{
  "_id": "6a23c7a0530b9bc726be07a3",
  "Package": "hamlet",
  "Type": "Package",
  "Title": "Hierarchical Optimal Matching and Machine Learning Toolbox",
  "Version": "0.9.8",
  "Date": "2025-12-08",
  "Authors@R": "person(given = c(\"Teemu\", \"Daniel\"),\nfamily = \"Laajala\",\nrole = c(\"aut\", \"cre\"),\nemail = \"teelaa@utu.fi\")",
  "Author": "Teemu Daniel Laajala [aut, cre]",
  "Maintainer": "Teemu Daniel Laajala <teelaa@utu.fi>",
  "Description": "Various functions and algorithms are provided here for\nsolving optimal matching tasks in the context of preclinical\ncancer studies. Further, various helper and plotting functions\nare provided for unsupervised and supervised machine learning\nas well as longitudinal mixed-effects modeling of tumor growth\nresponse patterns.",
  "License": "GPL (>= 2)",
  "Repository": "https://syksy.r-universe.dev",
  "Date/Publication": "2025-12-08 23:04:09 UTC",
  "RemoteUrl": "https://github.com/syksy/hamlet",
  "RemoteRef": "HEAD",
  "RemoteSha": "7e571f481a816d7c3ce11b14c5423d8d6cc96259",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-06 07:06:24 UTC",
    "User": "root"
  },
  "MD5sum": "37f113572f6a976bf44df044d2eaca6b",
  "_user": "syksy",
  "_type": "src",
  "_file": "hamlet_0.9.8.tar.gz",
  "_fileid": "66aa6bd599d4ea9d05cf41042a5c759610b1fe52b2dca0eb7d5ede1fbf5b03d6",
  "_filesize": 722993,
  "_sha256": "66aa6bd599d4ea9d05cf41042a5c759610b1fe52b2dca0eb7d5ede1fbf5b03d6",
  "_created": "2026-06-06T07:06:24.000Z",
  "_published": "2026-06-06T07:09:20.171Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79859762537,
      "time": 148,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7452270240"
    },
    {
      "job": 79859762532,
      "time": 125,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7452267593"
    },
    {
      "job": 79859762520,
      "time": 89,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7452262754"
    },
    {
      "job": 79859762538,
      "time": 90,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7452263097"
    },
    {
      "job": 79859590279,
      "time": 172,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7452251394"
    },
    {
      "job": 79859762530,
      "time": 103,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7452264816"
    },
    {
      "job": 79859762549,
      "time": 93,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7452263389"
    },
    {
      "job": 79859762534,
      "time": 85,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7452262300"
    },
    {
      "job": 79859762559,
      "time": 130,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7452268218"
    }
  ],
  "_buildurl": "https://github.com/r-universe/syksy/actions/runs/27055706343",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/syksy/hamlet",
  "_commit": {
    "id": "7e571f481a816d7c3ce11b14c5423d8d6cc96259",
    "author": "Syksy <teemu.daniel.laajala@gmail.com>",
    "committer": "Syksy <teemu.daniel.laajala@gmail.com>",
    "message": "NEWS for version 0.9.8\n",
    "time": 1765235049
  },
  "_maintainer": {
    "name": "Teemu Daniel Laajala",
    "email": "teelaa@utu.fi",
    "login": "syksy",
    "description": "Finn with a knack for bioinformatics (mostly cancer), artificial intelligence, machine learning, game jams, and all that jazz.",
    "uuid": 36551395
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "lme4",
      "role": "Suggests"
    },
    {
      "package": "nlme",
      "role": "Suggests"
    },
    {
      "package": "amap",
      "role": "Suggests"
    },
    {
      "package": "nbpMatching",
      "role": "Suggests"
    },
    {
      "package": "lattice",
      "role": "Suggests"
    },
    {
      "package": "lmerTest",
      "role": "Suggests"
    },
    {
      "package": "xtable",
      "role": "Suggests"
    },
    {
      "package": "Cairo",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "MASS",
      "role": "Suggests"
    }
  ],
  "_owner": "syksy",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-50",
      "n": 7
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "syksy",
      "count": 13,
      "uuid": 36551395
    }
  ],
  "_userbio": {
    "uuid": 36551395,
    "type": "user",
    "name": "T. D. Laajala",
    "description": "Finn with a knack for bioinformatics (mostly cancer), artificial intelligence, machine learning, game jams, and all that jazz."
