{
  "_id": "6a1edd30b401979e7340ffae",
  "Package": "FunChisq",
  "Type": "Package",
  "Version": "2.5.4",
  "Date": "2024-05-10",
  "Title": "Model-Free Functional Chi-Squared and Exact Tests",
  "Authors@R": "c(\nperson(\"Yang\", \"Zhang\", role = \"aut\"),\nperson(\"Hua\", \"Zhong\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-1962-2603\")),\nperson(\"Hien\", \"Nguyen\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-7237-4752\")),\nperson(\"Ruby\", \"Sharma\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-7774-4065\")),\nperson(\"Sajal\", \"Kumar\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-0930-1582\")),\nperson(\"Yiyi\", \"Li\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-8859-3987\")),\nperson(\"Joe\", \"Song\", role = c(\"aut\", \"cre\"),\nemail = \"joemsong@cs.nmsu.edu\",\ncomment = c(ORCID = \"0000-0002-6883-6547\")))",
  "Author": "Yang Zhang [aut], Hua Zhong [aut]\n(<https://orcid.org/0000-0003-1962-2603>), Hien Nguyen [aut]\n(<https://orcid.org/0000-0002-7237-4752>), Ruby Sharma [aut]\n(<https://orcid.org/0000-0001-7774-4065>), Sajal Kumar [aut]\n(<https://orcid.org/0000-0003-0930-1582>), Yiyi Li [aut]\n(<https://orcid.org/0000-0001-8859-3987>), Joe Song [aut, cre]\n(<https://orcid.org/0000-0002-6883-6547>)",
  "Maintainer": "Joe Song <joemsong@cs.nmsu.edu>",
  "Description": "Statistical hypothesis testing methods for inferring\nmodel-free functional dependency using asymptotic chi-squared\nor exact distributions. Functional test statistics are\nasymmetric and functionally optimal, unique from other related\nstatistics. Tests in this package reveal evidence for causality\nbased on the causality-by- functionality principle. They\ninclude asymptotic functional chi-squared tests (Zhang & Song\n2013) <doi:10.48550/arXiv.1311.2707>, an adapted functional\nchi-squared test (Kumar & Song 2022)\n<doi:10.1093/bioinformatics/btac206>, and an exact functional\ntest (Zhong & Song 2019) <doi:10.1109/TCBB.2018.2809743>\n(Nguyen et al. 2020) <doi:10.24963/ijcai.2020/372>. The\nnormalized functional chi-squared test was used by Best\nPerformer 'NMSUSongLab' in HPN-DREAM (DREAM8) Breast Cancer\nNetwork Inference Challenges (Hill et al. 2016)\n<doi:10.1038/nmeth.3773>. A function index (Zhong & Song 2019)\n<doi:10.1186/s12920-019-0565-9> (Kumar et al. 2018)\n<doi:10.1109/BIBM.2018.8621502> derived from the functional\ntest statistic offers a new effect size measure for the\nstrength of functional dependency, a better alternative to\nconditional entropy in many aspects. For continuous data, these\ntests offer an advantage over regression analysis when a\nparametric functional form cannot be assumed; for categorical\ndata, they provide a novel means to assess directional\ndependency not possible with symmetrical Pearson's chi-squared\nor Fisher's exact tests.",
  "License": "LGPL (>= 3)",
  "Encoding": "UTF-8",
  "RdMacros": "Rdpack",
  "NeedsCompilation": "yes",
  "URL": "https://www.cs.nmsu.edu/~joemsong/publications/",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Packaged": {
    "Date": "2026-05-20 08:15:38 UTC",
    "User": "root"
  },
  "Repository": "https://joemsong.r-universe.dev",
  "Date/Publication": "2024-05-11 02:33:53 UTC",
  "RemoteUrl": "https://github.com/cran/FunChisq",
  "RemoteRef": "HEAD",
  "RemoteSha": "90eb2fc97bc3584be02471ecf12d73d427952447",
  "MD5sum": "284f967be64ed1a7203e849b3e45c9ad",
  "_user": "joemsong",
  "_type": "src",
  "_file": "FunChisq_2.5.4.tar.gz",
  "_fileid": "968b127667b9d2e0def3dad73c4a0d51f395958386284937380d1786cd6601e9",
  "_filesize": 852811,
  "_sha256": "968b127667b9d2e0def3dad73c4a0d51f395958386284937380d1786cd6601e9",
  "_created": "2026-05-20T08:15:38.000Z",
  "_published": "2026-06-02T13:40:00.262Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79084062416,
      "time": 171,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7104776757"
    },
    {
      "job": 79084062451,
      "time": 163,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7104774209"
    },
    {
      "job": 79084062821,
