{
  "_id": "6ac24698d743750d376d7aa4",
  "Package": "PeakSegOptimal",
  "Authors@R": "person(given = c(\"Toby\", \"Dylan\"),\nfamily = \"Hocking\",\nrole = c(\"aut\", \"cre\"),\nemail = \"toby.hocking@r-project.org\")",
  "Version": "2024.10.1",
  "License": "GPL-3",
  "URL": "https://github.com/tdhock/PeakSegOptimal",
  "BugReports": "https://github.com/tdhock/PeakSegOptimal/issues",
  "Title": "Optimal Segmentation Subject to Up-Down Constraints",
  "Description": "Computes optimal changepoint models using the Poisson\nlikelihood for non-negative count data, subject to the PeakSeg\nconstraint: the first change must be up, second change down,\nthird change up, etc. For more info about the models and\nalgorithms, read \"Constrained Dynamic Programming and\nSupervised Penalty Learning Algorithms for Peak Detection\"\n<https://jmlr.org/papers/v21/18-843.html> by TD Hocking et al.",
  "Remotes": [
    "tdhock/cosegData"
  ],
  "Repository": "https://tdhock.r-universe.dev",
  "Date/Publication": "2026-03-27 18:50:00 UTC",
  "RemoteUrl": "https://github.com/tdhock/peaksegoptimal",
  "RemoteRef": "HEAD",
  "RemoteSha": "40b762a4ac7f0ff13455848029e686248a6f63d5",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-04 12:22:43 UTC",
    "User": "root"
  },
  "Author": "Toby Dylan Hocking [aut, cre]",
  "Maintainer": "Toby Dylan Hocking <toby.hocking@r-project.org>",
  "_user": "tdhock",
  "_type": "src",
  "_file": "PeakSegOptimal_2024.10.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/abe288c03f00c82ab2774ad1b3354fabfdd39d64aec9d8f3279776cf5753a02c",
  "_filesize": 263782,
  "_sha256": "abe288c03f00c82ab2774ad1b3354fabfdd39d64aec9d8f3279776cf5753a02c",
  "_expires": "2027-01-12T12:29:10.000Z",
  "_created": "2026-10-04T12:22:43.000Z",
  "_published": "2026-10-04T12:29:12.144Z",
  "_jobs": [
    {
      "job": 111435181751,
      "time": 132,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11302409727"
    },
    {
      "job": 111435181715,
      "time": 183,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11303426786"
    },
    {
      "job": 111435181745,
      "time": 125,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11302244927"
    },
    {
      "job": 111435181764,
      "time": 156,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11303296202"
    },
    {
      "job": 111435181700,
      "time": 144,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11303815040"
    },
    {
      "job": 111435181752,
      "time": 234,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11303815141"
    },
    {
      "job": 111435181684,
      "time": 150,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11303182265"
    },
    {
      "job": 111435181649,
      "time": 243,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11302992933"
    },
    {
      "job": 111434622725,
      "time": 194,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11302649273"
    },
    {
      "job": 111435181609,
      "time": 104,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11303197109"
    },
    {
      "job": 111435181723,
      "time": 300,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11303591338"
    },
    {
      "job": 111435181670,
      "time": 345,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11303142774"
    },
    {
      "job": 111435181682,
      "time": 295,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11303392064"
    },
    {
      "job": 111435181719,
      "time": 278,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11303112795"
    },
    {
      "job": 111435181774,
      "time": 259,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11302943204"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115",
  "_status": "success",
  "_upstream": "https://github.com/tdhock/peaksegoptimal",
  "_commit": {
    "id": "40b762a4ac7f0ff13455848029e686248a6f63d5",
    "author": "Toby Dylan Hocking <toby.hocking@r-project.org>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #25 from williamzhang7792/github-actions\n\nconvert CI from Travis to GitHub Actions",
