{ "_id": "6ad0b891b0a1b4b4099d7533", "Package": "BMhyb", "Version": "2.1.5", "Date": "2019-08-02", "Type": "Package", "Title": "Comparative Methods for Phylogenetic Networks", "Authors@R": "c(person(\"Dwueng-Chwuan\", \"Jhwueng\", role = c(\"aut\", \"cre\"),\nemail = \"djhwueng@umail.iu.edu\"),\nperson(\"Brian C.\", \"O'Meara\", role = c(\"aut\"),\nemail = \"omeara.brian@gmail.com\"))", "Description": "Analyze the phenotypic evolution of species of hybrid\norigin on a phylogenetic network. This can detect a burst of\nvariation at the formation of a hybrid as well as an increase\nor decrease in trait value at a hybridization event. Parameters\nare estimated by maximum likelihood, and model averaging can be\ndone automatically. Users need to enter a comparative data set\nand a phylogenetic network.", "License": "GPL (>=2)", "URL": "http://github.com/bomeara/BMhyb", "BugReports": "https://github.com/bomeara/BMhyb/issues", "RoxygenNote": "7.1.1", "Encoding": "UTF-8", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibglpk-dev make libicu-dev libxml2-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2021-11-08 16:09:12 UTC", "RemoteUrl": "https://github.com/bomeara/BMhyb", "RemoteRef": "HEAD", "RemoteSha": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-15 11:21:53 UTC", "User": "root" }, "Author": "Dwueng-Chwuan Jhwueng [aut, cre],\nBrian C. O'Meara [aut]", "Maintainer": "Dwueng-Chwuan Jhwueng ", "_user": "phylotastic", "_type": "src", "_file": "BMhyb_2.1.5.tar.gz", "_fileid": "https://r2.ropensci.org/3be8a3519ea3a0b39dc55141b0b90afda34fbf46b462670f6ff26dc05a12903b", "_filesize": 193674, "_sha256": "3be8a3519ea3a0b39dc55141b0b90afda34fbf46b462670f6ff26dc05a12903b", "_expires": "2027-01-23T11:27:11.000Z", "_created": "2026-10-15T11:21:53.000Z", "_published": "2026-10-15T11:27:13.886Z", "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726399542", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116394659630, "time": 205, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11968453850" }, { "job": 116394659483, "time": 214, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11968780032" }, { "job": 116394659428, "time": 208, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11967669970" }, { "job": 116394659432, "time": 169, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11967294935" }, { "job": 116393350428, "time": 195, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11968078418" }, { "job": 116394659486, "time": 152, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11968423800" }, { "job": 116394659594, "time": 278, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11969080041" }, { "job": 116394659635, "time": 229, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11967894315" }, { "job": 116394659606, "time": 288, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11968424232" } ], "_upstream": "https://github.com/bomeara/BMhyb", "_commit": { "id": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "author": "Brian O'Meara ", "committer": "Brian O'Meara ", "message": "updating to fix failed git issue\n", "time": 1636387752 }, "_maintainer": { "name": "Dwueng-Chwuan Jhwueng", "email": "djhwueng@umail.iu.edu" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "corpcor", "role": "Imports" }, { "package": "numDeriv", "role": "Imports" }, { "package": "geiger", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "TreeSim", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "lhs", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "DEoptim", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "metR", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "phytools", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bomeara", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "bomeara", "count": 265, "uuid": 1612612 } ], "_userbio": { "uuid": 1652822, "type": "organization", "name": "phylotastic", "followers": 5 }, "_downloads": { "count": 30, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BMhyb" }, "_devurl": "https://github.com/bomeara/bmhyb", "_searchresults": 137, "_rbuild": "4.6.1", "_assets": [ "extra/BMhyb.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_releases": [ { "version": "1.5.1", "date": "2017-09-11" }, { "version": "1.5.2", "date": "2017-10-08" }, { "version": "2.1.5", "date": "2019-08-02" } ], "_exports": [ "AddHybridization", "BMhyb", "BMhybExhaustive", "ComputeLikelihood", "ComputeVCV", "ConvertEvonetToIgraphWithNodeNumbers", "CreateHybridlessEvonet", "MergeExhaustiveForPlotting", "SimulateNetwork", "SimulateTips" ], "_datasets": [ { "name": "cichlid", "title": "Cichlid dataset", "object": "cichlid", "file": "cichlid.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "nicotiana", "title": "Nicotiana dataset", "object": "nicotiana", "file": "nicotiana.