description": "Estimates rates for continuous character evolution under\nBrownian motion and a new set of Ornstein-Uhlenbeck based\nHansen models that allow both the strength of the pull and\nstochastic motion to vary across selective regimes. Beaulieu et\nal (2012).", "URL": "https://github.com/thej022214/OUwie", "License": "GPL (>= 2)", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake libglpk-dev libgmp3-dev make libicu-dev\nlibpng-dev libxml2-dev libmpfr-dev", "Repository": "https://thej022214.r-universe.dev", "Date/Publication": "2026-04-28 02:16:04 UTC", "RemoteUrl": "https://github.com/thej022214/ouwie", "RemoteRef": "HEAD", "RemoteSha": "ef777e56099c111426a21a5c3861af78c2d244f0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 06:51:29 UTC", "User": "root" }, "MD5sum": "b76e8f8842870f5966322c042e3e56c3", "_user": "thej022214", "_type": "src", "_file": "OUwie_3.02.tar.gz", "_fileid": "1b8c031ba27eb2e55863cc0e0732421d3ce12ddbbadb11ba21f291eecebc2103", "_filesize": 3453628, "_sha256": "1b8c031ba27eb2e55863cc0e0732421d3ce12ddbbadb11ba21f291eecebc2103", "_created": "2026-05-15T06:51:29.000Z", "_published": "2026-06-02T19:53:18.632Z", "_distro": "noble", "_jobs": [ { "job": 79159068449, "time": 200, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7011757262" }, { "job": 79159068097, "time": 197, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7011756631" }, { "job": 79159068159, "time": 171, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7011763897" }, { "job": 79159068298, "time": 145, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7011764879" }, { "job": 79159067933, "time": 357, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7011711733" }, { "job": 79159067655, "time": 130, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7368281406" }, { "job": 79159068068, "time": 201, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7011757322" }, { "job": 79159068835, "time": 143, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7011744666" }, { "job": 79159068763, "time": 152, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7011746728" } ], "_buildurl": "https://github.com/r-universe/thej022214/actions/runs/25904497749", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/thej022214/ouwie", "_commit": { "id": "ef777e56099c111426a21a5c3861af78c2d244f0", "author": "Brian O'Meara ", "committer": "Brian O'Meara ", "message": "updated correction page\n", "time": 1777342564 }, "_maintainer": { "name": "Jeremy Beaulieu", "email": "jmbeauli@uark.edu", "login": "thej022214", "uuid": 10247702 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2.0", "role": "Depends" }, { "package": "ape", "role": "Depends" }, { "package": "corpcor", "role": "Depends" }, { "package": "nloptr", "role": "Depends" }, { "package": "geiger", "role": "Depends" }, { "package": "RColorBrewer", "role": "Depends" }, { "package": "igraph", "role": "Imports" }, { "package": "numDeriv", "role": "Imports" }, { "package": "phytools", "role": "Imports" }, { "package": "paleotree", "role": "Imports" }, { "package": "phangorn", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "lhs", "role": "Imports" }, { "package": "interp", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "phylolm", "role": "Imports" }, { "package": "GenSA", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "corHMM", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "expm", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "thej022214", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-32", "n": 1 }, { "week": "2025-36", "n": 2 }, { "week": "2025-38", "n": 2 }, { "week": "2025-40", "n": 1 }, { "week": "2026-10", "n": 5 }, { "week": "2026-11", "n": 1 }, { "week": "2026-13", "n": 2 }, { "week": "2026-16", "n": 2 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_stars": 10, "_contributors": [ { "user": "jboyko", "count": 84, "uuid": 44244507 }, { "user": "bomeara", "count": 62, "uuid": 1612612 }, { "user": "thej022214", "count": 2, "uuid": 10247702 }, { "user": "sborstein", "count": 2, "uuid": 15037889 }, { "user": "irmoodie", "count": 1, "uuid": 38960700 } ], "_userbio": { "uuid": 10247702, "type": "user", "name": "Jeremy Beaulieu" }, "_downloads": { "count": 509, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/OUwie" }, "_devurl": "https://github.com/thej022214/ouwie", "_searchresults": 223, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/OUwie.