{
  "_id": "6a1933a7acfb0bcc41dd1918",
  "Package": "CFAcoop",
  "Type": "Package",
  "Title": "Colony Formation Assay: Taking into Account Cellular Cooperation",
  "Version": "1.0.0",
  "Authors@R": "c(\nperson(\"Daniel\", \"Samaga\",\nemail = \"daniel.samaga@helmholtz-muenchen.de\",\nrole = c(\"cre\",\"aut\")),\nperson(\"Nikko\", \"Brix\",\nrole = \"aut\"),\nperson(\"Kirsten\", \"Lauber\",\nrole = \"aut\"),\nperson(\"Horst\", \"Zitzelsberger\",\nrole = \"aut\"))",
  "Maintainer": "Daniel Samaga <daniel.samaga@helmholtz-muenchen.de>",
  "URL": "https://github.com/ZytoHMGU/CFAcoop",
  "BugReports": "https://github.com/ZytoHMGU/CFAcoop/issues",
  "Description": "Cellular cooperation compromises the plating\nefficiency-based analysis of clonogenic survival data. This\ntool provides functions that enable a robust analysis of colony\nformation assay (CFA) data in presence or absence of cellular\ncooperation. The implemented method has been described in Brix\net al. (2020). (Brix, N., Samaga, D., Hennel, R. et al. \"The\nclonogenic assay: robustness of plating efficiency-based\nanalysis is strongly compromised by cellular cooperation.\"\nRadiat Oncol 15, 248 (2020). <doi:10.1186/s13014-020-01697-y>)\nPower regression for parameter estimation, calculation of\nsurvival fractions, uncertainty analysis and plotting functions\nare provided.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.1.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://zytohmgu.r-universe.dev",
  "Date/Publication": "2021-06-11 08:20:35 UTC",
  "RemoteUrl": "https://github.com/zytohmgu/cfacoop",
  "RemoteRef": "HEAD",
  "RemoteSha": "39bb6d02387d0f00f2cad4f03e38901c078d4cc4",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 06:15:42 UTC",
    "User": "root"
  },
  "Author": "Daniel Samaga [cre, aut],\nNikko Brix [aut],\nKirsten Lauber [aut],\nHorst Zitzelsberger [aut]",
  "MD5sum": "05a01d0ebe9a7c632ad2c2b42ba9c18a",
  "_user": "zytohmgu",
  "_type": "src",
  "_file": "CFAcoop_1.0.0.tar.gz",
  "_fileid": "3ed8fff64d1304f8b8e7e0d0fa7dfe63f9ffc65e9aa2b7c2b62acee3e10a6b87",
  "_filesize": 545063,
  "_sha256": "3ed8fff64d1304f8b8e7e0d0fa7dfe63f9ffc65e9aa2b7c2b62acee3e10a6b87",
  "_created": "2026-05-29T06:15:42.000Z",
  "_published": "2026-05-29T06:35:19.462Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78448277585,
      "time": 147,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7284361212"
    },
    {
      "job": 78448277583,
      "time": 145,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284360430"
    },
    {
      "job": 78448277594,
      "time": 163,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7284589016"
    },
    {
      "job": 78448277580,
      "time": 159,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284576826"
    },
    {
      "job": 78447912293,
      "time": 190,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284326435"
    },
    {
      "job": 78448277564,
      "time": 127,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284356003"
    },
    {
      "job": 78448277586,
      "time": 143,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7284360124"
    },
    {
      "job": 78448277579,
      "time": 88,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7284347325"
    },
    {
      "job": 78448277591,
      "time": 92,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284347968"
    }
  ],
  "_buildurl": "https://github.com/r-universe/zytohmgu/actions/runs/26621373901",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/zytohmgu/cfacoop",
  "_commit": {
    "id": "39bb6d02387d0f00f2cad4f03e38901c078d4cc4",
    "author": "ZytoHMGU <daniel.samaga@helmholtz-muenchen.de>",
    "committer": "ZytoHMGU <daniel.samaga@helmholtz-muenchen.de>",
    "message": "Uncertainty by Taylor Expansion\n",
    "time": 1623399635
  },
  "_maintainer": {
    "name": "Daniel Samaga",
    "email": "daniel.samaga@helmholtz-muenchen.de",
    "login": "zytohmgu",
    "description": "",
    "uuid": 39589287
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Hmisc",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "zytohmgu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "zytohmgu",
      "count": 16,
      "uuid": 39589287
    }
  ],
  "_userbio": {
    "uuid": 39589287,
    "type": "user",
    "name": "ZytoHMGU"
  },
  "_downloads": {
    "count": 265,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CFAcoop"
  },
  "_devurl": "https://github.com/zytohmgu/cfacoop",
  "_searchresults": 3,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/CFAcoop.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/zytohmgu/cfacoop",
  "_realowner": "zytohmgu",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2020-11-25"
    },
    {
      "version": "1.0.0",
      "date": "2021-06-11"
    }
  ],
  "_exports": [
    "analyze_survival",
    "calculate_sf",
    "export_sf",
    "plot_sf",
    "pwr_reg"
  ],
  "_datasets": [
    {
      "name": "CFAdata",
      "title": "Colony Formation Assay data on cellular cooperation",
      "object": "CFAdata",
      "class": [
        "data.frame"
      ],
      "fields": [