      "time": 168,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7104776199"
    },
    {
      "job": 79084062335,
      "time": 170,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7104776555"
    },
    {
      "job": 79084062659,
      "time": 276,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7104801938"
    },
    {
      "job": 79084062938,
      "time": 288,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7104809795"
    },
    {
      "job": 79084062585,
      "time": 151,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7104762992"
    },
    {
      "job": 79084062339,
      "time": 461,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7104862365"
    },
    {
      "job": 79084061954,
      "time": 237,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7104716678"
    },
    {
      "job": 79084061428,
      "time": 139,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 79084062390,
      "time": 149,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7104769308"
    },
    {
      "job": 79084062551,
      "time": 137,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7104765265"
    },
    {
      "job": 79084062174,
      "time": 142,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7104767139"
    }
  ],
  "_buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/FunChisq",
  "_commit": {
    "id": "90eb2fc97bc3584be02471ecf12d73d427952447",
    "author": "Joe Song <joemsong@cs.nmsu.edu>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.5.4\n",
    "time": 1715394833
  },
  "_maintainer": {
    "name": "Joe Song",
    "email": "joemsong@cs.nmsu.edu",
    "login": "joemsong",
    "description": "",
    "uuid": 28720910,
    "orcid": "0000-0002-6883-6547"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "BH",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "Rdpack",
      "version": ">= 0.6-1",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "dqrng",
      "role": "Imports"
    },
    {
      "package": "Ckmeans.1d.dp",
      "role": "Suggests"
    },
    {
      "package": "DescTools",
      "role": "Suggests"
    },
    {
      "package": "DiffXTables",
      "role": "Suggests"
    },
    {
      "package": "GridOnClusters",
      "role": "Suggests"
    },
    {
      "package": "infotheo",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "joemsong",
      "count": 29,
      "uuid": 28720910
    }
  ],
  "_userbio": {
    "uuid": 28720910,
    "type": "user",
    "name": "The Song Lab"
  },
  "_downloads": {
    "count": 216,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FunChisq"
  },
  "_mentions": 4,
  "_searchresults": 34,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/FunChisq.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "joemsong",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2014-03-07"
    },
    {
      "version": "2.0.0",
      "date": "2015-02-16"
    },
    {
      "version": "2.0.1",
      "date": "2015-02-24"
    },
    {
      "version": "2.0.2",
      "date": "2015-03-04"
    },
    {
      "version": "2.1.0",
      "date": "2015-06-29"
    },
    {
      "version": "2.2.0",
      "date": "2016-01-24"
    },
    {
      "version": "2.2.1",
      "date": "2016-01-25"
    },
    {
      "version": "2.2.2",
      "date": "2016-02-14"
    },
    {
      "version": "2.2.3",
      "date": "2016-04-01"
    },
    {
      "version": "2.2.4",
      "date": "2016-04-22"
    },
    {
      "version": "2.3.1",
      "date": "2016-05-02"
    },
    {
      "version": "2.3.2",
      "date": "2016-09-01"
    },
    {
      "version": "2.3.3",
      "date": "2016-09-02"
    },
    {
      "version": "2.4.0",
      "date": "2017-02-28"
    },
    {
      "version": "2.4.2",
      "date": "2017-04-24"
    },
    {
      "version": "2.4.3",
      "date": "2017-05-02"
    },
    {
      "version": "2.4.4",
      "date": "2018-02-06"
    },
    {
      "version": "2.4.5",
      "date": "2018-02-20"
    },
    {
      "version": "2.4.5-1",
      "date": "2018-06-16"
    },
    {
      "version": "2.4.5-2",
      "date": "2018-10-23"