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/thej022214/ouwie", "_realowner": "thej022214", "_cranurl": true, "_releases": [ { "version": "1.2", "date": "2011-09-17" }, { "version": "1.10", "date": "2011-12-20" }, { "version": "1.13", "date": "2012-02-21" }, { "version": "1.15", "date": "2012-03-02" }, { "version": "1.16", "date": "2012-03-14" }, { "version": "1.17", "date": "2012-03-15" }, { "version": "1.18", "date": "2012-04-17" }, { "version": "1.21", "date": "2012-05-04" }, { "version": "1.24", "date": "2012-06-13" }, { "version": "1.27", "date": "2012-09-10" }, { "version": "1.30", "date": "2012-11-11" }, { "version": "1.31", "date": "2012-11-26" }, { "version": "1.32", "date": "2013-01-30" }, { "version": "1.33", "date": "2013-03-23" }, { "version": "1.34", "date": "2013-05-24" }, { "version": "1.35", "date": "2013-11-11" }, { "version": "1.36", "date": "2013-11-22" }, { "version": "1.37", "date": "2013-12-11" }, { "version": "1.38", "date": "2014-02-03" }, { "version": "1.39", "date": "2014-02-10" }, { "version": "1.40", "date": "2014-02-18" }, { "version": "1.41", "date": "2014-03-14" }, { "version": "1.42", "date": "2014-04-01" }, { "version": "1.43", "date": "2014-07-26" }, { "version": "1.44", "date": "2015-02-19" }, { "version": "1.45", "date": "2015-03-09" }, { "version": "1.46", "date": "2015-09-06" }, { "version": "1.48", "date": "2016-01-07" }, { "version": "1.49", "date": "2016-02-28" }, { "version": "1.50", "date": "2016-06-18" }, { "version": "1.53", "date": "2019-06-11" }, { "version": "1.57", "date": "2019-12-06" }, { "version": "2.1", "date": "2020-05-12" }, { "version": "2.2", "date": "2020-06-15" }, { "version": "2.3", "date": "2020-06-25" }, { "version": "2.4", "date": "2020-08-05" }, { "version": "2.5", "date": "2020-10-20" }, { "version": "2.6", "date": "2021-02-04" }, { "version": "2.10", "date": "2022-06-15" } ], "_exports": [ "check.identify", "fix.kappa", "getModelAvgParams", "getModelTable", "getOUParamStructure", "hOUwie", "hOUwie.fixed", "hOUwie.recon", "hOUwie.sim", "hOUwie.thorough", "hOUwie.walk", "OUwie", "OUwie.anc", "OUwie.boot", "OUwie.contour", "OUwie.dredge", "OUwie.fixed", "OUwie.format", "OUwie.sim" ], "_datasets": [ { "name": "trait", "title": "An example dataset", "object": "sim.ex", "file": "sim.ex.rda", "class": [ "data.frame" ], "fields": [ "Genus_species", "Reg", "X" ], "rows": 64, "table": true, "tojson": true }, { "name": "trait", "title": "An example dataset", "object": "tworegime", "file": "tworegime.rda", "class": [ "data.frame" ], "fields": [ "Genus_species", "Reg", "X" ], "rows": 64, "table": true, "tojson": true }, { "name": "tree", "title": "An example dataset", "object": "sim.ex", "file": "sim.ex.rda", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree", "title": "An example dataset", "object": "tworegime", "file": "tworegime.rda", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "check.identify", "title": "A test of regime identifiability", "topics": [ "check.identify" ] }, { "page": "dent_likelihood", "title": "Dents the likelihood surface This takes any values that are better (lower) than the desired negative log likelihood and reflects them across the best_neglnL + delta line, \"denting\" the likelihood surface.", "topics": [ "dent_likelihood" ] }, { "page": "dent_propose", "title": "Propose new values This proposes new values using a normal distribution centered on the original parameter values, with desired standard deviation. If any proposed values are outside the bounds, it will propose again.", "topics": [ "dent_propose" ] }, { "page": "dent_walk", "title": "Sample points from along a ridge This \"dents\" the likelihood surface by reflecting points better than a threshold back across the threshold (think of taking a hollow plastic model of a mountain and punching the top so it's a volcano). It then uses essentially a Metropolis-Hastings walk to wander around the new rim. It adjusts the proposal width so that it samples points around the desired likelihood. This is better than using the curvature at the maximum likelihood estimate since it can actually sample points in case the assumptions of the curvature method do not hold. It is better than varying one parameter at a time while holding others constant because that could miss