{
  "_id": "6a12bf71acfb0bcc41d1d843",
  "Package": "rhierbaps",
  "Type": "Package",
  "Title": "Clustering Genetic Sequence Data Using the HierBAPS Algorithm",
  "Version": "1.1.3",
  "Authors@R": "person(\"Gerry\", \"Tonkin-Hill\", email = \"g.tonkinhill@gmail.com\", role = c(\"cre\", \"aut\"))",
  "Description": "Implements the hierarchical Bayesian analysis of\npopulations structure (hierBAPS) algorithm of Cheng et al.\n(2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences\nfrom multiple sequence alignments in FASTA format. The\nimplementation includes improved defaults and plotting\ncapabilities and unlike the original 'MATLAB' version removes\nsingleton SNPs by default.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.1.0",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/gtonkinhill/rhierbaps",
  "BugReports": "https://github.com/gtonkinhill/rhierbaps/issues",
  "Repository": "https://gtonkinhill.r-universe.dev",
  "Date/Publication": "2026-02-23 05:32:54 UTC",
  "RemoteUrl": "https://github.com/gtonkinhill/rhierbaps",
  "RemoteRef": "HEAD",
  "RemoteSha": "da7f1159d9dcf5347c93684be6ed4ae5380b0544",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-24 09:01:56 UTC",
    "User": "root"
  },
  "Author": "Gerry Tonkin-Hill [cre, aut]",
  "Maintainer": "Gerry Tonkin-Hill <g.tonkinhill@gmail.com>",
  "MD5sum": "aa94d34317065438a2ebbc32dfd02d0a",
  "_user": "gtonkinhill",
  "_type": "src",
  "_file": "rhierbaps_1.1.3.tar.gz",
  "_fileid": "0bf833dad74205f188080f4bb25a6e7dd06a6b1c5a41dc1442ebc5e289faa33c",
  "_filesize": 1455151,
  "_sha256": "0bf833dad74205f188080f4bb25a6e7dd06a6b1c5a41dc1442ebc5e289faa33c",
  "_created": "2026-05-24T09:01:56.000Z",
  "_published": "2026-05-24T09:05:53.693Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77585556332,
      "time": 154,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7183878525"
    },
    {
      "job": 77585556338,
      "time": 145,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7183877704"
    },
    {
      "job": 77585556369,
      "time": 205,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7183879984"
    },
    {
      "job": 77585556329,
      "time": 185,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7183878207"
    },
    {
      "job": 77585268776,
      "time": 294,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7183861008"
    },
    {
      "job": 77585556325,
      "time": 117,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7183874460"
    },
    {
      "job": 77585556349,
      "time": 115,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7183874146"
    },
    {
      "job": 77585556351,
      "time": 87,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7183871237"
    },
    {
      "job": 77585556331,
      "time": 96,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7183872253"
    }
  ],
  "_buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/26356927501",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/gtonkinhill/rhierbaps",
  "_commit": {
    "id": "da7f1159d9dcf5347c93684be6ed4ae5380b0544",
    "author": "Gerry Tonkin-Hill <gqt20@cam.ac.uk>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Refactor R-CMD-check workflow for efficiency",
    "time": 1771824774
  },
  "_maintainer": {
    "name": "Gerry Tonkin-Hill",
    "email": "g.tonkinhill@gmail.com",
    "login": "gtonkinhill",
    "description": "Research group leader at Peter Mac & Doherty Institute\n| previously at UiO, Sanger & Cambridge\n| microbial genomics, statistics, machine learning",
    "uuid": 10625107
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "ggtree",
      "role": "Suggests"
    },
    {
      "package": "phytools",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "formatR",
      "role": "Suggests"
    }
  ],
  "_owner": "gtonkinhill",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-09",
      "n": 4
    }
  ],
  "_tags": [],
  "_topics": [
    "population-genetics",
    "population-genomics",
    "population-structure"
  ],
  "_stars": 36,
  "_contributors": [
    {
      "user": "gtonkinhill",
      "count": 47,
      "uuid": 10625107
    }
  ],
  "_userbio": {
    "uuid": 10625107,
    "type": "user",
    "name": "Gerry Tonkin-Hill",
    "description": "Research group leader at Peter Mac & Doherty Institute\r\n| previously at UiO, Sanger & Cambridge\r\n| microbial genomics, statistics, machine learning"
  },
  "_downloads": {
    "count": 271,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rhierbaps"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/gtonkinhill/rhierbaps",
  "_searchresults": 38,
  "_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/readme.html",
    "extra/readme.md",
    "extra/rhierbaps.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/gtonkinhill/rhierbaps",
  "_realowner": "gtonkinhill",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2018-07-20"
    },
    {
      "version": "1.1.0",
      "date": "2018-10-10"
    },
    {
      "version": "1.1.2",
      "date": "2019-05-10"
    },
    {
      "version": "1.1.3",
      "date": "2019-12-11"
    },
    {
      "version": "1.1.4",
      "date": "2022-11-18"