  },
  "_downloads": {
    "count": 192,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hamlet"
  },
  "_devurl": "https://github.com/syksy/hamlet",
  "_searchresults": 26,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/hamlet.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/syksy/hamlet",
  "_realowner": "syksy",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.7",
      "date": "2014-05-29"
    },
    {
      "version": "0.9.4",
      "date": "2015-08-04"
    },
    {
      "version": "0.9.4-2",
      "date": "2015-10-15"
    },
    {
      "version": "0.9.5",
      "date": "2016-10-25"
    },
    {
      "version": "0.9.5-2",
      "date": "2017-10-04"
    },
    {
      "version": "0.9.6",
      "date": "2018-05-26"
    },
    {
      "version": "0.9.8",
      "date": "2025-12-11"
    }
  ],
  "_exports": [
    "extendsymrange",
    "hmap",
    "hmap.annotate",
    "hmap.key",
    "match.allocate",
    "match.bb",
    "match.dummy",
    "match.ga",
    "match.mat2vec",
    "match.vec2mat",
    "mem.getcomp",
    "mem.plotran",
    "mem.plotresid",
    "mem.powersimu",
    "mix.binary",
    "mix.fun",
    "mixplot",
    "smartjitter"
  ],
  "_datasets": [
    {
      "name": "orxlong",
      "title": "Long-format longitudinal data for the ORX study",
      "object": "orxlong",
      "file": "orxlong.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "PSA",
        "log2PSA",
        "Day",
        "TrDay",
        "Date",
        "Group",
        "Submatch",
        "ORXTx",
        "ORX",
        "Intact"
      ],
      "rows": 392,
      "table": true,
      "tojson": true
    },
    {
      "name": "orxwide",
      "title": "Wide-format baseline data for the ORX study",
      "object": "orxwide",
      "file": "orxwide.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "Group",
        "Submatch",
        "Volume",
        "PSA",
        "High",
        "BodyWeight",
        "PSAChange"
      ],
      "rows": 109,
      "table": true,
      "tojson": true
    },
    {
      "name": "vcaplong",
      "title": "Long-format data of the Castration-resistant Prostate Cancer experiment using the VCaP cell line.",
      "object": "vcaplong",
      "file": "vcaplong.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "PSA",
        "log2PSA",
        "BW",
        "Submatch",
        "ID",
        "Week",
        "DrugWeek",
        "Group",
        "Vehicle",
        "ARN",
        "MDV"
      ],
      "rows": 225,
      "table": true,
      "tojson": true
    },
    {
      "name": "vcapwide",
      "title": "Wide-format data of the Castration-resistant Prostate Cancer experiment using the VCaP cell line.",
      "object": "vcapwide",
      "file": "vcapwide.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "CastrationDate",
        "CageAtAllocation",
        "Group",
        "TreatmentInitiationWeek",
        "Submatch",
        "ID",
        "PSAWeek2",
        "PSAWeek3",
        "PSAWeek4",
        "PSAWeek5",
        "PSAWeek6",
        "PSAWeek7",
        "PSAWeek8",
        "PSAWeek9",
        "PSAWeek10",
        "PSAWeek11",
        "PSAWeek12",
        "PSAWeek13",
        "PSAWeek14",
        "BWWeek0",
        "BWWeek1",
        "BWWeek2",
        "BWWeek3",
        "BWWeek4",
        "BWWeek5",
        "BWWeek6",
        "BWWeek7",
        "BWWeek8",
        "BWWeek9",
        "BWWeek10",
        "BWWeek11",
        "BWWeek12",
        "BWWeek13",
        "BWWeek14"
      ],
      "rows": 45,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "hamlet-package",
      "title": "Hierarchical Optimal Matching and Machine Learning Toolbox",
      "topics": [
        "hamlet-package",
        "hamlet"
      ]
    },
    {
      "page": "extendsymrange",
      "title": "Extend range of variable limits while retaining a point of symmetricity",
      "topics": [
        "extendsymrange"
      ]
    },
    {
      "page": "hmap",
      "title": "Plot-region based heatmap",
      "topics": [
        "hmap"
      ]
    },
    {
      "page": "hmap.annotate",
      "title": "Add a row and column annotations to a plot-region based heatmap built with 'hmap'",
      "topics": [
        "hmap.annotate"
      ]
    },
    {
      "page": "hmap.key",
      "title": "Add a color key to a plot-region based heatmap built with 'hmap'",
      "topics": [
        "hmap.key"
      ]
    },
    {
      "page": "match.allocate",
      "title": "Allocation of matched units to intervention arms",
      "topics": [
        "match.allocate"
      ]
    },
    {
      "page": "match.bb",
      "title": "Branch and Bound algorithm implementation for performing multigroup non-bipartite matching",
      "topics": [
        "match.bb"
      ]
    },
    {
      "page": "match.dummy",
      "title": "Create dummy individuals or sinks to a data matrix or a distance/dissimilarity matrix",
      "topics": [
        "match.dummy"
      ]
    },
    {
      "page": "match.ga",
      "title": "Non-bipartite matching using the Genetic Algorithm (GA)",
      "topics": [
        "match.ga"
      ]
    },
    {
      "page": "match.mat2vec",
      "title": "Transform a binary matching matrix to a matching vector",
      "topics": [
        "match.mat2vec"
      ]
    },
    {
      "page": "match.vec2mat",
      "title": "Transform a matching vector to a binary matching matrix",
