{
  "_id": "6a197eb1acfb0bcc41df7b83",
  "Package": "MDDC",
  "Type": "Package",
  "Title": "Modified Detecting Deviating Cells Algorithm in\nPharmacovigilance",
  "Version": "1.1.0",
  "Authors@R": "c(\nperson(given = \"Anran\", family = \"Liu\", role = c(\"aut\", \"cre\"),\nemail = \"anranliu@buffalo.edu\",\ncomment = c(ORCID = \"0000-0002-4504-9786\")),\nperson(given = \"Raktim\", family = \"Mukhopadhyay\",\nrole = c(\"aut\"), email = \"raktimmu@buffalo.edu\",\ncomment = c(ORCID = \"0009-0007-8972-6682\")),\nperson(given = \"Marianthi\", family = \"Markatou\",\nrole = c(\"aut\"), email = \"markatou@buffalo.edu\",\ncomment = c(ORCID = \"0000-0002-1453-8229\"))\n)",
  "Maintainer": "Anran Liu <anranliu@buffalo.edu>",
  "Description": "Methods for detecting signals related to (adverse event,\nmedical product e.g. drugs, vaccines) pairs, a data generation\nfunction for simulating pharmacovigilance datasets, and various\nutility functions. For more details please see Liu A.,\nMukhopadhyay R., and Markatou M.\n<doi:10.48550/arXiv.2410.01168>.",
  "URL": "https://github.com/niuniular/MDDC",
  "BugReports": "https://github.com/niuniular/MDDC/issues",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Language": "en-US",
  "Repository": "https://niuniular.r-universe.dev",
  "Date/Publication": "2025-04-07 16:27:33 UTC",
  "RemoteUrl": "https://github.com/niuniular/mddc",
  "RemoteRef": "HEAD",
  "RemoteSha": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-29 11:23:30 UTC",
    "User": "root"
  },
  "Author": "Anran Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-4504-9786>),\nRaktim Mukhopadhyay [aut] (ORCID:\n<https://orcid.org/0009-0007-8972-6682>),\nMarianthi Markatou [aut] (ORCID:\n<https://orcid.org/0000-0002-1453-8229>)",
  "MD5sum": "8e049c6e1d202dc8ac9bd687cc061801",
  "_user": "niuniular",
  "_type": "src",
  "_file": "MDDC_1.1.0.tar.gz",
  "_fileid": "886551f078617626ec3a6a52d7028c23cfb5205164941832c421395e68ee5209",
  "_filesize": 509190,
  "_sha256": "886551f078617626ec3a6a52d7028c23cfb5205164941832c421395e68ee5209",
  "_created": "2026-05-29T11:23:30.000Z",
  "_published": "2026-05-29T11:55:29.778Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78491176052,
      "time": 148,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7289555661"
    },
    {
      "job": 78491176073,
      "time": 151,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7289556480"
    },
    {
      "job": 78491176062,
      "time": 139,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7289552952"
    },
    {
      "job": 78491176217,
      "time": 148,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7289555662"
    },
    {
      "job": 78491176067,
      "time": 191,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7290045371"
    },
    {
      "job": 78491176069,
      "time": 286,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7289588443"
    },
    {
      "job": 78491176105,
      "time": 89,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7290018566"
    },
    {
      "job": 78491176066,
      "time": 223,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7289579240"
    },
    {
      "job": 78490664559,
      "time": 215,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7289512016"
    },
    {
      "job": 78491176034,
      "time": 107,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7289543573"
    },
    {
      "job": 78491176074,
      "time": 146,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7289554662"
    },
    {
      "job": 78491176042,
      "time": 125,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7289548818"
    },
    {
      "job": 78491176096,
      "time": 138,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7289552385"
    }
  ],
  "_buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/niuniular/mddc",
  "_commit": {
    "id": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
    "author": "Raktim Mukhopadhyay <rmj.3197@gmail.com>",
    "committer": "Raktim Mukhopadhyay <rmj.3197@gmail.com>",
    "message": "updated man\n",
    "time": 1744043253
  },
  "_maintainer": {
    "name": "Anran Liu",
    "email": "anranliu@buffalo.edu",
    "orcid": "0000-0002-4504-9786"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "niuniular",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "pharmacovigilance",
    "cpp"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "rmj3197",
      "count": 131,
      "uuid": 54344732
    }
  ],
  "_userbio": {
    "uuid": 75549823,
    "type": "user",
    "name": "Anran Liu"
  },
  "_downloads": {
    "count": 145,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MDDC"
  },
  "_devurl": "https://github.com/niuniular/mddc",
