{
  "_id": "6a1f2944b401979e73423ec1",
  "Package": "BREADR",
  "Title": "Estimates Degrees of Relatedness (Up to the Second Degree) for\nExtreme Low-Coverage Data",
  "Version": "1.0.4",
  "Authors@R": "c(\nperson(\ngiven = \"Jono\",\nfamily = \"Tuke\",\nemail = \"simon.tuke@adelaide.edu.au\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1688-8951\")\n),\nperson(\ngiven = \"Adam B.\",\nfamily = \"Rohrlach\",\nemail = \"adam.rohrlach@adelaide.edu.au\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-4204-5018\")\n),\nperson(\ngiven = \"Wolfgang\",\nfamily = \"Haak\",\nemail = \"wolfgang_haak@eva.mpg.de\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-2475-2007\")\n),\nperson(\ngiven = \"Divyaratan\",\nfamily = \"Popli\",\nemail = \"divyaratan_popli@eva.mpg.de\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-0305-6427\")\n)\n)",
  "Description": "The goal of the package is to provide an easy-to-use\nmethod for estimating degrees of relatedness (up to the second\ndegree) for extreme low-coverage data. The package also allows\nusers to quantify and visualise the level of confidence in the\nestimated degrees of relatedness.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/jonotuke/BREADR,\nhttps://jonotuke.github.io/BREADR/",
  "BugReports": "https://github.com/jonotuke/BREADR/issues",
  "Config/testthat/edition": "3",
  "LazyData": "true",
  "Language": "en-US",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake libgmp3-dev make libicu-dev libmpfr-dev\npari-gp libx11-dev",
  "Repository": "https://jonotuke.r-universe.dev",
  "Date/Publication": "2026-04-15 23:58:36 UTC",
  "RemoteUrl": "https://github.com/jonotuke/breadr",
  "RemoteRef": "HEAD",
  "RemoteSha": "ed27851c7af621cac76a8513e1a918ec04a74acd",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-16 05:04:45 UTC",
    "User": "root"
  },
  "Author": "Jono Tuke [aut, cre] (ORCID: <https://orcid.org/0000-0002-1688-8951>),\nAdam B. Rohrlach [aut] (ORCID: <https://orcid.org/0000-0002-4204-5018>),\nWolfgang Haak [aut] (ORCID: <https://orcid.org/0000-0003-2475-2007>),\nDivyaratan Popli [aut] (ORCID: <https://orcid.org/0000-0002-0305-6427>)",
  "Maintainer": "Jono Tuke <simon.tuke@adelaide.edu.au>",
  "MD5sum": "3429cf611d98d82a445775314ee49823",
  "_user": "jonotuke",
  "_type": "src",
  "_file": "BREADR_1.0.4.tar.gz",
  "_fileid": "d06d4de897274c4b2d96a0f9153d0b7655cb0e8b07c38fcd1308a0ec106477d6",
  "_filesize": 1997632,
  "_sha256": "d06d4de897274c4b2d96a0f9153d0b7655cb0e8b07c38fcd1308a0ec106477d6",
  "_created": "2026-05-16T05:04:45.000Z",
  "_published": "2026-06-02T19:04:36.873Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79149920024,
      "time": 196,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7030671905"
    },
    {
      "job": 79149920412,
      "time": 182,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7030670464"
    },
    {
      "job": 79149920271,
      "time": 138,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7030663699"
    },
    {
      "job": 79149919533,
      "time": 137,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7030663482"
    },
    {
      "job": 79149919680,
      "time": 419,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7030651372"
    },
    {
      "job": 79149918800,
      "time": 185,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7367242962"
    },
    {
      "job": 79149919617,
      "time": 109,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7030662964"
    },
    {
      "job": 79149919561,
      "time": 87,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7030660624"
    },
    {
      "job": 79149919731,
      "time": 104,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7030662276"
    }
  ],
  "_buildurl": "https://github.com/r-universe/jonotuke/actions/runs/25953296882",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/jonotuke/breadr",
  "_commit": {
    "id": "ed27851c7af621cac76a8513e1a918ec04a74acd",
    "author": "Jonathan Tuke <jonotuke@gmail.com>",
    "committer": "Jonathan Tuke <jonotuke@gmail.com>",
    "message": "prep for CRAN submission\n",
    "time": 1776297516
  },
  "_maintainer": {
    "name": "Jono Tuke",
    "email": "simon.tuke@adelaide.edu.au",
    "login": "jonotuke",
    "uuid": 1281470,
    "orcid": "0000-0002-1688-8951"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "forcats",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "ggstatsplot",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "fs",
      "role": "Suggests"
    }
  ],
  "_owner": "jonotuke",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-28",