    },
    {
      "version": "2.4.5-3",
      "date": "2018-12-06"
    },
    {
      "version": "2.4.8-1",
      "date": "2019-09-08"
    },
    {
      "version": "2.4.9.1",
      "date": "2019-09-24"
    },
    {
      "version": "2.4.9.2",
      "date": "2020-03-14"
    },
    {
      "version": "2.5.0",
      "date": "2020-04-25"
    },
    {
      "version": "2.5.1",
      "date": "2020-06-14"
    },
    {
      "version": "2.5.2",
      "date": "2021-05-19"
    },
    {
      "version": "2.5.3",
      "date": "2023-05-25"
    },
    {
      "version": "2.5.4",
      "date": "2024-05-10"
    }
  ],
  "_exports": [
    "add.candle.noise",
    "add.house.noise",
    "add.noise",
    "cond.fun.chisq.test",
    "cp.chisq.test",
    "cp.fun.chisq.test",
    "EFTDP",
    "EFTDQP",
    "fun.chisq.test",
    "plot_table",
    "simulate_tables",
    "test.interactions"
  ],
  "_help": [
    {
      "page": "FunChisq-package",
      "title": "Model-Free Functional Chi-Squared and Exact Tests",
      "topics": [
        "FunChisq-package"
      ]
    },
    {
      "page": "noise_model",
      "title": "Apply Noise to Discrete-Valued Tables",
      "concept": [
        "noise model"
      ],
      "topics": [
        "add.candle.noise",
        "add.house.noise",
        "add.noise"
      ]
    },
    {
      "page": "cond.fun.chisq.test",
      "title": "Conditional Functional Chi-Squared Test",
      "topics": [
        "cond.fun.chisq.test"
      ]
    },
    {
      "page": "cp.fun.chisq.test",
      "title": "Comparative Chi-Squared Test for Model-Free Functional Heterogeneity",
      "topics": [
        "cp.fun.chisq.test"
      ]
    },
    {
      "page": "EFT",
      "title": "Exact Functional Test on Two Discrete Random Variables",
      "topics": [
        "EFTDP",
        "EFTDQP",
        "Exact Functional Test"
      ]
    },
    {
      "page": "fun.chisq.test",
      "title": "Model-Free Functional Chi-Squared and Exact Tests",
      "topics": [
        "fun.chisq.test"
      ]
    },
    {
      "page": "FunChisq-deprecated",
      "title": "Deprecated Functions in Package 'FunChisq'",
      "topics": [
        "cp.chisq.test",
        "FunChisq-deprecated"
      ]
    },
    {
      "page": "plot_table",
      "title": "Plot a Table Using Color Intensity for Counts",
      "topics": [
        "plot_table"
      ]
    },
    {
      "page": "simulate_tables",
      "title": "Simulate Noisy Contingency Tables to Represent Diverse Discrete Patterns",
      "topics": [
        "simulate_tables"
      ]
    },
    {
      "page": "test.interactions",
      "title": "Functional Chi-Squared Test of Functional Dependency among Many Variables in a Data Set",
      "topics": [
        "test.interactions"
      ]
    }
  ],
  "_readme": "https://github.com/cran/FunChisq/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "dqrng",
    "rbibutils",
    "Rcpp",
    "Rdpack",
    "sitmo"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "adapted.fun.chisq.test.Rmd",
      "filename": "adapted.fun.chisq.test.html",
      "title": "Adapted versus original functional chi-squared tests and conditional entropy",
      "author": "Sajal Kumar and Joe Song",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Detecting functional direction",
        "Example 1. A function in a square table versus its inverse",
        "Example 2. A function in a landscape table versus its inverse",
        "Example 3. A function in a portrait table versus its inverse",
        "Detecting functional strength",
        "Example 4. Functional versus independent patterns",
        "Conclusion"
      ],
      "created": "2021-05-19 20:00:02",
      "modified": "2023-05-25 09:30:08",
      "commits": 2
    },
    {
      "source": "patterns.Rmd",
      "filename": "patterns.html",
      "title": "Examples of discrete patterns",
      "author": "Joe Song",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Perfect functional patterns",
        "Imperfect patterns"
      ],
      "created": "2018-12-06 12:50:03",
