{
  "_id": "6a2d03e93efcd9bda42e9fb9",
  "Type": "Package",
  "Package": "AgeingError",
  "Title": "Estimating ageing error with 'TMB' from double reads",
  "Version": "2.1.1",
  "Date": "2026-05-14",
  "Authors@R": "c(\nperson(c(\"Andre\", \"E.\"), \"Punt\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-8489-2488\")),\nperson(c(\"Kelli\", \"F.\"), \"Johnson\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-9563-1937\")),\nperson(c(\"James\", \"T.\"), \"Thorson\", role = c(\"ctb\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-7415-1010\")),\nperson(c(\"Ian\", \"G.\"), \"Taylor\", , \"ian.taylor@noaa.gov\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-8489-2488\")),\nperson(\"Paul\", \"Burch\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-9853-462X\")),\nperson(c(\"Ian\", \"J.\"), \"Stewart\", role = \"ctb\"),\nperson(c(\"Melissa\", \"A.\"), \"Haltuch\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-2821-1267\"))\n)",
  "Description": "Implements Generalized Linear Mixed Effect Models (GLMMs)\nusing TMB to estimate ageing error from double reads of\notoliths.  The original analysis (Punt et al. 2008;\n<doi:10.1139/F08-111>) was written in ADMB and focused on\nestimating imprecision and bias. The newer version of the\nsoftware allows for random effects using TMB.",
  "License": "GPL-3",
  "URL": "https://pfmc-assessments.github.io/AgeingError/",
  "BugReports": "https://github.com/pfmc-assessments/AgeingError/issues",
  "VignetteBuilder": "litedown",
  "ByteCompile": "true",
  "Config/roxygen2/version": "8.0.0",
  "Config/testthat/edition": "3",
  "Config/testthat/parallel": "true",
  "Copyright": "inst/COPYRIGHTS",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "Roxygen": "list(markdown = TRUE)",
  "SystemRequirements": "GNU make, C++17",
  "Config/pak/sysreqs": "cmake make libuv1-dev libx11-dev",
  "Repository": "https://noaa-fisheries-integrated-toolbox.r-universe.dev",
  "Date/Publication": "2026-05-14 22:34:23 UTC",
  "RemoteUrl": "https://github.com/pfmc-assessments/AgeingError",
  "RemoteRef": "HEAD",
  "RemoteSha": "846ff30ab0a486eba89e495672699073740ee279",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-13 07:09:02 UTC",
    "User": "root"
  },
  "Author": "Andre E. Punt [aut] (ORCID: <https://orcid.org/0000-0001-8489-2488>),\nKelli F. Johnson [aut] (ORCID: <https://orcid.org/0000-0001-9563-1937>),\nJames T. Thorson [ctb, cph] (ORCID:\n<https://orcid.org/0000-0001-7415-1010>),\nIan G. Taylor [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8489-2488>),\nPaul Burch [aut] (ORCID: <https://orcid.org/0000-0002-9853-462X>),\nIan J. Stewart [ctb],\nMelissa A. Haltuch [ctb] (ORCID:\n<https://orcid.org/0000-0003-2821-1267>)",
  "Maintainer": "Ian G. Taylor <ian.taylor@noaa.gov>",
  "MD5sum": "369f19098214e85bc8ac8e20ff4068a5",
  "_user": "noaa-fisheries-integrated-toolbox",
  "_type": "src",
  "_file": "AgeingError_2.1.1.tar.gz",
  "_fileid": "d49d3c23bf28a6ef9d0b91ff69346c54d42fc738c0a1de6d6ed4cadca4ee41fa",
  "_filesize": 316348,
  "_sha256": "d49d3c23bf28a6ef9d0b91ff69346c54d42fc738c0a1de6d6ed4cadca4ee41fa",
  "_created": "2026-06-13T07:09:02.000Z",
  "_published": "2026-06-13T07:16:57.233Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 81171711350,
      "time": 287,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7608508982"
    },
    {
      "job": 81171711353,
      "time": 138,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7608490225"
    },
    {
      "job": 81171711386,
      "time": 210,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7608499440"
    },
    {
      "job": 81171711352,
      "time": 177,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7608495980"
    },
    {
      "job": 81171711376,
      "time": 142,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7608524677"
    },
    {
      "job": 81171711399,
      "time": 275,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7608508244"
    },
    {
      "job": 81171711377,
      "time": 156,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7608501334"
    },
    {
      "job": 81171711378,
      "time": 375,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7608521251"
    },
    {
      "job": 81171334837,
      "time": 364,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7608472634"
    },
    {
      "job": 81171711322,
      "time": 140,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7608490351"
    },
    {
      "job": 81171711351,
      "time": 185,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7608496352"
    },
    {
      "job": 81171711374,
      "time": 139,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7608490731"
    },
    {
      "job": 81171711360,
      "time": 166,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7608494257"
    }
  ],
  "_buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/pfmc-assessments/AgeingError",
  "_commit": {
    "id": "846ff30ab0a486eba89e495672699073740ee279",
    "author": "iantaylor-NOAA <ian.taylor@noaa.gov>",
    "committer": "iantaylor-NOAA <ian.taylor@noaa.gov>",
    "message": "update WORDLIST after failed github action\n",
