{ "_id": "6a1f29f0b401979e7342426c", "Package": "extendedSurface", "Type": "Package", "Title": "Fit Complex Multi-OU Models by Extending SURFACE and Providing\nan Interface with OUwie", "Version": "0.1.0", "Authors@R": "person(\"Nicolas\", \"Mongiardino Koch\", email = \"mongiar@hotmail.com\", role = c(\"aut\", \"cre\"))", "Description": "Multi Ornstein Uhlenbeck (OUM) models are routinely\nemployed to describe the phenotypic evolution of clades across\na macroevolutionary adaptive landscape. Multiple\nimplementations exist, including those that require an a priori\nassigment of lineages to adaptive regimes (e.g., OUwie), and\nthose that infer the location of such regimes shifts (e.g.,\nSURFACE). However, SURFACE has been found to favor overly\ncomplex models, which is likely a consequence of fixing a\nsingle rate of evolution and force of attraction for the entire\ntree. Although these parameters can be optimized for each\nregime by using the SURFACE output as the set of regime shifts\nrequired by OUwie, such complex models often fail to be\noptimized. extendedSurface provides a solution by continuing\nthe backwards phase of SURFACE, merging regimes and generating\nsimpler (yet suboptimal) multiOU models. These are then fed to\nOUwie, where parameters for each regime can be independetly\noptimized. Using simpler OUM models as starting points improves\nthe probability of successful model fitting. The resulting\nmodels are more realistic, and have been found to be favored\nover others using empirical comparative datasets. The package\nallows the user to decide which models should be fit (OUMA,\nOUMV, OUMVA, with and without stationary root state), and plots\nthe fit of these against those explored by SURFACE to easily\ncompare model fit. Additionally, several approaches to record\nand plot the evolutionary dynamics of discrete traits through\ntime are also implemented.", "URL": "http://github.com/mongiardino/extendedSurface", "BugReports": "https://github.com/mongiardino/extendedSurface/issues", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.0", "Config/pak/sysreqs": "cmake libglpk-dev libgmp3-dev make libicu-dev\nlibpng-dev libxml2-dev libmpfr-dev", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2021-07-01 22:50:07 UTC", "RemoteUrl": "https://github.com/mongiardino/extendedSurface", "RemoteRef": "HEAD", "RemoteSha": "de922e5de538cb2cc0ad28ab5ce48ff964191444", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 19:02:34 UTC", "User": "root" }, "Author": "Nicolas Mongiardino Koch [aut, cre]", "Maintainer": "Nicolas Mongiardino Koch ", "MD5sum": "60cdefeba550d796d34c847471b1fc18", "_user": "phylotastic", "_type": "src", "_file": "extendedSurface_0.1.0.tar.gz", "_fileid": "770ed861c7e689f2559a13eed5669c3fa145714dda24de4dbab82e62422307b7", "_filesize": 2433797, "_sha256": "770ed861c7e689f2559a13eed5669c3fa145714dda24de4dbab82e62422307b7", "_created": "2026-06-02T19:02:34.000Z", "_published": "2026-06-02T19:07:28.188Z", "_distro": "noble", "_jobs": [ { "job": 79150246720, "time": 198, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7367286148" }, { "job": 79150246712, "time": 237, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7367299907" }, { "job": 79150246730, "time": 98, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7367300438" }, { "job": 79150246918, "time": 127, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7367306558" }, { "job": 79149581071, "time": 208, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7367213251" }, { "job": 79150246650, "time": 133, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7367261847" }, { "job": 79150246877, "time": 135, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7367262819" }, { "job": 79150246994, "time": 130, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7367260812" }, { "job": 79150246910, "time": 130, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7367260931" } ], "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26841494405", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/mongiardino/extendedSurface", "_commit": { "id": "de922e5de538cb2cc0ad28ab5ce48ff964191444", "author": "Nicolás Mongiardino Koch ", "committer": "GitHub ", "message": "Merge pull request #1 from bomeara/master\n\nkeeping dimension of data when subsetting", "time": 1625179807 }, "_maintainer": { "name": "Nicolas Mongiardino Koch", "email": "mongiar@hotmail.com" }, 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