{
  "_id": "6a2e5c0a3efcd9bda430cfd7",
  "Type": "Package",
  "Package": "phenomix",
  "Title": "Fit Density Curves to Peak Timing Data that Varies over Time",
  "Version": "1.0.5",
  "Authors@R": "c(person(given = c(\"Eric\", \"J.\"),\nfamily = \"Ward\",\nrole = c(\"aut\", \"cre\"),\nemail = \"eric.ward@noaa.gov\"),\nperson(given = c(\"Samantha\", \"M.\"),\nfamily = \"Wilson\",\nrole = c(\"ctb\")),\nperson(given = c(\"Joseph\", \"H.\"),\nfamily = \"Anderson\",\nrole = c(\"ctb\")))",
  "Description": "The 'phenomix' package fits time-varying density curves to\nrun timing type data commonly encountered in fisheries and\necology. Example applications include to peak run timing curves\ncollected for juvenile or adult Pacific salmon, though could\nalso be applied to other kinds of data such as hydrographs,\nplant phenology (flowering, leaf out).",
  "License": "GPL (>=3)",
  "URL": "https://nwfsc-cb.github.io/phenomix,\nhttps://github.com/nwfsc-cb/phenomix",
  "VignetteBuilder": "knitr",
  "ByteCompile": "true",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Repository": "https://nmfs-opensci.r-universe.dev",
  "Date/Publication": "2026-01-14 13:23:26 UTC",
  "RemoteUrl": "https://github.com/nwfsc-cb/phenomix",
  "RemoteRef": "HEAD",
  "RemoteSha": "361b04dbb0344d4b3e28ff90af14e7c203f33f87",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-14 07:40:08 UTC",
    "User": "root"
  },
  "Author": "Eric J. Ward [aut, cre],\nSamantha M. Wilson [ctb],\nJoseph H. Anderson [ctb]",
  "Maintainer": "Eric J. Ward <eric.ward@noaa.gov>",
  "MD5sum": "a041168790630dd32031725e9d59efcc",
  "_user": "nmfs-opensci",
  "_type": "src",
  "_file": "phenomix_1.0.5.tar.gz",
  "_fileid": "d6b58248d7e3db5372bfb5dedcc2ff058b3c56450916d73f9aaa199a4e1783a4",
  "_filesize": 1048094,
  "_sha256": "d6b58248d7e3db5372bfb5dedcc2ff058b3c56450916d73f9aaa199a4e1783a4",
  "_created": "2026-06-14T07:40:08.000Z",
  "_published": "2026-06-14T07:45:14.403Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 81259343183,
      "time": 257,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7618779968"
    },
    {
      "job": 81259343166,
      "time": 256,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7618778679"
    },
    {
      "job": 81259343168,
      "time": 151,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7618763026"
    },
    {
      "job": 81259343185,
      "time": 219,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7618772777"
    },
    {
      "job": 81259123934,
      "time": 208,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7618741271"
    },
    {
      "job": 81259343178,
      "time": 109,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7618756879"
    },
    {
      "job": 81259343177,
      "time": 228,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7618774569"
    },
    {
      "job": 81259343188,
      "time": 187,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7618768105"
    },
    {
      "job": 81259343176,
      "time": 211,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7618772394"
    }
  ],
  "_buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/27492102910",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/nwfsc-cb/phenomix",
  "_commit": {
    "id": "361b04dbb0344d4b3e28ff90af14e7c203f33f87",
    "author": "Eric Ward <5046884+ericward-noaa@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #3 from nwfsc-cb/dev\n\nrefactor -> RTMB",
    "time": 1768397006
  },
  "_maintainer": {
    "name": "Eric J. Ward",
    "email": "eric.ward@noaa.gov",
    "login": "ericward-noaa",
    "linkedin": "in/eric-ward-42b76b3",
    "description": "Statistics, fisheries, conservation biology @ Northwest Fisheries Science Center, Seattle WA ",
    "uuid": 5046884
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "gnorm",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "RTMB",
      "role": "Imports"
    },
    {
      "package": "nlme",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "nwfsc-cb",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-03",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "v1.0.5",
      "date": "2026-01-14"
    }
  ],
  "_stars": 6,
  "_contributors": [
    {
      "user": "ericward-noaa",
      "count": 148,
      "uuid": 5046884
    },
    {
      "user": "eric-ward",
      "count": 2,
      "uuid": 159983626
    }
  ],
  "_userbio": {
    "uuid": 110112201,
    "type": "organization",
    "name": "nmfs-opensci",
    "followers": 144,
    "description": "GiHub org for NMFS Open Science"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phenomix"
  },
  "_devurl": "https://github.com/nwfsc-cb/phenomix",
  "_pkgdown": "https://nwfsc-cb.github.io/phenomix",
  "_searchresults": 34,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/phenomix.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "create_data",
    "extract_all",
    "extract_annual",
    "extract_lower",
    "extract_means",
    "extract_sigma",
    "extract_theta",
    "extract_upper",
    "fit",
    "pars",
    "plot_diagnostics"
  ],
  "_datasets": [
    {
      "name": "chum",
      "title": "Count data collected by Washington Department of Fish and Wildlife on chum salmon from the Skagit River (Washington state). Each row of the dataframe contains an observation (\"number\") on a given date (\"date\"). The year (\"year\") and calendar day (\"doy\") are also included.",
      "object": "chum",
      "class": [
        "data.frame"
      ],
      "fields": [
        "date",
