{
  "_id": "6a141eccacfb0bcc41d3e0bd",
  "Package": "cpam",
  "Title": "Changepoint Additive Models for Time Series Omics Data",
  "Version": "0.2.1",
  "Authors@R": "c(person(\"Luke\", \"Yates\", email = \"luke.yates@utas.edu.au\", role = c(\"aut\", \"cre\",\"cph\"),\ncomment = c(ORCID = \"0000-0002-1685-3169\")),\nperson(\"Michael\", \"Charleston\", role = \"aut\"),\nperson(\"Jazmine\", \"Humphreys\", role = \"aut\"),\nperson(\"Steven\", \"Smith\", role = \"aut\"))",
  "Description": "Provides a comprehensive framework for time series omics\nanalysis, integrating changepoint detection, smooth and\nshape-constrained trends, and uncertainty quantification. It\nsupports gene- and transcript-level inferences, p-value\naggregation for improved power, and both case-only and\ncase-control designs. It includes an interactive 'shiny'\ninterface. The methods are described in Yates et al. (2024)\n<doi:10.1101/2024.12.22.630003>.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "URL": "https://l-a-yates.github.io/cpam/,\nhttps://github.com/l-a-yates/cpam",
  "Config/testthat/edition": "3",
  "BugReports": "https://github.com/l-a-yates/cpam/issues",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev",
  "Repository": "https://l-a-yates.r-universe.dev",
  "Date/Publication": "2026-03-26 04:18:23 UTC",
  "RemoteUrl": "https://github.com/l-a-yates/cpam",
  "RemoteRef": "HEAD",
  "RemoteSha": "9ebd3295f58cd1fb1bd97b8bcb5079df7eda42c6",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-25 10:00:48 UTC",
    "User": "root"
  },
  "Author": "Luke Yates [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0002-1685-3169>),\nMichael Charleston [aut],\nJazmine Humphreys [aut],\nSteven Smith [aut]",
  "Maintainer": "Luke Yates <luke.yates@utas.edu.au>",
  "MD5sum": "0a8077584ebe8c72e0cd9d33fed8dd39",
  "_user": "l-a-yates",
  "_type": "src",
  "_file": "cpam_0.2.1.tar.gz",
  "_fileid": "69e89dc49c68a9ec59ea986b7d859dc2b14296a500da423bf7ebc92820021052",
  "_filesize": 2667773,
  "_sha256": "69e89dc49c68a9ec59ea986b7d859dc2b14296a500da423bf7ebc92820021052",
  "_created": "2026-05-25T10:00:48.000Z",
  "_published": "2026-05-25T10:05:00.745Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77692817100,
      "time": 180,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7196040945"
    },
    {
      "job": 77692817091,
      "time": 179,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7196040855"
    },
    {
      "job": 77692817142,
      "time": 178,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7196031674"
    },
    {
      "job": 77692817102,
      "time": 221,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7196040770"
    },
    {
      "job": 77692260808,
      "time": 254,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7195994509"
    },
    {
      "job": 77692817160,
      "time": 138,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7196030465"
    },
    {
      "job": 77692817113,
      "time": 137,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7196030888"
    },
    {
      "job": 77692817144,
      "time": 125,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7196027374"
    },
    {
      "job": 77692817154,
      "time": 127,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7196028002"
    }
  ],
  "_buildurl": "https://github.com/r-universe/l-a-yates/actions/runs/26394618044",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/l-a-yates/cpam",
  "_commit": {
    "id": "9ebd3295f58cd1fb1bd97b8bcb5079df7eda42c6",
    "author": "l-a-yates <luke.yates@utas.edu.au>",
    "committer": "l-a-yates <luke.yates@utas.edu.au>",
    "message": "Increment version number to 0.2.1\n",
    "time": 1774498703
  },
  "_maintainer": {
    "name": "Luke Yates",
    "email": "luke.yates@utas.edu.au",
    "login": "l-a-yates",
    "description": "",
    "uuid": 57280417,
    "orcid": "0000-0002-1685-3169"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "bslib",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "mgcv",
      "role": "Imports"
    },
    {
      "package": "mvnfast",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "pbmcapply",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "scam",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "shinyjs",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tximport",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "l-a-yates",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-49",
      "n": 1
    },
    {
      "week": "2026-10",
      "n": 11
    },
    {
      "week": "2026-13",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "l-a-yates",
      "count": 132,
      "uuid": 57280417
    }
  ],
  "_userbio": {
    "uuid": 57280417,
    "type": "user",
    "name": "l-a-yates"
  },
  "_downloads": {
    "count": 479,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cpam"
  },
  "_devurl": "https://github.com/l-a-yates/cpam",
  "_pkgdown": "https://l-a-yates.github.io/cpam/",
  "_searchresults": 20,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/cpam.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/l-a-yates/cpam",
  "_realowner": "l-a-yates",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.3",
      "date": "2025-03-13"
    },
    {
      "version": "0.2.0",
      "date": "2026-03-04"
    },
    {
      "version": "0.2.1",
      "date": "2026-03-27"
    }
  ],
  "_exports": [
    "%>%",
    "acat",
    "compute_p_values",
    "estimate_changepoint",
    "lancaster",
    "plot_cluster",
    "plot_cpam",
    "prepare_cpam",
    "results",
    "select_shape",
    "ts_filter",
    "visualise"
  ],
  "_help": [
    {
      "page": "acat",
      "title": "Aggregated Cauchy Association Test",
      "topics": [
        "acat"
      ]
    },
    {
      "page": "compute_p_values",
      "title": "Compute p-values for each target ID",
      "topics": [
        "compute_p_values"
