{ "_id": "6a5013b9c30f0868bbf1f88f", "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": "2026-07-09 21:24:06 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/916ece55e135bb4a34ec8ab8b5253108ab0254be814fc42a4298e7fba398b654", "_filesize": 198839, "_sha256": "916ece55e135bb4a34ec8ab8b5253108ab0254be814fc42a4298e7fba398b654", "_expires": "2026-10-17T21:33:43.000Z", "_created": "2026-07-09T21:24:06.000Z", "_published": "2026-07-09T21:33:45.490Z", "_jobs": [ { "job": 86232283709, "time": 300, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8211983309" }, { "job": 86232283702, "time": 260, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8211970327" }, { "job": 86232283672, "time": 208, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8212065156" }, { "job": 86232283697, "time": 161, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8212051735" }, { "job": 86231532739, "time": 238, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8211881245" }, { "job": 86232283648, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8211925153" }, { "job": 86232283727, "time": 326, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8211992751" }, { "job": 86232283728, "time": 260, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8211969988" }, { "job": 86232283707, "time": 319, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8211990118" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051024630", "_status": "success", "_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": 9, "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/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_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" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.1.5", "date": "2026-07-09T21:26:42.000Z", "distro": "resolute", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/8693ac706914696c2ebe0af0d8f4bddfe9b250ef0fe5d5198a59bb88824882ce", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051024630" }, { "r": "4.6.1", "os": "linux", "version": "2.1.5", "date": "2026-07-09T21:26:40.000Z", "distro": "resolute", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/3aaf213ea91985a150eb9b8b5fc328124105647a0c3c26e958b43a32779ba9ba", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051024630" }, { "r": "4.5.3", "os": "mac", "version": "2.1.5", "date": "2026-07-09T21:31:27.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/483b2033039a04920028729cc6899cd93c686b942a8ad9d945a059ce446b5b88", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051024630" }, { "r": "4.6.1", "os": "mac", "version": "2.1.5", "date": "2026-07-09T21:31:19.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/2aeeef6040e3dae22d7274b5aeb3bcc271d5888bb073de1c748ae135bf8f26f2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051024630" }, { "r": "4.6.0", "os": "wasm", "version": "2.1.5", "date": "2026-07-09T21:26:31.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/49b6c6f0a41bbcbf92aaac529ad3e16d127d01bd3f01d82e989ce73afb590f16", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051024630" }, { "r": "4.7.0", "os": "win", "version": "2.1.5", "date": "2026-07-09T21:25:26.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/a33624add8817dd987a5a1c3ababa5328fccbaf151cd0831574bdaff5da20862", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051024630" }, { "r": "4.5.3", "os": "win", "version": "2.1.5", "date": "2026-07-09T21:25:28.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/e7be400c0538d38375818d0d14941eec05eea66ade32f6a347ca33d3f59c0df1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051024630" }, { "r": "4.6.1", "os": "win", "version": "2.1.5", "date": "2026-07-09T21:25:44.000Z", "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8", "fileid": "https://r2.ropensci.org/af999e28b1296ab6512d2be5c880b90775d42558921a98508b54819471a27d46", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051024630" } ] }