  "_searchresults": 4,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MDDC.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/niuniular/mddc",
  "_realowner": "niuniular",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2024-10-04"
    },
    {
      "version": "1.1.0",
      "date": "2025-04-07"
    }
  ],
  "_exports": [
    "check_and_fix_contin_table",
    "find_optimal_coef",
    "generate_contin_table_with_clustered_AE",
    "generate_contin_table_with_clustered_AE_with_tol",
    "get_expected_counts",
    "get_std_pearson_res",
    "mddc_boxplot",
    "mddc_mc",
    "plot_heatmap",
    "report_drug_AE_pairs"
  ],
  "_datasets": [
    {
      "name": "betablocker500",
      "title": "FDA dataset for beta blockers with 500 adverse events",
      "object": "betablocker500",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Acebutolol",
        "Atenolol",
        "Bisoprolol",
        "Carvedilol",
        "Metoprolol",
        "Nadolol",
        "Propranolol",
        "Timolol",
        "Other"
      ],
      "rows": 501,
      "table": true,
      "tojson": true
    },
    {
      "name": "sedative1000",
      "title": "FDA dataset for sedatives with 1000 adverse events",
      "object": "sedative1000",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Clonazepam",
        "Dexmedetomidine",
        "Diazepam",
        "Diphenhydramine",
        "Doxepin",
        "Lorazepam",
        "Midazolam",
        "Mirtazapine",
        "Nitrazepam",
        "Temazepam",
        "Other"
      ],
      "rows": 1001,
      "table": true,
      "tojson": true
    },
    {
      "name": "statin101",
      "title": "FDA statin dataset with 101 adverse events",
      "object": "statin101",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Atorvastatin",
        "Fluvastatin",
        "Rosuvastatin",
        "Simvastatin",
        "Other"
      ],
      "rows": 102,
      "table": true,
      "tojson": true
    },
    {
      "name": "statin49",
      "title": "FDA statin dataset with 49 adverse events",
      "object": "statin49",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Atorvastatin",
        "Fluvastatin",
        "Lovastatin",
        "Pravastatin",
        "Rosuvastatin",
        "Simvastatin",
        "Other"
      ],
      "rows": 50,
      "table": true,
      "tojson": true
    },
    {
      "name": "statin49_AE_idx",
      "title": "Cluster index of the FDA statin dataset with 49 adverse events",
      "object": "statin49_AE_idx",
      "class": [
        "data.frame"
      ],
      "fields": [
        "idx",
        "AE"
      ],
      "rows": 50,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "MDDC-package",
      "title": "Modified Detecting Deviating Cells Algorithm in Pharmacovigilance",
      "topics": [
        "MDDC-package",
        "MDDC"
      ]
    },
    {
      "page": "betablocker500",
      "title": "FDA dataset for beta blockers with 500 adverse events",
      "topics": [
        "betablocker500"
      ]
    },
    {
      "page": "check_and_fix_contin_table",
      "title": "Verifying and correcting the input I by J contingency table",
      "topics": [
        "check_and_fix_contin_table"
      ]
    },
    {
      "page": "find_optimal_coef",
      "title": "Find Adaptive Boxplot Coefficient `coef` via Grid Search",
      "topics": [
        "find_optimal_coef"
      ]
    },
    {
      "page": "generate_contin_table_with_clustered_AE",
      "title": "Generate simulated contingency tables with the option of incorporating adverse event correlation within clusters.",
      "topics": [
        "generate_contin_table_with_clustered_AE"
      ]
    },
    {
      "page": "generate_contin_table_with_clustered_AE_with_tol",
      "title": "Generate simulated contingency tables with the option of incorporating adverse event correlation within clusters and tolerance for total report count.",
      "topics": [
        "generate_contin_table_with_clustered_AE_with_tol"
      ]
    },
    {
      "page": "get_expected_counts",
      "title": "Compute the Expected Count Matrix from a Contingency Table",
      "topics": [
        "get_expected_counts"
      ]
    },
    {
      "page": "get_std_pearson_res",
      "title": "Computing the standardized Pearson residuals for a given I \\times J contingency table",
      "topics": [
        "get_std_pearson_res"
      ]
    },
    {
      "page": "mddc_boxplot",
      "title": "Modified Detecting Deviating Cells (MDDC) algorithm for adverse event signal identification with boxplot method for cutoff selection.",
      "topics": [
        "mddc_boxplot"
      ]
    },
    {
      "page": "mddc_mc",
      "title": "Modified Detecting Deviating Cells (MDDC) algorithm for adverse event signal identification with Monte Carlo (MC) method for cutoff selection.",