    "time": 1778798063
  },
  "_maintainer": {
    "name": "Ian G. Taylor",
    "email": "ian.taylor@noaa.gov",
    "login": "iantaylor-noaa",
    "orcid": "0000-0001-8489-2488",
    "description": "Fisheries stock assessment scientist at NOAA's Northwest Fisheries Science Center",
    "uuid": 4992918
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "TMB",
      "role": "LinkingTo"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "fs",
      "role": "Imports"
    },
    {
      "package": "lifecycle",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "TMB",
      "version": ">= 1.8.0",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "litedown",
      "role": "Suggests"
    },
    {
      "package": "remotes",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "pfmc-assessments",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-25",
      "n": 2
    },
    {
      "week": "2026-20",
      "n": 4
    }
  ],
  "_tags": [
    {
      "name": "v2.1.1",
      "date": "2026-05-14"
    }
  ],
  "_stars": 11,
  "_contributors": [
    {
      "user": "iantaylor-noaa",
      "count": 117,
      "uuid": 4992918
    },
    {
      "user": "kellijohnson-noaa",
      "count": 20,
      "uuid": 4108564
    },
    {
      "user": "james-thorson",
      "count": 13,
      "uuid": 7989837
    },
    {
      "user": "k-doering-noaa",
      "count": 1,
      "uuid": 48930335
    }
  ],
  "_userbio": {
    "uuid": 49974461,
    "type": "organization",
    "name": "NOAA Fisheries Integrated Toolbox",
    "description": "GitHub Organization to manage the NOAA FIT"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/AgeingError"
  },
  "_devurl": "https://github.com/pfmc-assessments/ageingerror",
  "_pkgdown": "https://pfmc-assessments.github.io/AgeingError/",
  "_searchresults": 9,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/AgeingError.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "ageing_comparison",
    "cMx",
    "CreateData",
    "CreateSpecs",
    "DoApplyAgeError",
    "estgrowth.vb",
    "fit",
    "load_data",
    "load_specs",
    "minimizer",
    "plot_output",
    "PlotOutputFn",
    "ProcessResults",
    "rMx",
    "run",
    "RunFn",
    "SimulatorFn",
    "StepwiseFn",
    "tally_repeats",
    "write_data_file",
    "write_files",
    "write_specs_file"
  ],
  "_help": [
    {
      "page": "ageing_comparison",
      "title": "Plot comparison of double age readings",
      "topics": [
        "ageing_comparison"
      ]
    },
    {
      "page": "cMx",
      "title": "Make a column matrix",
      "topics": [
        "cMx"
      ]
    },
    {
      "page": "CreateData",
      "title": "Deprecated function renamed to load_data()",
      "topics": [
        "CreateData"
      ]
    },
    {
      "page": "CreateSpecs",
      "title": "Deprecated function renamed to load_specs()",
      "topics": [
        "CreateSpecs"
      ]
    },
    {
      "page": "determine_n_sets",
      "title": "Determine the number of data sets in a data file",
      "topics": [
        "determine_n_sets"
      ]
    },
    {
      "page": "DoApplyAgeError",
      "title": "Run the ageing error optimization routine",
      "topics": [
        "DoApplyAgeError"
      ]
    },
    {
      "page": "estgrowth.vb",
      "title": "Calculate von Bertanlaffy Growth Parameters from Lengths and Ages",
      "topics": [
        "estgrowth.vb"
      ]
    },
    {
      "page": "fit",
      "title": "Fit an ageing error model using TMB",
      "topics": [
        "fit"
      ]
    },
    {
      "page": "load_data",
      "title": "Load the formatted ageing error data",
      "topics": [
        "load_data"
      ]
    },
    {
      "page": "load_specs",
      "title": "Read the ageing error specifications",
      "topics": [
        "load_specs"
      ]
    },
    {
      "page": "minimizer",
      "title": "Minimize the negative log likelihood",
      "topics": [
        "minimizer"
      ]
    },
    {
      "page": "plot_output",
      "title": "Plot output",
      "topics": [
        "plot_output"
      ]
    },
    {
      "page": "PlotOutputFn",
      "title": "Deprecated function replaced by plot_output()",
      "topics": [
        "PlotOutputFn"
      ]
    },
    {
      "page": "ProcessResults",
      "title": "Process results of the ageing error estimation",
      "topics": [
        "ProcessResults"
      ]
    },
    {
      "page": "rMx",
      "title": "Make a row matrix",
      "topics": [
        "rMx"
      ]
    },
    {
      "page": "run",
      "title": "Run ageing error routine",
      "topics": [
        "run"
      ]
    },
    {
      "page": "RunFn",
      "title": "Deprecated function replaced by run()",
      "topics": [
        "RunFn"
      ]
    },
    {
      "page": "SimulatorFn",
      "title": "Simulate double reading data",
      "topics": [
        "SimulatorFn"
      ]
    },
    {
      "page": "StepwiseFn",
      "title": "Step-wise model selection",
      "topics": [
        "StepwiseFn"
      ]
    },
    {
      "page": "tally_repeats",
      "title": "Tally repeated age reading combinations in a new count column",
