{ "_id": "6a1156d9acfb0bcc41ceb583", "Package": "phyloTop", "Title": "Calculating Topological Properties of Phylogenies", "Date": "2025-08-26", "Version": "2.1.3", "Authors@R": "c(MK=person(\"Michelle\", \"Kendall\", email=\"michelle.kendall@ndm.ox.ac.uk\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-7344-7071\")),\nMB=person(\"Michael\", \"Boyd\", email=\"mboyd855@gmail.com\", role = c(\"aut\")),\nCC=person(\"Caroline\", \"Colijn\", role = c(\"aut\")))", "Description": "Tools for calculating and viewing topological properties\nof phylogenetic trees.", "License": "GPL-2", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "URL": "https://michellekendall.github.io/phyloTop/,\nhttps://github.com/MichelleKendall/phyloTop", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libxml2-dev\nlibssl-dev", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2025-08-26 12:34:54 UTC", "RemoteUrl": "https://github.com/MichelleKendall/phyloTop", "RemoteRef": "HEAD", "RemoteSha": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-23 07:23:57 UTC", "User": "root" }, "Author": "Michelle Kendall [aut, cre] (ORCID:\n),\nMichael Boyd [aut],\nCaroline Colijn [aut]", "Maintainer": "Michelle Kendall ", "MD5sum": "e46f4bb1352556c27e409655a6a5e077", "_user": "phylotastic", "_type": "src", "_file": "phyloTop_2.1.3.tar.gz", "_fileid": "8694630844ea1c602684bfef0d62f9691075f3a4ff1f4b994efb2ca9e589e6ea", "_filesize": 183989, "_sha256": "8694630844ea1c602684bfef0d62f9691075f3a4ff1f4b994efb2ca9e589e6ea", "_created": "2026-05-23T07:23:57.000Z", "_published": "2026-05-23T07:27:21.252Z", "_distro": "noble", "_jobs": [ { "job": 77506105529, "time": 170, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7175292669" }, { "job": 77506105515, "time": 156, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7175291520" }, { "job": 77506105516, "time": 82, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7175284590" }, { "job": 77506105520, "time": 85, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7175284800" }, { "job": 77505952269, "time": 177, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7175276689" }, { "job": 77506105522, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7175289061" }, { "job": 77506105528, "time": 98, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7175286061" }, { "job": 77506105531, "time": 108, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7175287000" }, { "job": 77506105533, "time": 99, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7175286081" } ], "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26326798405", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/MichelleKendall/phyloTop", "_commit": { "id": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "author": "Michelle Kendall ", "committer": "Michelle Kendall ", "message": "Update to satisfy CRAN requirements\n\nLinks in Rd files to external packages now explicitly defined.\n", "time": 1756211694 }, "_maintainer": { "name": "Michelle Kendall", "email": "michelle.kendall@ndm.ox.ac.uk", "login": "michellekendall", "bluesky": "@mishkendall.bsky.social", "description": "I specialise in developing and communicating statistical methods, software and results for public health protection. Based in the @BDI-pathogens group.", "uuid": 10987259, "orcid": "0000-0001-7344-7071" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2.2", "role": "Depends" }, { "package": "ape", "role": "Depends" }, { "package": "igraph", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "NHPoisson", "role": "Imports" }, { "package": "phylobase", "role": "Imports" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "michellekendall", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-35", "n": 1 } ], "_tags": [ { "name": "v2.1.3", "date": "2025-08-26" } ], "_stars": 1, "_userbio": { "uuid": 1652822, "type": "organization", "name": "phylotastic" }, "_downloads": { "count": 398, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phyloTop" }, "_mentions": 2, "_devurl": "https://github.com/michellekendall/phylotop", "_pkgdown": "https://michellekendall.github.io/phyloTop/", "_searchresults": 62, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/phyloTop.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/michellekendall/phylotop", "_realowner": "michellekendall", "_cranurl": true, "_releases": [ { "version": "1.0", "date": "2013-07-30" }, { "version": "1.1", "date": "2014-05-10" }, { "version": "1.1.1", "date": "2014-05-13" }, { "version": "2.0.0", "date": "2016-04-15" }, { "version": "2.0.1", "date": "2017-04-04" }, { "version": "2.1.0", "date": "2017-10-10" }, { "version": "2.1.1", "date": "2018-02-21" }, { "version": "2.1.2", "date": "2023-01-24" }, { "version": "2.1.3", "date": "2025-08-27" } ], "_exports": [ "avgLadder", "cherries", "colless.phylo", "configShow", "getDepths", "getLabGenealogy", "ILnumber", "ladderShow", "ladderSizes", "makeEpiRecord", "makePhyloTree", "maxHeight", "nConfig", "nodeDepth", "nodeDepthFrac", "nodeImb", "nodeImbFrac", "phyloCheck", "phyloTop", "pitchforks", "rtree4", "sackin.phylo", "splitTop", "stairs", "subtreeShow", "treeImb", "widths" ], "_help": [ { "page": "avgLadder", "title": "Average ladder size", "topics": [ "avgLadder" ] }, { "page": "cherries", "title": "Cherry number", "topics": [ "cherries" ] }, { "page": "colless.phylo", "title": "Colless number", "topics": [ "colless.phylo" ] }, { "page": "configShow", "title": "Plot a tree highlighting configurations", "topics": [ "configShow" ] }, { "page": "getDepths", "title": "Find the depth of each node", "topics": [ "getDepths" ] }, { "page": "getLabGenealogy", "title": "Create genealogy", "topics": [ "getLabGenealogy" ] }, { "page": "ILnumber", "title": "IL number", "topics": [ "ILnumber" ] }, { "page": "ladderShow", "title": "Show ladders", "topics": [ "ladderShow" ] }, { "page": "ladderSizes", "title": "Ladder sizes", "topics": [ "ladderSizes" ] }, { "page": "makeEpiRecord", "title": "Simulate epidemiological record", "topics": [ "makeEpiRecord" ] }, { "page": "maxHeight", "title": "Maximum tree height", "topics": [ "maxHeight" ] }, { "page": "nConfig", "title": "Configuration sizes in a tree", "topics": [ "nConfig" ] }, { "page": "nodeDepth", "title": "Node depth", "topics": [ "nodeDepth" ] }, { "page": "nodeDepthFrac", "title": "Fraction of nodes beyond a given depth", "topics": [ "nodeDepthFrac" ] }, { "page": "nodeImb", "title": "Node imbalance", "topics": [ "nodeImb" ] }, { "page": "nodeImbFrac", "title": "Fraction of nodes with given imbalance", "topics": [ "nodeImbFrac" ] }, { "page": "phyloTop", "title": "phyloTop: topological properties of phylogenies", "topics": [ "phyloTop" ] }, { "page": "pitchforks", "title": "Number of pitchforks", "topics": [ "pitchforks" ] }, { "page": "rtree4", "title": "Random phylo4 tree", "topics": [ "rtree4" ] }, { "page": "sackin.phylo", "title": "Sackin index", "topics": [ "sackin.phylo" ] }, { "page": "splitTop", "title": "Split topology", "topics": [ "splitTop" ] }, { "page": "stairs", "title": "Stairs", "topics": [ "stairs" ] }, { "page": "subtreeShow", "title": "Highlight a subtree", "topics": [ "subtreeShow" ] }, { "page": "treeImb", "title": "Tree imbalance", "topics": [ "treeImb" ] }, { "page": "widths", "title": "Number of nodes at each depth", "topics": [ "widths" ] } ], "_readme": "https://github.com/MichelleKendall/phyloTop/raw/HEAD/README.md", "_rundeps": [ "abind", "ade4", "ape", "askpass", "backports", "boot", "broom", "car", "carData", "cli", "colorspace", "cowplot", "cpp11", "crayon", "curl", "Deriv", "digest", "doBy", "dplyr", "farver", "forecast", "Formula", "fracdiff", "generics", "ggplot2", "glue", "gtable", "hms", "httr", "igraph", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "mgcv", "microbenchmark", "mime", "minqa", "modelr", "NHPoisson", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "pbkrtest", "phylobase", "pillar", "pixmap", "pkgconfig", "plyr", "prettyunits", "progress", "purrr", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "reshape2", "rlang", "rncl", "RNeXML", "S7", "scales", "sp", "SparseM", "stringi", "stringr", "survival", "sys", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "uuid", "vctrs", "viridisLite", "withr", "XML", "xml2", "zoo" ], "_score": 3.792391689498254, "_indexed": false, "_nocasepkg": "phylotop", "_universes": [ "phylotastic" ], "_indexurl": "https://michellekendall.r-universe.dev/phyloTop", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.1.3", "date": "2026-05-23T07:26:30.000Z", "distro": "noble", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "4d7224bf8fc1fdeaf8dae811c1ab8e4191988f10bbeb595bbcb48d0db42ea3e1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26326798405" }, { "r": "4.6.0", "os": "linux", "version": "2.1.3", "date": "2026-05-23T07:26:21.000Z", "distro": "noble", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "a93253ec81f5d54afadf3c18abca085b191cbd396958bf0d2f04c189c74628f0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26326798405" }, { "r": "4.5.3", "os": "mac", "version": "2.1.3", "date": "2026-05-23T07:25:21.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "7bc895f55c520b902d3f642d46834d00296e80ca890a229aac93f65d9cb548be", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26326798405" }, { "r": "4.6.0", "os": "mac", "version": "2.1.3", "date": "2026-05-23T07:25:23.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "cf0451dd57f18b5f520b989e5fe306003609750ec4d7ad06de602e63ff79d1fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26326798405" }, { "r": "4.6.0", "os": "wasm", "version": "2.1.3", "date": "2026-05-23T07:26:27.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "222772f479e732b75f637b289debf210676c98929874fec2d5efa21d59aa574a", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26326798405" }, { "r": "4.7.0", "os": "win", "version": "2.1.3", "date": "2026-05-23T07:25:17.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "98f3846156e767c455e92e0caf1c2ab2bde1accd9d004491f7072bc6ce471a5b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26326798405" }, { "r": "4.5.3", "os": "win", "version": "2.1.3", "date": "2026-05-23T07:25:26.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "70fd7ff080cee84dfafe586ab7cfa904f3bc3d27c753088bbbac4b4a6beacfec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26326798405" }, { "r": "4.6.0", "os": "win", "version": "2.1.3", "date": "2026-05-23T07:25:17.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "921b2b63613b4dff3f66e33913da1fc91a146b519a8690641b1d67db02ac4772", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26326798405" } ] }