{ "_id": "6a115760acfb0bcc41ceb62e", "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://michellekendall.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 07:25:48 UTC", "User": "root" }, "Author": "Michelle Kendall [aut, cre] (ORCID:\n),\nMichael Boyd [aut],\nCaroline Colijn [aut]", "Maintainer": "Michelle Kendall ", "MD5sum": "0fd719e2864ce3059fecb0dcc85645e8", "_user": "michellekendall", "_type": "src", "_file": "phyloTop_2.1.3.tar.gz", "_fileid": "8fc867e346b8669cc031d5d493077a1782f9465f221615ae5b989c0b33984c8f", "_filesize": 184055, "_sha256": "8fc867e346b8669cc031d5d493077a1782f9465f221615ae5b989c0b33984c8f", "_created": "2026-05-23T07:25:48.000Z", "_published": "2026-05-23T07:29:36.418Z", "_distro": "noble", "_jobs": [ { "job": 77506198001, "time": 176, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7175303384" }, { "job": 77506198122, "time": 185, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7175304211" }, { "job": 77506197998, "time": 146, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7175298885" }, { "job": 77506198005, "time": 130, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7175297506" }, { "job": 77506045000, "time": 183, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7175287102" }, { "job": 77506197995, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7175299343" }, { "job": 77506198080, "time": 111, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7175297669" }, { "job": 77506198083, "time": 113, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7175297730" }, { "job": 77506198063, "time": 112, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7175297607" } ], "_buildurl": "https://github.com/r-universe/michellekendall/actions/runs/26326828025", "_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": true, "_usedby": 0, "_updates": [ { "week": "2025-35", "n": 1 } ], "_tags": [ { "name": "v2.1.3", "date": "2025-08-26" } ], "_stars": 1, "_userbio": { "uuid": 10987259, "type": "user", "name": "Michelle Kendall", "description": "I specialise in developing and communicating statistical methods, software and results for public health protection. Based in the @BDI-pathogens group." }, "_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": true, "_nocasepkg": "phylotop", "_universes": [ "michellekendall" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.1.3", "date": "2026-05-23T07:28:33.000Z", "distro": "noble", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "5f0a968528906ad5a17e568446f8f84e791ea132026b40e5d0b5d33dd1b87f17", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/michellekendall/actions/runs/26326828025" }, { "r": "4.6.0", "os": "linux", "version": "2.1.3", "date": "2026-05-23T07:28:39.000Z", "distro": "noble", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "af16f16d054d1be70b848a61acf7a7fa120908760ab1d1b6975230a5911997b6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/michellekendall/actions/runs/26326828025" }, { "r": "4.5.3", "os": "mac", "version": "2.1.3", "date": "2026-05-23T07:27:56.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "5bbad10c17a33aab56a50b22b5ddff7870403a93133533ebff9d7a9ab899dea4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/michellekendall/actions/runs/26326828025" }, { "r": "4.6.0", "os": "mac", "version": "2.1.3", "date": "2026-05-23T07:27:39.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "2886d5d97cd3ecb67789c69fe963cefa381d3d0503b06753d6dc4cd8fadc140a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/michellekendall/actions/runs/26326828025" }, { "r": "4.6.0", "os": "wasm", "version": "2.1.3", "date": "2026-05-23T07:28:21.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "9a5b48ec00f0610988c0dc6c92b3c9291c4ded72433c0db4f5e019dcb9a86505", "status": "success", "buildurl": "https://github.com/r-universe/michellekendall/actions/runs/26326828025" }, { "r": "4.7.0", "os": "win", "version": "2.1.3", "date": "2026-05-23T07:27:23.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "1cd25251b575c546571fd41db84e4234ec736cff03c68ebd3ed19c7d660623f5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/michellekendall/actions/runs/26326828025" }, { "r": "4.5.3", "os": "win", "version": "2.1.3", "date": "2026-05-23T07:27:14.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "ab4a8c08b28a987e719cba6cc0dcb6455e034a0a9c1f3c59651555ce4f4c81b6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/michellekendall/actions/runs/26326828025" }, { "r": "4.6.0", "os": "win", "version": "2.1.3", "date": "2026-05-23T07:27:19.000Z", "commit": "7043fa2d120f6d08231dbe6c3a8cc5bc84bf80ed", "fileid": "16dffc9c417016f3ba5f2d8e7d3a198f5f449568ff905d6c1fef27ee69f62a7c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/michellekendall/actions/runs/26326828025" } ] }