      "topics": [
        "mddc_mc"
      ]
    },
    {
      "page": "plot_heatmap",
      "title": "Plot Heatmap",
      "topics": [
        "plot_heatmap"
      ]
    },
    {
      "page": "report_drug_AE_pairs",
      "title": "Report the potential adverse events for drugs from contingency table",
      "topics": [
        "report_drug_AE_pairs"
      ]
    },
    {
      "page": "sedative1000",
      "title": "FDA dataset for sedatives with 1000 adverse events",
      "topics": [
        "sedative1000"
      ]
    },
    {
      "page": "statin101",
      "title": "FDA statin dataset with 101 adverse events",
      "topics": [
        "statin101"
      ]
    },
    {
      "page": "statin49",
      "title": "FDA statin dataset with 49 adverse events",
      "topics": [
        "statin49"
      ]
    },
    {
      "page": "statin49_AE_idx",
      "title": "Cluster index of the FDA statin dataset with 49 adverse events",
      "topics": [
        "statin49_AE_idx"
      ]
    }
  ],
  "_readme": "https://github.com/niuniular/mddc/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "codetools",
    "cpp11",
    "doParallel",
    "farver",
    "foreach",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "iterators",
    "labeling",
    "lifecycle",
    "MASS",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_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": "Introduction_to_MDDC.Rmd",
      "filename": "Introduction_to_MDDC.html",
      "title": "Usage Examples for MDDC in R",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Dataset",
        "Adverse Event (AE) Identification with MDDC",
        "Using Boxplot Method",
        "Function for Finding Optimal Boxplot Coefficient",
        "Using the Monte Carlo Method",
        "Function for Reporting",
        "Simulating datasets with grouped AEs",
        "Visualization"
      ],
      "created": "2024-08-20 22:08:48",
      "modified": "2025-04-05 06:18:57",
      "commits": 15
    }
  ],
  "_score": 4.176091259055681,
  "_indexed": true,
  "_nocasepkg": "mddc",
  "_universes": [
    "niuniular"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-29T11:25:47.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "4aa9b231296764c7bfe298879ad50fc5eef6969a7f7895071f6e043b921f8224",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-29T11:25:46.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "3e2e2b1fa9bfa9ec46ee1ed88518bd8573bd330240aacebc39e2f333102b1da6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-29T11:25:41.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "2f86825b114e8fdc9a30edc7f54e6c9b692a9b585fc9a5e0db4f2184638211b4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-05-29T11:25:43.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "fb808b89e5f37988d85c55159c1cd5a49b9b452e6f62add8d5cf86ba9318749b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-29T11:54:04.000Z",
      "arch": "aarch64",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "84b8ef9c9958a76153a91cbb75fa2679c0d4c06b65d1d818fcdeb82ac76f5763",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-29T11:27:17.000Z",
      "arch": "x86_64",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "c2b2b579f1bb80ec2d6f01827bb14197e264bd496d3936bc384ac0fa0c32cffa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-29T11:53:03.000Z",
      "arch": "aarch64",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "60f910f8e9182f9079a2f642b8a10eeba54745eeea650efa5a9a04c6f34ee6a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-05-29T11:26:47.000Z",
      "arch": "x86_64",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "f538675d7547026e0b98a49dd2d4a46f17e4343b3414ce6b0923cfa3f646fc84",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-05-29T11:25:36.000Z",
      "arch": "emscripten",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "90e14826ee28d1d5899481fa173bc09d5c17307a740bcc99389105fc18d553e3",
      "status": "success",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-29T11:24:56.000Z",
      "arch": "x86_64",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "28053030c299b3c9640e1b12f70869f3b044d51286d14e63abc72342fd243ccc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-29T11:24:46.000Z",
      "arch": "x86_64",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "2e4db4f7d330ea987922d3e46bed71866445395d91777df1f65d88578b7c3501",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-05-29T11:24:50.000Z",
      "arch": "x86_64",
      "commit": "1b7975d68407ae2211a877355d1638b2d8a8dd15",
      "fileid": "e628bf13b6609ddc8be3c2a967f2feb4b4e34087a0c95f3679d1ef4913e61066",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/niuniular/actions/runs/26634311032"
    }
  ]
}