ridges: if I am fitting 5=x+y, and get a point estimate of (3,2), the reality is that there are an infinite range of values of x and y that will sum to 5, but if I hold x constant it looks like y is estimated very precisely. Of course, one could just fully embrace the Metropolis-Hastings lifestyle and use a full Bayesian approach.", "topics": [ "dent_walk" ] }, { "page": "Example", "title": "An example dataset", "topics": [ "trait", "tree" ] }, { "page": "fix.kappa", "title": "Adjust tree for matrix condition", "topics": [ "fix.kappa" ] }, { "page": "getModelAvgParams", "title": "Model average the parameter estimates over severl hOUwie fits.", "topics": [ "getModelAvgParams" ] }, { "page": "getModelTable", "title": "Generate a table from a set of hOUwie models describing their relative fit to data.", "topics": [ "getModelTable" ] }, { "page": "getOUParamStructure", "title": "Generate a continuous model parameter structure", "topics": [ "getOUParamStructure" ] }, { "page": "hOUwie", "title": "Fit a joint model of discrete and continuous characters via maximum-likelihood.", "topics": [ "hOUwie" ] }, { "page": "hOUwie.fixed", "title": "Fit a joint model of discrete and continuous characters via maximum-likelihood with fixed regimes.", "topics": [ "hOUwie.fixed" ] }, { "page": "hOUwie.recon", "title": "Reconstruct the marginal probability of discrete node states under the hOUwie model.", "topics": [ "hOUwie.recon" ] }, { "page": "hOUwie.sim", "title": "Simulate a discrete and continuous character following a Markov and Ornstein-Uhlenbeck model.", "topics": [ "hOUwie.sim" ] }, { "page": "hOUwie.thorough", "title": "Rerun a set of hOUwie models with the best mappings of the set.", "topics": [ "hOUwie.thorough" ] }, { "page": "hOUwie.walk", "title": "Sample points from along a ridge for a hOUwie model", "topics": [ "hOUwie.walk" ] }, { "page": "OUwie", "title": "Generalized Hansen models", "topics": [ "OUwie" ] }, { "page": "OUwie.anc", "title": "Estimate ancestral states given a fitted OUwie model", "topics": [ "OUwie.anc" ] }, { "page": "OUwie.boot", "title": "Parametric bootstrap function", "topics": [ "OUwie.boot" ] }, { "page": "OUwie.contour", "title": "Generates data for contour plot of likelihood surface", "topics": [ "OUwie.contour" ] }, { "page": "OUwie.dredge", "title": "Generalized Detection of shifts in OU process", "topics": [ "OUwie.dredge" ] }, { "page": "OUwie.fixed", "title": "Generalized Hansen model likelihood calculator", "topics": [ "OUwie.fixed" ] }, { "page": "OUwie.format", "title": "Format data and tree for OUwie", "topics": [ "OUwie.format" ] }, { "page": "OUwie.sim", "title": "Generalized Hansen model simulator", "topics": [ "OUwie.sim" ] }, { "page": "plot.dentist", "title": "Plot the dented samples This will show the univariate plots of the parameter values versus the likelihood as well as bivariate plots of pairs of parameters to look for ridges.", "topics": [ "plot.dentist" ] }, { "page": "plot.OUwie.contour", "title": "Contour plot", "topics": [ "plot.OUwie.contour" ] }, { "page": "print.dentist", "title": "Print dentist print summary of output from dent_walk", "topics": [ "print.dentist" ] }, { "page": "summary.dentist", "title": "Summarize dentist Display summary of output from dent_walk", "topics": [ "summary.dentist" ] } ], "_readme": "https://github.com/thej022214/ouwie/raw/HEAD/README.md", "_rundeps": [ "ape", "bitops", "cli", "clusterGeneration", "coda", "codetools", "colorspace", "combinat", "corHMM", "corpcor", "cpp11", "data.table", "deldir", "DEoptim", "deSolve", "digest", "doParallel", "expm", "farver", "fastmatch", "foreach", "future", "future.apply", "geiger", "generics", "GenSA", "ggplot2", "globals", "glue", "gmp", "gridExtra", "gtable", "igraph", "interp", "isoband", "iterators", "jsonlite", "labeling", "lattice", "lhs", "lifecycle", "listenv", "magrittr", "maps", "MASS", "Matrix", "mnormt", "mvtnorm", "ncbit", "nlme", "nloptr", "nnet", "numDeriv", "optimParallel", "paleotree", "parallelly", "phangorn", "phylolm", "phytools", "pkgconfig", "plyr", "png", "quadprog", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "reshape2", "rlang", "Rmpfr", "RTMB", "S7", "scales", "scatterplot3d", "stringi", "stringr", "subplex", "TMB", "vctrs", "viridis", "viridisLite", "withr" ], "_vignettes": [ { "source": "calculationUpdate.Rmd", "filename": "calculationUpdate.html", "title": "Calculation