      "topics": [
        "tally_repeats"
      ]
    },
    {
      "page": "write_data_file",
      "title": "Write a data file for the AgeingError package",
      "topics": [
        "write_data_file"
      ]
    },
    {
      "page": "write_files",
      "title": "Write the input files (data and specifications) for the AgeingError package",
      "topics": [
        "write_files"
      ]
    },
    {
      "page": "write_specs_file",
      "title": "Write a specifications file for the AgeingError package",
      "topics": [
        "write_specs_file"
      ]
    }
  ],
  "_readme": "https://github.com/pfmc-assessments/AgeingError/raw/HEAD/README.md",
  "_rundeps": [
    "bit",
    "bit64",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "dplyr",
    "fs",
    "generics",
    "glue",
    "hms",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "R6",
    "Rcpp",
    "RcppEigen",
    "readr",
    "rlang",
    "tibble",
    "tidyselect",
    "TMB",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "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": "getting_started.Rmd",
      "filename": "getting_started.html",
      "title": "Estimating ageing error using the TMB model written by André Punt",
      "author": "Paul Burch and Ian Taylor based on documentation written by André Punt",
      "engine": "litedown::vignette",
      "headings": [
        "Introduction",
        "R package",
        "Input files",
        "Data file",
        "Separate Data Sets",
        "Combined Data Set",
        "Other Considerations",
        "Specifications file",
        "Bias options",
        "Sigma options",
        "Example Specifications file",
        "Examples",
        "Blue Grenadier",
        "Bight Redfish",
        "School Whiting",
        "Sablefish",
        "Trouble Shooting",
        "Acknowledgements",
        "References"
      ],
      "created": "2024-05-29 23:55:15",
      "modified": "2025-05-01 15:30:41",
      "commits": 8
    }
  ],
  "_score": 4.518513939877888,
  "_indexed": false,
  "_nocasepkg": "ageingerror",
  "_universes": [
    "noaa-fisheries-integrated-toolbox"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.1",
      "date": "2026-06-13T07:13:44.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "5522dd8f61016a26093d6aaef5b374f35e7de42df009567e03c74e00559d5508",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.1",
      "date": "2026-06-13T07:11:20.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "dbd5bf36e1fd7bc5a6432fe248c42b1e3caf5eae4b147bb961093e9f6cf9e8f1",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.1.1",
      "date": "2026-06-13T07:12:27.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "8072d98bed119a2c1f4e0b006ced936934206146bc7af4c9cd722e609968e74d",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.1.1",
      "date": "2026-06-13T07:12:01.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "539e4c48186a90009e858537229d2efb8049d9cad004cc2321c1508c2641a8a4",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.1",
      "date": "2026-06-13T07:15:50.000Z",
      "arch": "aarch64",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "53250abc43493dca33463fc8950a795e801ba9175e8f2ccbe564bee8c70d7506",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.1",
      "date": "2026-06-13T07:12:56.000Z",
      "arch": "x86_64",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "6a872317583ee3beb5e9947a1349ad05100815abd15e54570d9447f9e90976a4",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.1.1",
      "date": "2026-06-13T07:12:38.000Z",
      "arch": "aarch64",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "4065bb19b16856f0403efd80e302a9095c4e0cc72c92594afc930063c6f1d827",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.1.1",
      "date": "2026-06-13T07:13:06.000Z",
      "arch": "x86_64",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "7d572c36c6c13b01853700ec6aeabf7c20c55d94537984e75ad05476c2a2d7a6",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.1.1",
      "date": "2026-06-13T07:11:56.000Z",
      "arch": "emscripten",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "fe3388fb7549ec9c8f494e28577472a2e2d18eb603faf6838c9edad68917fad5",
      "status": "success",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.1.1",
      "date": "2026-06-13T07:11:34.000Z",
      "arch": "x86_64",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "be4465413d1e396cb650b23b53a9c398c17503833e9bf304c4322eedf4ecc361",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.1.1",
      "date": "2026-06-13T07:10:42.000Z",
      "arch": "x86_64",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "33f305b8e831a820d3efdea789269b4d4c6c278080f786815d748943874e7298",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.1.1",
      "date": "2026-06-13T07:11:03.000Z",
      "arch": "x86_64",
      "commit": "846ff30ab0a486eba89e495672699073740ee279",
      "fileid": "18c1ddd441605763d9aa36957c32585bfd7ba5fca9ef203e4e30922dbbbd80ec",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/noaa-fisheries-integrated-toolbox/actions/runs/27459831062"
    }
  ]
}