      "n": 1
    },
    {
      "week": "2025-35",
      "n": 1
    },
    {
      "week": "2026-16",
      "n": 11
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "jonotuke",
      "count": 119,
      "uuid": 1281470
    },
    {
      "user": "spholmes",
      "count": 1,
      "uuid": 1203389
    }
  ],
  "_userbio": {
    "uuid": 1281470,
    "type": "user",
    "name": "Jonathan Tuke"
  },
  "_downloads": {
    "count": 589,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BREADR"
  },
  "_devurl": "https://github.com/jonotuke/breadr",
  "_pkgdown": "https://jonotuke.github.io/BREADR/",
  "_searchresults": 6,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BREADR.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"
  ],
  "_homeurl": "https://github.com/jonotuke/breadr",
  "_realowner": "jonotuke",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2023-04-07"
    },
    {
      "version": "1.0.1",
      "date": "2023-04-12"
    },
    {
      "version": "1.0.2",
      "date": "2024-09-09"
    },
    {
      "version": "1.0.3",
      "date": "2025-04-14"
    },
    {
      "version": "1.1.0",
      "date": "2026-04-16"
    }
  ],
  "_exports": [
    "%>%",
    "callRelatedness",
    "get_column_new",
    "plotDOUGH",
    "plotLOAF",
    "plotSLICE",
    "priorSensitivity",
    "processEigenstrat",
    "processEigenstrat_old",
    "read_ind",
    "read_snp",
    "saveSLICES",
    "sim_geno",
    "split_line",
    "test_degree"
  ],
  "_datasets": [
    {
      "name": "counts_example",
      "title": "counts_example",
      "object": "counts_example",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "pair",
        "nsnps",
        "mismatch",
        "pmr"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    },
    {
      "name": "relatedness_example",
      "title": "relatedness_example",
      "object": "relatedness_example",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "row",
        "pair",
        "relationship",
        "pmr",
        "sd",
        "mismatch",
        "nsnps",
        "ave_rel",
        "Same_Twins",
        "First_Degree",
        "Second_Degree",
        "Unrelated"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "callRelatedness",
      "title": "callRelatedness",
      "topics": [
        "callRelatedness"
      ]
    },
    {
      "page": "counts_example",
      "title": "counts_example",
      "topics": [
        "counts_example"
      ]
    },
    {
      "page": "get_column_new",
      "title": "get column",
      "topics": [
        "get_column_new"
      ]
    },
    {
      "page": "plotDOUGH",
      "title": "plotDOUGH",
      "topics": [
        "plotDOUGH"
      ]
    },
    {
      "page": "plotLOAF",
      "title": "plotLOAF",
      "topics": [
        "plotLOAF"
      ]
    },
    {
      "page": "plotSLICE",
      "title": "plotSLICE",
      "topics": [
        "plotSLICE"
      ]
    },
    {
      "page": "priorSensitivity",
      "title": "priorSensitivity",
      "topics": [
        "priorSensitivity"
      ]
    },
    {
      "page": "processEigenstrat",
      "title": "process Eigenstrat data - alternative version",
      "topics": [
        "processEigenstrat"
      ]
    },
    {
      "page": "processEigenstrat_old",
      "title": "process Eigenstrat data",
      "topics": [
        "processEigenstrat_old"
      ]
    },
    {
      "page": "read_ind",
      "title": "read_ind",
      "topics": [
        "read_ind"
      ]
    },
    {
      "page": "read_snp",
      "title": "read_snp",
      "topics": [
        "read_snp"
      ]
    },
    {
      "page": "relatedness_example",
      "title": "relatedness_example",
      "topics": [
        "relatedness_example"
      ]
    },
    {
      "page": "saveSLICES",
      "title": "saveSLICES",
      "topics": [
        "saveSLICES"
      ]
    },
    {
      "page": "sim_geno",
      "title": "sim_geno",
      "topics": [
        "sim_geno"
      ]
    },
    {
      "page": "split_line",
      "title": "split line",
      "topics": [
        "split_line"
      ]
    },
    {
      "page": "test_degree",
      "title": "test_degree",
      "topics": [
        "test_degree"
      ]
    }
  ],
  "_readme": "https://github.com/jonotuke/breadr/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "afex",
    "backports",
    "BayesFactor",
    "bayestestR",
    "bit",
    "bit64",
    "boot",
    "broom",
    "BWStest",
    "cachem",
    "car",
    "carData",
    "cli",
    "clipr",
    "coda",
    "colorspace",
    "contfrac",
    "correlation",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "data.table",