    "time": 1774637400
  },
  "_maintainer": {
    "name": "Toby Dylan Hocking",
    "email": "toby.hocking@r-project.org",
    "login": "tdhock",
    "description": "",
    "uuid": 932850
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "penaltyLearning",
      "role": "Imports"
    },
    {
      "package": "PeakSegDP",
      "version": ">= 2016.08.06",
      "role": "Suggests"
    },
    {
      "package": "cosegData",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "data.table",
      "version": ">= 1.9.8",
      "role": "Suggests"
    }
  ],
  "_owner": "tdhock",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-13",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 6,
  "_contributors": [
    {
      "user": "tdhock",
      "count": 253,
      "uuid": 932850
    },
    {
      "user": "williamzhang7792",
      "count": 6,
      "uuid": 141804129
    },
    {
      "user": "azamlynny",
      "count": 1,
      "uuid": 32941757
    }
  ],
  "_userbio": {
    "uuid": 932850,
    "type": "user",
    "name": "Toby Dylan Hocking",
    "followers": 433
  },
  "_downloads": {
    "count": 315,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PeakSegOptimal"
  },
  "_devurl": "https://github.com/tdhock/peaksegoptimal",
  "_searchresults": 40,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/PeakSegOptimal.html"
  ],
  "_homeurl": "https://github.com/tdhock/peaksegoptimal",
  "_realowner": "tdhock",
  "_cranurl": true,
  "_releases": [
    {
      "version": "2017.06.20",
      "date": "2017-06-21"
    },
    {
      "version": "2017.07.11",
      "date": "2017-07-11"
    },
    {
      "version": "2017.07.12",
      "date": "2017-07-12"
    },
    {
      "version": "2018.05.25",
      "date": "2018-05-25"
    },
    {
      "version": "2024.1.24",
      "date": "2024-01-24"
    },
    {
      "version": "2024.10.1",
      "date": "2024-10-02"
    }
  ],
  "_exports": [
    "oracleModelComplexity",
    "PeakSegFPOP",
    "PeakSegFPOPchrom",
    "PeakSegPDPA",
    "PeakSegPDPAchrom",
    "PeakSegPDPAInf",
    "PoissonLoss"
  ],
  "_datasets": [
    {
      "name": "H3K4me3_PGP_immune_chunk24",
      "title": "H3K4me3_PGP_immune ChIP-seq data set chunk 24",
      "object": "H3K4me3_PGP_immune_chunk24",
      "file": "H3K4me3_PGP_immune_chunk24.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "cell.type",
        "sample.id",
        "chromStart",
        "chromEnd",
        "coverage"
      ],
      "rows": 66713,
      "table": true,
      "tojson": true
    },
    {
      "name": "H3K4me3_XJ_immune_chunk1",
      "title": "H3K4me3_XJ_immune chunk 1",
      "object": "H3K4me3_XJ_immune_chunk1",
      "file": "H3K4me3_XJ_immune_chunk1.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "cell.type",
        "sample.id",
        "chromStart",
        "chromEnd",
        "coverage"
      ],
      "rows": 18027,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "H3K4me3_PGP_immune_chunk24",
      "title": "H3K4me3_PGP_immune ChIP-seq data set chunk 24",
      "topics": [
        "H3K4me3_PGP_immune_chunk24"
      ]
    },
    {
      "page": "H3K4me3_XJ_immune_chunk1",
      "title": "H3K4me3_XJ_immune chunk 1",
      "topics": [
        "H3K4me3_XJ_immune_chunk1"
      ]
    },
    {
      "page": "oracleModelComplexity",
      "title": "oracleModelComplexity",
      "topics": [
        "oracleModelComplexity"
      ]
    },
    {
      "page": "PeakSegFPOP",
      "title": "PeakSegFPOP",
      "topics": [
        "PeakSegFPOP"
      ]
    },
    {
      "page": "PeakSegFPOPchrom",
      "title": "PeakSegFPOPchrom",
      "topics": [
        "PeakSegFPOPchrom"
      ]
    },
    {
      "page": "PeakSegPDPA",
      "title": "PeakSegPDPA",
      "topics": [
        "PeakSegPDPA"
      ]
    },
    {
      "page": "PeakSegPDPAchrom",
      "title": "PeakSegPDPAchrom",
      "topics": [
        "PeakSegPDPAchrom"
      ]
    },
    {
      "page": "PeakSegPDPAInf",
