{
  "_id": "6a5749ecff0138dec5d700ea",
  "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": "2026-07-15 08:46:57 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>",
  "_user": "jonotuke",
  "_type": "src",
  "_file": "BREADR_1.0.4.tar.gz",
  "_fileid": "https://r2.ropensci.org/ae357f26415439ca03e6f872ee272f6a8cf9411f35a5117a043d9b6fac9d1b61",
  "_filesize": 2000186,
  "_sha256": "ae357f26415439ca03e6f872ee272f6a8cf9411f35a5117a043d9b6fac9d1b61",
  "_expires": "2026-10-23T08:50:50.000Z",
  "_created": "2026-07-15T08:46:57.000Z",
  "_published": "2026-07-15T08:50:52.548Z",
  "_jobs": [
    {
      "job": 87308630204,
      "time": 200,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8337518298"
    },
    {
      "job": 87308630265,
      "time": 193,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8337515592"
    },
    {
      "job": 87308630331,
      "time": 95,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8337473577"
    },
    {
      "job": 87308630305,
      "time": 100,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8337475368"
    },
    {
      "job": 87307206767,
      "time": 430,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8337432057"
    },
    {
      "job": 87308630222,
      "time": 164,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8337502885"
    },
    {
      "job": 87308630264,
      "time": 120,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8337485172"
    },
    {
      "job": 87308630251,
      "time": 106,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8337478232"
    },
    {
      "job": 87308630260,
      "time": 165,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8337503448"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/jonotuke/actions/runs/29401590893",
  "_status": "success",
  "_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",
    "description": "",
    "uuid": 1281470,
    "orcid": "0000-0002-1688-8951"
  },
  "_distro": "resolute",
  "_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": "2025-35",
      "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",
    "followers": 18
  },
  "_downloads": {
    "count": 514,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BREADR"
  },
  "_devurl": "https://github.com/jonotuke/breadr",
  "_pkgdown": "https://jonotuke.github.io/BREADR/",
  "_searchresults": 8,
  "_rbuild": "4.6.1",
  "_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",
    "LICENSE",
    "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",
    "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,
  "_indexed": true,
  "_nocasepkg": "breadr",
  "_universes": [
    "jonotuke"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.4",
      "date": "2026-07-15T08:50:10.000Z",
      "distro": "resolute",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "https://r2.ropensci.org/16d05f587e538e907af9703a673e073fe45958670ce36f053042c27d772be344",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/29401590893"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0.4",
      "date": "2026-07-15T08:50:04.000Z",
      "distro": "resolute",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "https://r2.ropensci.org/cb86773829e8f443b221f46aae28f97177eeca2c15d85dbfd1fb5d30c6fb6595",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/29401590893"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.4",
      "date": "2026-07-15T08:48:32.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "https://r2.ropensci.org/7806bf28aa140158dea263a748bd460a9e4f8df310a44a07f04f2f8d0bea5c7f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/29401590893"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0.4",
      "date": "2026-07-15T08:48:35.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "https://r2.ropensci.org/21b49a561de0f23fd8d04670b44ee6d19fb3100f616b8fa98f6d9f20cc76e3d3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/29401590893"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.4",
      "date": "2026-07-15T08:49:56.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "https://r2.ropensci.org/8ec1860711d39a865b8271a961832e949705a971a2f31713332f2bdb8748552a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/29401590893"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-07-15T08:48:44.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "https://r2.ropensci.org/403a53e984c833c0aaec0d90dd70d428d8ea728b6a0690093b971648e1f1e516",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/29401590893"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-07-15T08:48:27.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "https://r2.ropensci.org/2afdac077d7a03a848c3742c005d5b8e3d67a17ff3a4ef0fd705c6b224befd11",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/29401590893"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0.4",
      "date": "2026-07-15T08:49:30.000Z",
      "commit": "ed27851c7af621cac76a8513e1a918ec04a74acd",
      "fileid": "https://r2.ropensci.org/034ef728ddef69984055e878164293aae35c5f35fe896cdf0afdbcf050335c62",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/jonotuke/actions/runs/29401590893"
    }
  ]
}