        "cell.line",
        "Cells seeded",
        "0 Gy",
        "1 Gy",
        "2 Gy",
        "4 Gy",
        "6 Gy",
        "8 Gy"
      ],
      "rows": 454,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "analyze_survival",
      "title": "analyze_survival",
      "topics": [
        "analyze_survival"
      ]
    },
    {
      "page": "calculate_sf",
      "title": "calculate_sf",
      "topics": [
        "calculate_sf"
      ]
    },
    {
      "page": "CFAdata",
      "title": "Colony Formation Assay data on cellular cooperation",
      "topics": [
        "CFAdata"
      ]
    },
    {
      "page": "export_sf",
      "title": "export_sf",
      "topics": [
        "export_sf"
      ]
    },
    {
      "page": "plot_SF",
      "title": "plot_sf",
      "topics": [
        "plot_sf"
      ]
    },
    {
      "page": "pwr_reg",
      "title": "pwr_reg",
      "topics": [
        "pwr_reg"
      ]
    }
  ],
  "_rundeps": [
    "backports",
    "base64enc",
    "bslib",
    "cachem",
    "checkmate",
    "cli",
    "cluster",
    "colorspace",
    "cpp11",
    "data.table",
    "digest",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "foreign",
    "Formula",
    "fs",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lifecycle",
    "magrittr",
    "memoise",
    "mime",
    "nnet",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "rlang",
    "rmarkdown",
    "rpart",
    "rstudioapi",
    "S7",
    "sass",
    "scales",
    "stringi",
    "stringr",
    "tinytex",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "CFAcoop.Rmd",
      "filename": "CFAcoop.html",
      "title": "CFAcoop",
      "engine": "knitr::rmarkdown",
      "headings": [
        "How to use this package (and why)",
        "Introduction",
        "Cellular Cooperation",
        "Clonogenic Survival",
        "Getting Started",
        "Fast Analysis and Plotting of Results",
        "Details for Focussed Analysis",
        "Assess Cellular Cooperation",
        "Determine Clonogenic Survival Fractions",
        "Remark on Ignoring Cellular Cooperation",
        "Determine Uncertainty of Survival Fractions",
        "What's the problem with PE-based analysis?",
        "(1) The non-cooperative case",
        "(2) The cooperative case",
        "Conclusion from (1) and (2)"
      ],
      "created": "2020-11-06 11:18:39",
      "modified": "2021-06-11 08:20:35",
      "commits": 4
    }
  ],
  "_score": 3,
  "_indexed": true,
  "_nocasepkg": "cfacoop",
  "_universes": [
    "zytohmgu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-29T06:17:56.000Z",
      "distro": "noble",
      "commit": "39bb6d02387d0f00f2cad4f03e38901c078d4cc4",
      "fileid": "6e5a5a8347cc971eac0674239b5477618c010b8af6dd2d99d922da5b0ca2c664",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zytohmgu/actions/runs/26621373901"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.0",
      "date": "2026-05-29T06:17:55.000Z",
      "distro": "noble",
      "commit": "39bb6d02387d0f00f2cad4f03e38901c078d4cc4",
      "fileid": "476e8ebeb880f319cd3d9175f3040538e3b041b675fbff5e7421b9d6c6c2ef20",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zytohmgu/actions/runs/26621373901"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-29T06:34:17.000Z",
      "commit": "39bb6d02387d0f00f2cad4f03e38901c078d4cc4",
      "fileid": "5121ce45a863f398bb7db6552934d1b61f83540315678e87a2880a6228ed5a09",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zytohmgu/actions/runs/26621373901"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.0",
      "date": "2026-05-29T06:33:31.000Z",
      "commit": "39bb6d02387d0f00f2cad4f03e38901c078d4cc4",
      "fileid": "2af6f4b47e49d0993dac8f1d71e41068597c29d90dc9cda1e0148a342524bd1e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zytohmgu/actions/runs/26621373901"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.0",
      "date": "2026-05-29T06:18:02.000Z",
      "commit": "39bb6d02387d0f00f2cad4f03e38901c078d4cc4",
      "fileid": "3e2de9c215c7cd834eb08a078779cbc4d10a4a73369fdb0889cd558add9e713d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/zytohmgu/actions/runs/26621373901"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T06:17:41.000Z",
      "commit": "39bb6d02387d0f00f2cad4f03e38901c078d4cc4",
      "fileid": "85ddba3a1d0a53417d5ad78a9e1bcd0a6d58752531a7b04779ac1eb78f49b50e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zytohmgu/actions/runs/26621373901"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T06:16:54.000Z",
      "commit": "39bb6d02387d0f00f2cad4f03e38901c078d4cc4",
      "fileid": "c276a9b0de0a7f4a54cd54afab8164f95377f7f50e8700ca1c575eef8880f932",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zytohmgu/actions/runs/26621373901"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.0",
      "date": "2026-05-29T06:16:55.000Z",
      "commit": "39bb6d02387d0f00f2cad4f03e38901c078d4cc4",
      "fileid": "938301310e233eadebba82cb721191c1d97e0b066b6b78a44fda8e88772fe987",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/zytohmgu/actions/runs/26621373901"
    }
  ]
}