      ]
    },
    {
      "page": "cpam-class",
      "title": "The cpam class",
      "topics": [
        "cpam",
        "cpam-class"
      ]
    },
    {
      "page": "estimate_changepoint",
      "title": "Use model selection to estimate changepoints",
      "topics": [
        "estimate_changepoint"
      ]
    },
    {
      "page": "lancaster",
      "title": "Lancaster's method for p-value aggregation",
      "topics": [
        "lancaster"
      ]
    },
    {
      "page": "plot_cluster",
      "title": "Plot clustered targets",
      "topics": [
        "plot_cluster"
      ]
    },
    {
      "page": "plot_cpam",
      "title": "Plot fitted changepoint additive models",
      "topics": [
        "plot_cpam"
      ]
    },
    {
      "page": "prepare_cpam",
      "title": "Prepare a cpam object",
      "topics": [
        "prepare_cpam"
      ]
    },
    {
      "page": "results",
      "title": "Create a results table from a cpam object",
      "topics": [
        "results"
      ]
    },
    {
      "page": "select_shape",
      "title": "Use model selection to select a shape for each target",
      "topics": [
        "select_shape"
      ]
    },
    {
      "page": "ts_filter",
      "title": "Removes lowly expressed genes",
      "topics": [
        "ts_filter"
      ]
    },
    {
      "page": "visualise",
      "title": "Launches a Shiny app to visualise the data and fitted models of a cpam object",
      "topics": [
        "visualise",
        "visualize"
      ]
    }
  ],
  "_readme": "https://github.com/l-a-yates/cpam/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "BH",
    "bslib",
    "cachem",
    "cli",
    "commonmark",
    "cpp11",
    "digest",
    "dplyr",
    "edgeR",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "htmltools",
    "httpuv",
    "isoband",
    "jquerylib",
    "jsonlite",
    "labeling",
    "later",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "Matrix",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "mvnfast",
    "nlme",
    "otel",
    "pbmcapply",
    "pillar",
    "pkgconfig",
    "promises",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "S7",
    "sass",
    "scales",
    "scam",
    "shiny",
    "shinyjs",
    "sourcetools",
    "statmod",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "tximport",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xtable"
  ],
  "_vignettes": [
    {
      "source": "cpam.Rmd",
      "filename": "cpam.html",
      "title": "cpam",
      "engine": "knitr::rmarkdown",
      "headings": [
        "About",
        "Data",
        "Installation",
        "Getting started",
        "Load packages",
        "Experimental design",
        "Count matrix",
        "Fitting cpam",
        "Result tables",
        "Plotting genes and transcripts",
        "Clusters",
        "Many more options",
        "Session Info",
        "References"
      ],
      "created": "2025-02-28 05:18:07",
      "modified": "2025-03-06 00:42:03",
      "commits": 3
    }
  ],
  "_score": 4.778151250383644,
  "_indexed": true,
  "_nocasepkg": "cpam",
  "_universes": [
    "l-a-yates"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.1",
      "date": "2026-05-25T10:03:20.000Z",
      "distro": "noble",
      "commit": "9ebd3295f58cd1fb1bd97b8bcb5079df7eda42c6",
      "fileid": "7993e3468a547cb12328151685f1e77946c041371e35eddd48b0ce55885356a8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/l-a-yates/actions/runs/26394618044"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.2.1",
      "date": "2026-05-25T10:03:17.000Z",
      "distro": "noble",
      "commit": "9ebd3295f58cd1fb1bd97b8bcb5079df7eda42c6",
      "fileid": "4d611ab227132c2132db5b344339c459d7cc8fa46e938f6f2a900ad5f2f930b0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/l-a-yates/actions/runs/26394618044"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.1",
      "date": "2026-05-25T10:02:59.000Z",
      "commit": "9ebd3295f58cd1fb1bd97b8bcb5079df7eda42c6",
      "fileid": "fd4e76fc0dddb0c867dcde7fe19875cc41fc93037e61486824f7b92b1f0fc90e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/l-a-yates/actions/runs/26394618044"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.2.1",
      "date": "2026-05-25T10:03:17.000Z",
      "commit": "9ebd3295f58cd1fb1bd97b8bcb5079df7eda42c6",
      "fileid": "bb5f23ad9813230b5d7c27e7e13474cbed8dbbd349d619df26189985e0129314",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/l-a-yates/actions/runs/26394618044"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.1",
      "date": "2026-05-25T10:03:20.000Z",
      "commit": "9ebd3295f58cd1fb1bd97b8bcb5079df7eda42c6",
      "fileid": "274d37d5cd4c463a13988f52ca433a8c852a17fb645c57a7efe969896e9c7103",
      "status": "success",
      "buildurl": "https://github.com/r-universe/l-a-yates/actions/runs/26394618044"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.1",
      "date": "2026-05-25T10:02:28.000Z",
      "commit": "9ebd3295f58cd1fb1bd97b8bcb5079df7eda42c6",
      "fileid": "d7c9aaf74001452370a2d3bccab813cbe0dc1dacde7514ea185ca91ca5ec349c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/l-a-yates/actions/runs/26394618044"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.1",
      "date": "2026-05-25T10:02:12.000Z",
      "commit": "9ebd3295f58cd1fb1bd97b8bcb5079df7eda42c6",
      "fileid": "69363fc0af58371b37f29ebf53a22a5b6102bcff38b72e2b22ff88a51cf3a0b3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/l-a-yates/actions/runs/26394618044"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.2.1",
      "date": "2026-05-25T10:02:16.000Z",
      "commit": "9ebd3295f58cd1fb1bd97b8bcb5079df7eda42c6",
      "fileid": "2d6ac3eb12b90dbde465f9d7bece83cedc4bec1380d2e5c6b3a4e6022a3e1ad7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/l-a-yates/actions/runs/26394618044"
    }
  ]
}