{
  "_id": "6a104b64acfb0bcc41c9fe94",
  "Package": "assignPOP",
  "Type": "Package",
  "Title": "Population Assignment using Genetic, Non-Genetic or Integrated\nData in a Machine Learning Framework",
  "Version": "1.3.1",
  "Authors@R": "c(person(given = c(\"Kuan-Yu\",\"(Alex)\"), family = \"Chen\", email = \"alexkychen@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(given = c(\"Elizabeth\", \"A.\"), family = \"Marschall\",role = \"aut\"),\nperson(given = c(\"Michael\", \"G.\"),family = \"Sovic\",role = \"aut\"),\nperson(given = c(\"Anthony\", \"C.\"),family = \"Fries\", role = \"aut\"),\nperson(given = c(\"H.\", \"Lisle\"), family = \"Gibbs\",role = \"aut\"),\nperson(given = c(\"Stuart\", \"A.\"), family = \"Ludsin\", role = \"aut\"))",
  "Maintainer": "Kuan-Yu (Alex) Chen <alexkychen@gmail.com>",
  "Description": "Use Monte-Carlo and K-fold cross-validation coupled with\nmachine- learning classification algorithms to perform\npopulation assignment, with functionalities of evaluating\ndiscriminatory power of independent training samples,\nidentifying informative loci, reducing data dimensionality for\ngenomic data, integrating genetic and non-genetic data, and\nvisualizing results.",
  "URL": "https://github.com/alexkychen/assignPOP",
  "License": "GPL (>= 2)",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://alexkychen.r-universe.dev",
  "Date/Publication": "2025-09-12 17:37:41 UTC",
  "RemoteUrl": "https://github.com/alexkychen/assignpop",
  "RemoteRef": "HEAD",
  "RemoteSha": "b1d6ec604274a838591eeb33abc527f64059a228",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-10 07:54:28 UTC",
    "User": "root"
  },
  "Author": "Kuan-Yu (Alex) Chen [aut, cre],\nElizabeth A. Marschall [aut],\nMichael G. Sovic [aut],\nAnthony C. Fries [aut],\nH. Lisle Gibbs [aut],\nStuart A. Ludsin [aut]",
  "MD5sum": "71ff323e42bca4f521148070e44de3ce",
  "_user": "alexkychen",
  "_type": "src",
  "_file": "assignPOP_1.3.1.tar.gz",
  "_fileid": "c92e00b445c215b30a78e024bde93161d93fa093d062daf2c308d05ee907a3c5",
  "_filesize": 231972,
  "_sha256": "c92e00b445c215b30a78e024bde93161d93fa093d062daf2c308d05ee907a3c5",
  "_created": "2026-05-10T07:54:28.000Z",
  "_published": "2026-05-22T12:26:12.756Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77378911663,
      "time": 202,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6902128748"
    },
    {
      "job": 77378911711,
      "time": 198,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6902128381"
    },
    {
      "job": 77378911688,
      "time": 185,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6902124838"
    },
    {
      "job": 77378911211,
      "time": 216,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6902126091"
    },
    {
      "job": 77378910674,
      "time": 244,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6902108676"
    },
    {
      "job": 77378910893,
      "time": 134,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7160423730"
    },
    {
      "job": 77378911511,
      "time": 134,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6902122285"
    },
    {
      "job": 77378911673,
      "time": 133,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6902122271"
    },
    {
      "job": 77378911850,
      "time": 128,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6902121524"
    }
  ],
  "_buildurl": "https://github.com/r-universe/alexkychen/actions/runs/25623326052",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/alexkychen/assignpop",
  "_commit": {
    "id": "b1d6ec604274a838591eeb33abc527f64059a228",
    "author": "alexkychen <alexkychen@gmail.com>",
    "committer": "alexkychen <alexkychen@gmail.com>",
    "message": "update testthat to meet ggplot2 requirements\n",
    "time": 1757698661
  },
  "_maintainer": {
    "name": "Kuan-Yu (Alex) Chen",
    "email": "alexkychen@gmail.com",
    "login": "alexkychen",
    "uuid": 11549861
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.3.2",
      "role": "Depends"
    },
    {
      "package": "caret",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "e1071",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "randomForest",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tree",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "gtable",
      "role": "Suggests"
    },
    {