      "topics": [
        "match.vec2mat"
      ]
    },
    {
      "page": "mem.getcomp",
      "title": "Extract per-observation components for fixed and random effects of a mixed-effects model",
      "topics": [
        "mem.getcomp"
      ]
    },
    {
      "page": "mem.plotran",
      "title": "Plot random effects histograms for a fitted mixed-effects model",
      "topics": [
        "mem.plotran"
      ]
    },
    {
      "page": "mem.plotresid",
      "title": "Plot residuals of a mixed-effects model along with trend lines",
      "topics": [
        "mem.plotresid"
      ]
    },
    {
      "page": "mem.powersimu",
      "title": "Power simulations for the fixed effects of a mixed-effects model through structured bootstrapping of the data and re-fitting of the model",
      "topics": [
        "mem.powersimu"
      ]
    },
    {
      "page": "mix.binary",
      "title": "Binary coding of categorical variables",
      "topics": [
        "mix.binary"
      ]
    },
    {
      "page": "mix.fun",
      "title": "Apply function to numerical columns of a mixed data.frame while ignoring non-numeric fields",
      "topics": [
        "mix.fun"
      ]
    },
    {
      "page": "mixplot",
      "title": "Scatterplot for mixed type data",
      "topics": [
        "mixplot"
      ]
    },
    {
      "page": "orxlong",
      "title": "Long-format longitudinal data for the ORX study",
      "topics": [
        "orxlong"
      ]
    },
    {
      "page": "orxwide",
      "title": "Wide-format baseline data for the ORX study",
      "topics": [
        "orxwide"
      ]
    },
    {
      "page": "smartjitter",
      "title": "Smart jittering function for deterministic shifting of overlapping values",
      "topics": [
        "smartjitter"
      ]
    },
    {
      "page": "vcaplong",
      "title": "Long-format data of the Castration-resistant Prostate Cancer experiment using the VCaP cell line.",
      "topics": [
        "vcaplong"
      ]
    },
    {
      "page": "vcapwide",
      "title": "Wide-format data of the Castration-resistant Prostate Cancer experiment using the VCaP cell line.",
      "topics": [
        "vcapwide"
      ]
    }
  ],
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "introduction.Rnw",
      "filename": "introduction.pdf",
      "title": "Introduction to hamlet",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2018-07-17 16:18:13",
      "modified": "2025-12-08 23:01:19",
      "commits": 2
    }
  ],
  "_score": 4.193124598354462,
  "_indexed": true,
  "_nocasepkg": "hamlet",
  "_universes": [
    "syksy"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.9.8",
      "date": "2026-06-06T07:08:47.000Z",
      "distro": "noble",
      "commit": "7e571f481a816d7c3ce11b14c5423d8d6cc96259",
      "fileid": "e8b78b2cc2003455616befc3aa290077d30c282f5d83b52cb0913f3449e2ee08",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/syksy/actions/runs/27055706343"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.9.8",
      "date": "2026-06-06T07:08:26.000Z",
      "distro": "noble",
      "commit": "7e571f481a816d7c3ce11b14c5423d8d6cc96259",
      "fileid": "7ab50f3f3687bde3996a45c9c3b1ab7c7f40e75c739dd2c7ce724ce0ede49828",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/syksy/actions/runs/27055706343"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.9.8",
      "date": "2026-06-06T07:07:53.000Z",
      "commit": "7e571f481a816d7c3ce11b14c5423d8d6cc96259",
      "fileid": "78629289b0398dedd10260b261bef77699d358df3bed30fcd45bf5e1965c8761",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/syksy/actions/runs/27055706343"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.9.8",
      "date": "2026-06-06T07:07:50.000Z",
      "commit": "7e571f481a816d7c3ce11b14c5423d8d6cc96259",
      "fileid": "a0cba6769227ad8353e41842a087f399d5df0efb6bf4f3cd5470affa53b14c3c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/syksy/actions/runs/27055706343"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.9.8",
      "date": "2026-06-06T07:08:23.000Z",
      "commit": "7e571f481a816d7c3ce11b14c5423d8d6cc96259",
      "fileid": "6e441b381c94261d35a094213d2c2ffcec65667c521d22584ddfb86e6a41ef73",
      "status": "success",
      "buildurl": "https://github.com/r-universe/syksy/actions/runs/27055706343"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.9.8",
      "date": "2026-06-06T07:07:45.000Z",
      "commit": "7e571f481a816d7c3ce11b14c5423d8d6cc96259",
      "fileid": "d4f9da075116f4e218906022ea82d925e2be92f34dc359a31d0c96bbe1ed36b4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/syksy/actions/runs/27055706343"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.9.8",
      "date": "2026-06-06T07:07:36.000Z",
      "commit": "7e571f481a816d7c3ce11b14c5423d8d6cc96259",
      "fileid": "8134c98cb570824e3f97cff8a85ce1c440339bcf75ba33d761b78ce71b9a4c2a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/syksy/actions/runs/27055706343"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.9.8",
      "date": "2026-06-06T07:08:21.000Z",
      "commit": "7e571f481a816d7c3ce11b14c5423d8d6cc96259",
      "fileid": "69f42d772af8b96bb00667cc1723717954ae0de8247fa52bb0a2231e12a3fe64",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/syksy/actions/runs/27055706343"
    }
  ]
}