    "datawizard",
    "Deriv",
    "desc",
    "deSolve",
    "doBy",
    "dplyr",
    "effectsize",
    "elliptic",
    "farver",
    "fastmap",
    "forcats",
    "forecast",
    "Formula",
    "fracdiff",
    "generics",
    "ggcorrplot",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggside",
    "ggsignif",
    "ggstatsplot",
    "glue",
    "gmp",
    "gridExtra",
    "gtable",
    "hms",
    "hypergeo",
    "insight",
    "isoband",
    "kSamples",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmerTest",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "multcompView",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "paletteer",
    "parameters",
    "patchwork",
    "pbapply",
    "pbkrtest",
    "performance",
    "pillar",
    "pkgconfig",
    "plyr",
    "PMCMRplus",
    "polynom",
    "prettyunits",
    "prismatic",
    "progress",
    "purrr",
    "quantreg",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppParallel",
    "Rdpack",
    "readr",
    "reformulas",
    "rematch2",
    "reshape",
    "reshape2",
    "rlang",
    "Rmpfr",
    "rstantools",
    "rstatix",
    "rstudioapi",
    "S7",
    "scales",
    "SparseM",
    "statsExpressions",
    "stringi",
    "stringr",
    "SuppDists",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "tzdb",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "WRS2",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "example-pipeline.Rmd",
      "filename": "example-pipeline.html",
      "title": "Example BREADR Analysis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "The theory behind BREADR",
        "Processing your data",
        "Processing only pairs within groups to save computational effort",
        "Calling degrees of relatedness from counts",
        "Assessing if groups can be merged",
        "Visualising overall relatedness patterns",
        "Visualising the relatedness information for two individuals",
        "Binomial tests for degrees of relatedness",
        "Sensitivity of the results to the prior distribution",
        "Acknowledgements"
      ],
      "created": "2025-04-02 00:06:34",
      "modified": "2026-04-15 23:58:36",
      "commits": 4
    }
  ],
  "_score": 4.176091259055681,
  "_indexed": true,
  "_nocasepkg": "breadr",
  "_universes": [
    "jonotuke"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.4",
      "date": "2026-05-16T05:08:00.000Z",
      "distro": "noble",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "682d3af1798aa9bcee634b6c864e70b5d5562756c8bd20acf5fe15c9d95f3159",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/25953296882"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.4",
      "date": "2026-05-16T05:07:48.000Z",
      "distro": "noble",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "807a2fdcf07ba46fb0e7ae8d83bf0a6ec4270ca37f7d47dc6d02f7a7914be79e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/25953296882"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.4",
      "date": "2026-05-16T05:06:53.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "8edadbd42fa948a739152594da0c2630761602db647ffbd005bc1d66c9bb5457",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/25953296882"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.4",
      "date": "2026-05-16T05:06:47.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "246c40bfc17d8b8b2dec1c46a23ade3cb144c89bf18e10d12394193f7fdeaf02",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/25953296882"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-05-16T05:06:27.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "7c7f7514001fd73ed3846eb1d823b778421feb44a4340d08a6ec0615534de33a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/25953296882"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-05-16T05:06:06.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "0478da8f739b4699499e5e876dc755f4ff4580f52096170bd0f04bca6bea8124",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/25953296882"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-05-16T05:06:18.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "9faededc7c1dbba7ec8ca2958385088cc5a3ec6ca4c12d868dca56124cf606f2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/25953296882"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.4",
      "date": "2026-06-02T19:04:18.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "595b66621b4016881f7d0be1cbdf435a5e2ceec22fdca17109e4626b2ce26cda",
      "status": "success",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/25953296882"
    }
  ]
}