      "title": "PeakSegPDPAInf",
      "topics": [
        "PeakSegPDPAInf"
      ]
    },
    {
      "page": "PoissonLoss",
      "title": "PoissonLoss",
      "topics": [
        "PoissonLoss"
      ]
    }
  ],
  "_rundeps": [
    "cli",
    "cpp11",
    "data.table",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "penaltyLearning",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 3.681241237375587,
  "_indexed": true,
  "_nocasepkg": "peaksegoptimal",
  "_universes": [
    "tdhock"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2024.10.1",
      "date": "2026-10-04T12:24:22.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/134ab578386ed2e4c1ea616c0f71d605ec84aeb15ca14beff3d261859dd88285",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2024.10.1",
      "date": "2026-10-04T12:25:14.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/327adc1b0b9eaa9d7aefb219b52081e8523cf9f233aaec820359ca5526c21d5e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2024.10.1",
      "date": "2026-10-04T12:24:17.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/6638516e050baa32bff9a499784bf1ab7a06b03026e44ac0eb4a576061a43b17",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2024.10.1",
      "date": "2026-10-04T12:24:32.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/13be53089c0518c8472d50819eefb93dd8cca081f32aa9bb434f5555023c6c88",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2024.10.1",
      "date": "2026-10-04T12:24:29.000Z",
      "arch": "aarch64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/4be30a45d7f740db8b5d8d54898401440b3183383a9c126978d4fb6be4c78c51",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2024.10.1",
      "date": "2026-10-04T12:25:23.000Z",
      "arch": "x86_64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/643fbc567c7e180cdf37199e6c497abf555798c786f0ae91cbea195516050d82",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2024.10.1",
      "date": "2026-10-04T12:24:40.000Z",
      "arch": "aarch64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/876af1287b07e9ee55165fdde0614f620d3d26ea8d4ab6ebb7adde3286b9b2da",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2024.10.1",
      "date": "2026-10-04T12:25:29.000Z",
      "arch": "x86_64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/388383b12f63cd9f11b7ab3f685abdfda6fe105076fb0a7a78a135180308a5b7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2024.10.1",
      "date": "2026-10-04T12:24:44.000Z",
      "arch": "emscripten",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/73202a056061cc6a612b15aef7b810bcf4c5d603805fc45df2b4842626f4bbc1",
      "status": "success",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2024.10.1",
      "date": "2026-10-04T12:26:49.000Z",
      "arch": "aarch64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/a48e30d1a5b6bb29ee80ba928890c7bc10f276a149afd8137ec98d7f2d1efeec",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2024.10.1",
      "date": "2026-10-04T12:24:05.000Z",
      "arch": "x86_64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/357d75e4f5326248d748c34b77931969303b4f9bbfb54354c6fce48e21622952",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2024.10.1",
      "date": "2026-10-04T12:24:00.000Z",
      "arch": "x86_64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/d3ad08beb5be25a329e1704193d6db9b871214d8c906687ca55db0daed534470",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2024.10.1",
      "date": "2026-10-04T12:26:31.000Z",
      "arch": "aarch64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/5d92fb4e17617374cf42171eafee511d1fab9eb7338ccd87231e1f5446625431",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2024.10.1",
      "date": "2026-10-04T12:23:55.000Z",
      "arch": "x86_64",
      "commit": "40b762a4ac7f0ff13455848029e686248a6f63d5",
      "fileid": "https://r2.ropensci.org/a77afc94f035b151b6c52466b2379597b921a9181baad426e9bf60f4a08b3a58",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tdhock/actions/runs/37201709115"
    }
  ]
}