      "package": "iterators",
      "role": "Suggests"
    },
    {
      "package": "klaR",
      "role": "Suggests"
    },
    {
      "package": "stringi",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "alexkychen",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-37",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "v1.3.1",
      "date": "2025-09-12"
    }
  ],
  "_topics": [
    "cross-validation",
    "data-integration",
    "gbs",
    "machine-learning",
    "population-assignment",
    "population-genomics",
    "radseq"
  ],
  "_stars": 16,
  "_contributors": [
    {
      "user": "alexkychen",
      "count": 200,
      "uuid": 11549861
    },
    {
      "user": "teunbrand",
      "count": 1,
      "uuid": 49372158
    }
  ],
  "_userbio": {
    "uuid": 11549861,
    "type": "user",
    "name": "Alex Chen",
    "description": "Data Scientist / Machine Learning / Bio-Cheminformatics"
  },
  "_downloads": {
    "count": 713,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/assignPOP"
  },
  "_mentions": 11,
  "_devurl": "https://github.com/alexkychen/assignpop",
  "_searchresults": 32,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/assignPOP.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/alexkychen/assignpop",
  "_realowner": "alexkychen",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.1.1",
      "date": "2016-12-29"
    },
    {
      "version": "1.1.2",
      "date": "2017-05-16"
    },
    {
      "version": "1.1.3",
      "date": "2017-06-15"
    },
    {
      "version": "1.1.4",
      "date": "2018-03-13"
    },
    {
      "version": "1.1.6",
      "date": "2019-06-09"
    },
    {
      "version": "1.1.7",
      "date": "2019-08-28"
    },
    {
      "version": "1.1.8",
      "date": "2020-03-02"
    },
    {
      "version": "1.1.9",
      "date": "2020-03-16"
    },
    {
      "version": "1.2.0",
      "date": "2020-07-25"
    },
    {
      "version": "1.2.1",
      "date": "2020-11-03"
    },
    {
      "version": "1.2.2",
      "date": "2020-11-17"
    },
    {
      "version": "1.2.4",
      "date": "2021-10-27"
    },
    {
      "version": "1.3.0",
      "date": "2024-03-13"
    },
    {
      "version": "1.3.1",
      "date": "2025-09-12"
    }
  ],
  "_exports": [
    "accuracy.kfold",
    "accuracy.MC",
    "accuracy.plot",
    "assign.kfold",
    "assign.matrix",
    "assign.MC",
    "assign.X",
    "check.loci",
    "compile.data",
    "membership.plot",
    "read.Genepop",
    "read.Structure",
    "reduce.allele"
  ],
  "_help": [
    {
      "page": "accuracy.kfold",
      "title": "Estimate assignment accuracies of K-fold cross-validation results",
      "topics": [
        "accuracy.kfold"
      ]
    },
    {
      "page": "accuracy.MC",
      "title": "Estimate assignment accuracy of Monte-Carlo cross-validation results",
      "topics": [
        "accuracy.MC"
      ]
    },
    {
      "page": "accuracy.plot",
      "title": "Make a boxplot (ggplot2 style) of assignment accuracy from cross-validation results",
      "topics": [
        "accuracy.plot"
      ]
    },
    {
      "page": "assign.kfold",
      "title": "Population assignment test using K-fold cross-validation",
      "topics": [
        "assign.kfold"
      ]
    },
    {
      "page": "assign.matrix",
      "title": "Make an assignment maxtrix from cross-validation results",
      "topics": [
        "assign.matrix"
      ]
    },
    {
      "page": "assign.MC",
      "title": "Population assignment test using Monte-Carlo cross-validation",
      "topics": [
        "assign.MC"
      ]
    },
    {
      "page": "assign.X",
      "title": "Perform a population assignment test on unknown individuals using known data",
      "topics": [
        "assign.X"
      ]
    },
    {
      "page": "check.loci",
      "title": "Check which loci frequently have high Fst across training sets",
      "topics": [
        "check.loci"
      ]
    },
    {
      "page": "compile.data",
      "title": "Compile genetic and other non-genetic data",
      "topics": [
        "compile.data"
      ]
    },
    {
      "page": "membership.plot",
      "title": "Make a membership probability plot using results from K-fold cross-validation (ggplot2 style)",
      "topics": [
        "membership.plot"
      ]
    },
    {
      "page": "read.Genepop",