      "modified": "2023-05-25 09:30:08",
      "commits": 2
    },
    {
      "source": "fun.chisq.test.Rmd",
      "filename": "fun.chisq.test.html",
      "title": "Measuring functional dependency model-free",
      "author": "Joe Song",
      "engine": "knitr::rmarkdown",
      "headings": [
        "$\\xi_f$       Yes             No              No          No             correlation coefficient      mean difference"
      ],
      "created": "2016-04-22 08:40:04",
      "modified": "2023-05-25 09:30:08",
      "commits": 7
    },
    {
      "source": "exact.fun.test.Rmd",
      "filename": "exact.fun.test.html",
      "title": "Using the exact functional test",
      "author": "Hua Zhong and Joe Song",
      "engine": "knitr::rmarkdown",
      "headings": [
        "References"
      ],
      "created": "2016-05-02 06:24:25",
      "modified": "2023-05-25 09:30:08",
      "commits": 4
    }
  ],
  "_score": 4.434568904034199,
  "_indexed": true,
  "_nocasepkg": "funchisq",
  "_universes": [
    "joemsong"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.5.4",
      "date": "2026-05-20T08:18:33.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "90eb2fc97bc3584be02471ecf12d73d427952447",
      "fileid": "6a96d5630803a128d85555ac2fe3756dbe8bdf9a5bff2d15f19288dc389b3f56",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.5.4",
      "date": "2026-05-20T08:18:26.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "90eb2fc97bc3584be02471ecf12d73d427952447",
      "fileid": "faaac89f33d6d78ca5206d9006c007e98139775e87447c9e3996e8a9409cb2ef",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.5.4",
      "date": "2026-05-20T08:18:35.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "90eb2fc97bc3584be02471ecf12d73d427952447",
      "fileid": "78a5a173ffbef92e4ac0a6e5a3e25faa5cdc7a36b14270a86d545fca1aa2c7e6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.5.4",
      "date": "2026-05-20T08:18:31.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "90eb2fc97bc3584be02471ecf12d73d427952447",
      "fileid": "4828dc945a93fb586c3260b3abb5747429fa9175d36b13e2886fc37f12570ffa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.5.4",
      "date": "2026-05-20T08:19:25.000Z",
      "arch": "aarch64",
      "commit": "90eb2fc97bc3584be02471ecf12d73d427952447",
      "fileid": "d64baf18917486912f4704af2bc5cf01fcdfac547de16cdc12c0eb1edf4ec9b9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.5.4",
      "date": "2026-05-20T08:19:39.000Z",
      "arch": "x86_64",
      "commit": "90eb2fc97bc3584be02471ecf12d73d427952447",
      "fileid": "ae494f7aff0a28e066f4c445ba06f5ff564003380b731e2183b0498f9a324c76",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.5.4",
      "date": "2026-05-20T08:17:54.000Z",
      "arch": "aarch64",
      "commit": "90eb2fc97bc3584be02471ecf12d73d427952447",
      "fileid": "91f24798d29e3b1a7680b19cbf2ca99a4714d9fa6a835712385356e55aad997d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.5.4",
      "date": "2026-05-20T08:21:17.000Z",
      "arch": "x86_64",
      "commit": "90eb2fc97bc3584be02471ecf12d73d427952447",
      "fileid": "5625f3ffb0d7143c6e782f7a13c9b3c8705e7951d0113fed1b4e652c9f4ad288",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.5.4",
      "date": "2026-05-20T08:17:40.000Z",
      "arch": "x86_64",
      "commit": "90eb2fc97bc3584be02471ecf12d73d427952447",
      "fileid": "cfc5668d581dd58f9b3668badfaa3c4960205c3ab9f1e06de70871f99f5278e7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.5.4",
      "date": "2026-05-20T08:17:33.000Z",
      "arch": "x86_64",
      "commit": "90eb2fc97bc3584be02471ecf12d73d427952447",
      "fileid": "1af0136fd6889b928f5548dd6d0f40140bd065a0aadad16118afbaefb885d5b7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.5.4",
      "date": "2026-05-20T08:17:31.000Z",
      "arch": "x86_64",
      "commit": "90eb2fc97bc3584be02471ecf12d73d427952447",
      "fileid": "f2d27db0056045753cb0e55480106833a16e4620355298e01c369c2a9bf59a7b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joemsong/actions/runs/26150063207"
    }
  ]
}