Update", "author": "Priscilla Lau, Bjørn Kopperud, Sebastian Höhna, Jeremy M. Beaulieu, and Brian C. O'Meara", "engine": "knitr::rmarkdown", "headings": [ "Timeline", "Rendered equation error in original Beaulieu et al. (2012)", "Variance-covariance matrix calculation error in OUwie", "Details of the issue", "General equations", "Expectation of the trait value for species i", "Covariance between species i and j", "A simple example", "FAQ" ], "created": "2026-03-06 15:02:50", "modified": "2026-04-27 13:50:22", "commits": 8 }, { "source": "hOUwieStarterGuide.Rmd", "filename": "hOUwieStarterGuide.pdf", "title": "hOUwie User Guide", "author": ".", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Preface", "Motivation", "The Actual Guide", "The dataset", "Basic usage", "Basic usage - model comparison", "Advanced usage", "Creating a custom model set", "Troubleshooting", "FAQs", "Why does joint modeling matter?", "Why doesn't discrete plus continuous likelihood equal total likelihood (lnLDisc + lnLCont = lnLTot)?", "How long is my run going to take?", "Why is hOUwie so slow?" ], "created": "2023-01-18 15:37:51", "modified": "2023-01-19 19:00:50", "commits": 2 }, { "source": "OUwie_2.1_adds.Rmd", "filename": "OUwie_2.1_adds.pdf", "title": "New additions as of OUwie 2.1", "author": "Jeremy M. Beaulieu and Brian C. O'Meara", "engine": "knitr::rmarkdown", "headings": [ "Bug fixes and deprecated functions", "New Features", "Idenfiability tests", "Contour plots", "Ancestral trait reconstruction", "Generalized three-point structured algorithm", "Estimating tip fog", "References" ], "created": "2020-05-12 13:31:52", "modified": "2024-08-27 18:32:08", "commits": 9 } ], "_score": 8.126456113431805, "_indexed": true, "_nocasepkg": "ouwie", "_universes": [ "thej022214" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.02", "date": "2026-05-15T06:54:11.000Z", "distro": "noble", "commit": "ef777e56099c111426a21a5c3861af78c2d244f0", "fileid": "4e863d8232b4b757b2a972871c1e7b23d165e77a4a491f1d10855b472950935f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/thej022214/actions/runs/25904497749" }, { "r": "4.6.0", "os": "linux", "version": "3.02", "date": "2026-05-15T06:54:08.000Z", "distro": "noble", "commit": "ef777e56099c111426a21a5c3861af78c2d244f0", "fileid": "43a81ee5468b253e749e3a25935ae0e0b32bc1aba7e0cf83aa2ebd8aa2d7b287", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/thej022214/actions/runs/25904497749" }, { "r": "4.5.3", "os": "mac", "version": "3.02", "date": "2026-05-15T06:54:46.000Z", "commit": "ef777e56099c111426a21a5c3861af78c2d244f0", "fileid": "1ea369a0f016da28ff40c5792bc67f2b572ec1449dc26bba090c3b4fce1e48c7", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/thej022214/actions/runs/25904497749" }, { "r": "4.6.0", "os": "mac", "version": "3.02", "date": "2026-05-15T06:54:50.000Z", "commit": "ef777e56099c111426a21a5c3861af78c2d244f0", "fileid": "5ac3c467d16dff0884516ab682c3a28289fc46afd7c9061e140b8127e8383870", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/thej022214/actions/runs/25904497749" }, { "r": "4.7.0", "os": "win", "version": "3.02", "date": "2026-05-15T06:54:09.000Z", "commit": "ef777e56099c111426a21a5c3861af78c2d244f0", "fileid": "32e56d4160c31c49dfa613ab059a366966ab7d85d8670386f73d0abbbf74feb7", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/thej022214/actions/runs/25904497749" }, { "r": "4.5.3", "os": "win", "version": "3.02", "date": "2026-05-15T06:52:57.000Z", "commit": "ef777e56099c111426a21a5c3861af78c2d244f0", "fileid": "6b4e07d470918980aafa47c9f80dfe14755d0e9853b13a82989cc2fd053a2d6b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/thej022214/actions/runs/25904497749" }, { "r": "4.6.0", "os": "win", "version": "3.02", "date": "2026-05-15T06:53:04.000Z", "commit": "ef777e56099c111426a21a5c3861af78c2d244f0", "fileid": "59a7a247265b22ed898f4176a49591dc97ee92b79e356938d26bae8e1cb8714d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/thej022214/actions/runs/25904497749" }, { "r": "4.6.0", "os": "wasm", "version": "3.02", "date": "2026-06-02T19:52:59.000Z", "commit": "ef777e56099c111426a21a5c3861af78c2d244f0", "fileid": "2067a402cbe94ed5de6fd2f7f8db72699184269d0c6c639cd99a9a5bcfdcf26b", "status": "success", "buildurl": "https://github.com/r-universe/thej022214/actions/runs/25904497749" } ] }