      "title": "Read GENEPOP format file",
      "topics": [
        "read.Genepop"
      ]
    },
    {
      "page": "read.Structure",
      "title": "Read Structure format file",
      "topics": [
        "read.Structure"
      ]
    },
    {
      "page": "reduce.allele",
      "title": "Remove low variance alleles (dimensionality reduction)",
      "topics": [
        "reduce.allele"
      ]
    }
  ],
  "_readme": "https://github.com/alexkychen/assignpop/raw/HEAD/README.md",
  "_rundeps": [
    "caret",
    "class",
    "cli",
    "clock",
    "codetools",
    "cpp11",
    "data.table",
    "diagram",
    "digest",
    "doParallel",
    "dplyr",
    "e1071",
    "farver",
    "foreach",
    "future",
    "future.apply",
    "generics",
    "ggplot2",
    "globals",
    "glue",
    "gower",
    "gtable",
    "hardhat",
    "ipred",
    "isoband",
    "iterators",
    "KernSmooth",
    "labeling",
    "lattice",
    "lava",
    "lifecycle",
    "listenv",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "ModelMetrics",
    "nlme",
    "nnet",
    "numDeriv",
    "parallelly",
    "pillar",
    "pkgconfig",
    "plyr",
    "pROC",
    "prodlim",
    "progressr",
    "proxy",
    "purrr",
    "R6",
    "randomForest",
    "RColorBrewer",
    "Rcpp",
    "recipes",
    "reshape2",
    "rlang",
    "rpart",
    "S7",
    "scales",
    "shape",
    "sparsevctrs",
    "SQUAREM",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "timeDate",
    "tree",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 5.40823996531185,
  "_indexed": true,
  "_nocasepkg": "assignpop",
  "_universes": [
    "alexkychen"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.1",
      "date": "2026-05-10T07:57:14.000Z",
      "distro": "noble",
      "commit": "b1d6ec604274a838591eeb33abc527f64059a228",
      "fileid": "f92f239b970cae24696b5b09b8e1a505771f2a3f1ac032000eb0f6243ba0d647",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alexkychen/actions/runs/25623326052"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.1",
      "date": "2026-05-10T07:57:13.000Z",
      "distro": "noble",
      "commit": "b1d6ec604274a838591eeb33abc527f64059a228",
      "fileid": "b43c8bd368076c9744774c7f9ef0d58879914b812787c11f50b4d88650aca1e9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alexkychen/actions/runs/25623326052"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.1",
      "date": "2026-05-10T07:56:52.000Z",
      "commit": "b1d6ec604274a838591eeb33abc527f64059a228",
      "fileid": "3e6b254980b06497988bd3b8865fc828b1afbda9b055154527547c6618a7d268",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alexkychen/actions/runs/25623326052"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.3.1",
      "date": "2026-05-10T07:56:44.000Z",
      "commit": "b1d6ec604274a838591eeb33abc527f64059a228",
      "fileid": "bef4ba8b31f5a1dafc280955c42dff5f4a68053344383480499304efcb61fcd7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alexkychen/actions/runs/25623326052"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.1",
      "date": "2026-05-10T07:55:57.000Z",
      "commit": "b1d6ec604274a838591eeb33abc527f64059a228",
      "fileid": "b048a5fa9c129774b382bfddb7dc8d01779d7c8d6c69fb1d9043890a4cb9e4b7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alexkychen/actions/runs/25623326052"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3.1",
      "date": "2026-05-10T07:55:55.000Z",
      "commit": "b1d6ec604274a838591eeb33abc527f64059a228",
      "fileid": "e27ad25d65fcaebba78965a598479fe37ba80348f7ec116e335c9a94c8dc7b18",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alexkychen/actions/runs/25623326052"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.3.1",
      "date": "2026-05-10T07:55:50.000Z",
      "commit": "b1d6ec604274a838591eeb33abc527f64059a228",
      "fileid": "254898ea2fdad761fd0d45795590eda9f8439eba84dfe704f92ec57493747a9b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/alexkychen/actions/runs/25623326052"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.1",
      "date": "2026-05-22T12:25:50.000Z",
      "commit": "b1d6ec604274a838591eeb33abc527f64059a228",
      "fileid": "b71f8d653f267a5cf2f9f8a38bbfed46fb2fb211e487d616cf644719a227630a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/alexkychen/actions/runs/25623326052"
    }
  ]
}