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "AddHybridization", "title": "Add hybrid events to a phy.graph", "topics": [ "AddHybridization" ] }, { "page": "BMhyb", "title": "Optimize model", "topics": [ "BMhyb" ] }, { "page": "BMhybExhaustive", "title": "Exhaustively evaluate models", "topics": [ "BMhybExhaustive" ] }, { "page": "cichlid", "title": "Cichlid dataset", "topics": [ "cichlid" ] }, { "page": "ComputeLikelihood", "title": "Compute the likelihood for a set of parameters", "topics": [ "ComputeLikelihood" ] }, { "page": "ComputeVCV", "title": "Compute the variance-covariance matrix", "topics": [ "ComputeVCV" ] }, { "page": "ConvertEvonetToIgraphWithNodeNumbers", "title": "Convert an evonet object into igraph", "topics": [ "ConvertEvonetToIgraphWithNodeNumbers" ] }, { "page": "CreateHybridlessEvonet", "title": "Convert phylo object to evonet", "topics": [ "CreateHybridlessEvonet" ] }, { "page": "GetConvexHull", "title": "Get convex hull at a given threshold", "topics": [ "GetConvexHull" ] }, { "page": "MergeExhaustiveForPlotting", "title": "Function to merge adaptive sampling sims for plotting", "topics": [ "MergeExhaustiveForPlotting" ] }, { "page": "nicotiana", "title": "Nicotiana dataset", "topics": [ "nicotiana" ] }, { "page": "plot.BMhybExhaustiveResult", "title": "Plot BMhybExhaustive result", "topics": [ "plot.BMhybExhaustiveResult" ] }, { "page": "plot.BMhybResult", "title": "Plot BMhyb result", "topics": [ "plot.BMhybResult" ] }, { "page": "print.BMhybExhaustiveResult", "title": "Print BMhybExhaustive result", "topics": [ "print.BMhybExhaustiveResult" ] }, { "page": "print.BMhybResult", "title": "Print BMhyb result", "topics": [ "print.BMhybResult" ] }, { "page": "SimulateNetwork", "title": "Simulate a phylogenetic network", "topics": [ "SimulateNetwork" ] }, { "page": "SimulateTips", "title": "Simulate trait data", "topics": [ "SimulateTips" ] }, { "page": "summary.BMhybExhaustiveResult", "title": "Summarize BMhybExhaustive result", "topics": [ "summary.BMhybExhaustiveResult" ] }, { "page": "summary.BMhybResult", "title": "Summarize BMhyb result", "topics": [ "summary.BMhybResult" ] } ], "_readme": "https://github.com/bomeara/BMhyb/raw/HEAD/README.md", "_rundeps": [ "ape", "backports", "cachem", "checkmate", "class", "classInt", "cli", "clusterGeneration", "coda", "codetools", "colorspace", "combinat", "corpcor", "cowplot", "cpp11", "data.table", "DBI", "DEoptim", "deSolve", "digest", "doParallel", "e1071", "expm", "farver", "fastmap", "foreach", "Formula", "formula.tools", "future", "future.apply", "geiger", "generics", "ggplot2", "globals", "glue", "gridExtra", "gtable", "igraph", "isoband", "iterators", "KernSmooth", "labeling", "lattice", "lhs", "lifecycle", "listenv", "lubridate", "magrittr", "maps", "MASS", "Matrix", "memoise", "metR", "mnormt", "mvtnorm", "ncbit", "nlme", "numDeriv", "operator.tools", "optimParallel", "osqp", "parallelly", "phangorn", "phytools", "pkgconfig", "plyr", "progressr", "proxy", "purrr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "s2", "S7", "scales", "scatterplot3d", "sf", "stringi", "stringr", "subplex", "timechange", "TreeSim", "units", "vctrs", "viridis", "viridisLite", "withr", "wk" ], "_score": 2.8356905714924254, "_indexed": false, "_nocasepkg": "bmhyb", "_universes": [ "phylotastic" ], "_indexurl": "https://bomeara.r-universe.dev/BMhyb", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.1.5", "date": "2026-10-15T11:23:54.000Z", "distro": "resolute", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/1acc6b8864e8d5084511087d838f0db4a321f2bb8e80d61d2b2a195cbaa916ca", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726399542" }, { "r": "4.6.1", "os": "linux", "version": "2.1.5", "date": "2026-10-15T11:24:10.000Z", "distro": "resolute", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/bb81960d3ec5199488264b951a6462d5834ea23118e2d5a49e597d03151bd4ec", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726399542" }, { "r": "4.5.3", "os": "mac", "version": "2.1.5", "date": "2026-10-15T11:24:10.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/a359a6f37ed0f8f04e86e4233c078b3b841343fe28f6085d091ed1c7991e569a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726399542" }, { "r": "4.6.1", "os": "mac", "version": "2.1.5", "date": "2026-10-15T11:23:39.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/80c7f4b52990e8e8f8b8786387aa62a0807d461f3f8abf429d796a86be251601", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726399542" }, { "r": "4.6.0", "os": "wasm", "version": "2.1.5", "date": "2026-10-15T11:24:34.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/76740ad0e1cccbee07d7a22d241e8d5dd106a6edaa64c2c1cbe6e0a771b9a0d0", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726399542" }, { "r": "4.7.0", "os": "win", "version": "2.1.5", "date": "2026-10-15T11:23:24.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/7ae96521a970489c4810cec5b7e0b27aa024877af0dcbe87ad2a6455211dbca9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726399542" }, { "r": "4.5.3", "os": "win", "version": "2.1.5", "date": "2026-10-15T11:23:18.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/08a6a8a3bfcf5b7e2fc30e8cefb98c66a8f23113d270b50d8253dcf6b006aa07", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726399542" }, { "r": "4.6.1", "os": "win", "version": "2.1.5", "date": "2026-10-15T11:23:06.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/364c21ff478dedd0fe3b66629f52f89dfa17f2552d447cdb7c8ea1affa5ebf47", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/38726399542" } ] }