    }
  ],
  "_exports": [
    "hierBAPS",
    "load_fasta",
    "plot_sub_cluster",
    "save_lml_logs"
  ],
  "_help": [
    {
      "page": "calc_change_in_ml",
      "title": "calc_change_in_ml",
      "topics": [
        "calc_change_in_ml"
      ]
    },
    {
      "page": "calc_log_ml",
      "title": "calc_log_ml",
      "topics": [
        "calc_log_ml"
      ]
    },
    {
      "page": "hierBAPS",
      "title": "hierBAPS",
      "topics": [
        "hierBAPS"
      ]
    },
    {
      "page": "join_units_2",
      "title": "join_units_2",
      "topics": [
        "join_units_2"
      ]
    },
    {
      "page": "load_fasta",
      "title": "load_fasta",
      "topics": [
        "load_fasta"
      ]
    },
    {
      "page": "model_search_parallel",
      "title": "model_search_parallel",
      "topics": [
        "model_search_parallel"
      ]
    },
    {
      "page": "move_units_1",
      "title": "move_units_1",
      "topics": [
        "move_units_1"
      ]
    },
    {
      "page": "plot_sub_cluster",
      "title": "plot_sub_cluster",
      "topics": [
        "plot_sub_cluster"
      ]
    },
    {
      "page": "preproc_alignment",
      "title": "preproc_alignment",
      "topics": [
        "preproc_alignment"
      ]
    },
    {
      "page": "reallocate_units_4",
      "title": "reallocate_units_4",
      "topics": [
        "reallocate_units_4"
      ]
    },
    {
      "page": "save_lml_logs",
      "title": "save_lml_logs",
      "topics": [
        "save_lml_logs"
      ]
    },
    {
      "page": "split_clusters_3",
      "title": "split_clusters_3",
      "topics": [
        "split_clusters_3"
      ]
    }
  ],
  "_readme": "https://github.com/gtonkinhill/rhierbaps/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "cli",
    "cpp11",
    "digest",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "matrixStats",
    "nlme",
    "patchwork",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "Introduction to rhierbaps",
      "author": "Gerry Tonkin-Hill",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Libraries",
        "Loading data",
        "Running hierBAPS",
        "Plotting results",
        "Caculating assignment probabilities",
        "Saving results",
        "Citing rhierbaps",
        "References",
        "Session Information"
      ],
      "created": "2017-11-24 15:03:35",
      "modified": "2019-05-09 21:00:36",
      "commits": 14
    }
  ],
  "_score": 5.835056101720117,
  "_indexed": true,
  "_nocasepkg": "rhierbaps",
  "_universes": [
    "gtonkinhill"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.3",
      "date": "2026-05-24T09:04:19.000Z",
      "distro": "noble",
      "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544",
      "fileid": "1a924fade2e597594dad4f9c931a42d11622c02a6ee73a32f71510933b294afc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/26356927501"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.3",
      "date": "2026-05-24T09:04:13.000Z",
      "distro": "noble",
      "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544",
      "fileid": "cea34506da92d5315c3cdd312f1a294dad62ba8a241bf65bedecb2974c7546e1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/26356927501"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.3",
      "date": "2026-05-24T09:04:39.000Z",
      "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544",
      "fileid": "fc5d094529d19167125bf98e865f62bb5d2ca9f6165f2e562ff20a657244d70b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/26356927501"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.3",
      "date": "2026-05-24T09:04:20.000Z",
      "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544",
      "fileid": "e63e821232d4ba54236dfdce724087bb7bfc97fc4d67dc46d11577fec8947174",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/26356927501"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.3",
      "date": "2026-05-24T09:04:09.000Z",
      "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544",
      "fileid": "436943180fc675a81823640e493939a88d33840aef8aed23b15c8212bc3a89b4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/26356927501"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.3",
      "date": "2026-05-24T09:03:39.000Z",
      "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544",
      "fileid": "22354287bb14fdf7cae53ffa950595a9d0528df5c11c07299de3a21ade8500f5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/26356927501"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.3",
      "date": "2026-05-24T09:03:07.000Z",
      "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544",
      "fileid": "3dcf563ac1020a5e208ff620901f2f4563d9c199af800cbc4ad5a78cc72d592b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/26356927501"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.3",
      "date": "2026-05-24T09:03:15.000Z",
      "commit": "da7f1159d9dcf5347c93684be6ed4ae5380b0544",
      "fileid": "037f7d17b179a3a603a2d80f8a2e9a52dfac710c8e972fb582c8725c3e0cec9c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gtonkinhill/actions/runs/26356927501"
    }
  ]
}