        "year",
        "number",
        "doy"
      ],
      "rows": 7540,
      "table": true,
      "tojson": true
    },
    {
      "name": "fishdist",
      "title": "Example simulate data for fish distributions from multiple years",
      "object": "fishdist",
      "class": [
        "data.frame"
      ],
      "fields": [
        "year",
        "number",
        "doy"
      ],
      "rows": 1005,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "create_data",
      "title": "Create data file for fitting time varying run timing distributions with TMB",
      "topics": [
        "create_data"
      ]
    },
    {
      "page": "extract_all",
      "title": "Output processing function to be called by user",
      "topics": [
        "extract_all"
      ]
    },
    {
      "page": "extract_annual",
      "title": "Output processing function to be called by user",
      "topics": [
        "extract_annual"
      ]
    },
    {
      "page": "extract_lower",
      "title": "Output processing function to be called by user",
      "topics": [
        "extract_lower"
      ]
    },
    {
      "page": "extract_means",
      "title": "Output processing function to be called by user",
      "topics": [
        "extract_means"
      ]
    },
    {
      "page": "extract_sigma",
      "title": "Output processing function to be called by user",
      "topics": [
        "extract_sigma"
      ]
    },
    {
      "page": "extract_theta",
      "title": "Output processing function to be called by user",
      "topics": [
        "extract_theta"
      ]
    },
    {
      "page": "extract_upper",
      "title": "Output processing function to be called by user",
      "topics": [
        "extract_upper"
      ]
    },
    {
      "page": "fit",
      "title": "Fitting function to be called by user",
      "topics": [
        "fit"
      ]
    },
    {
      "page": "fixef.phenomix",
      "title": "Get fixed effects parameters from model object, copying glmmTMB 'fast' implementation",
      "topics": [
        "fixef.phenomix"
      ]
    },
    {
      "page": "limits",
      "title": "Internal function to assign upper and lower bounds to parameters, based on their names",
      "topics": [
        "limits"
      ]
    },
    {
      "page": "plot_diagnostics",
      "title": "Plotting function to be called by user",
      "topics": [
        "plot_diagnostics"
      ]
    },
    {
      "page": "ranef.phenomix",
      "title": "Get random effects parameters from model object, copying glmmTMB 'fast' implementation",
      "topics": [
        "ranef.phenomix"
      ]
    }
  ],
  "_readme": "https://github.com/nwfsc-cb/phenomix/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gnorm",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "nlme",
    "pillar",
    "pkgconfig",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "rlang",
    "RTMB",
    "S7",
    "scales",
    "tibble",
    "tidyselect",
    "TMB",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "a4_derived.Rmd",
      "filename": "a4_derived.html",
      "title": "Extracting estimated and derived parameters",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Extracting parameters manually",
        "Helper functions",
        "Annual summaries"
      ],
      "created": "2023-05-03 12:01:26",
      "modified": "2026-01-14 13:23:26",
      "commits": 5
    },
    {
      "source": "a1_examples.Rmd",
      "filename": "a1_examples.html",
      "title": "Fitting time varying phenology models with the phenomix package",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Manipulating data for estimation",
        "Fitting the model",
        "Getting coefficients",
        "Getting predicted values",
        "Plotting results",
        "Additional examples",
        "Diagnosing lack of convergence"
      ],
      "created": "2022-03-03 00:53:09",
      "modified": "2026-01-14 13:23:26",
      "commits": 7
    },
    {
      "source": "a2_covariates.Rmd",
      "filename": "a2_covariates.html",
      "title": "Including covariates",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Covariates"
      ],
      "created": "2022-03-03 00:53:09",
      "modified": "2026-01-14 13:23:26",
      "commits": 4
    },
    {
      "source": "a3_troubleshooting.Rmd",
      "filename": "a3_troubleshooting.html",
      "title": "Troubleshooting",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Troubleshooting",
        "Using initial values",
        "Specifying limits"
      ],
      "created": "2022-03-03 00:53:09",
      "modified": "2026-01-14 13:23:26",
      "commits": 4
    }
  ],
  "_score": 4.6106601630898805,
  "_indexed": false,
  "_nocasepkg": "phenomix",
  "_universes": [
    "nmfs-opensci"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.5",
      "date": "2026-06-14T07:42:22.000Z",
      "distro": "noble",
      "commit": "361b04dbb0344d4b3e28ff90af14e7c203f33f87",
      "fileid": "259abd46742f45650ec73e6a904670bc9cc8bb78bda5a59fcc2260d5b5a3db72",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/27492102910"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.5",
      "date": "2026-06-14T07:42:48.000Z",
      "distro": "noble",
      "commit": "361b04dbb0344d4b3e28ff90af14e7c203f33f87",
      "fileid": "d0ee6b2b40f459662d6057452dca6281418d08b35ca0584db0e98502bd3be73b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/27492102910"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.5",
      "date": "2026-06-14T07:41:43.000Z",
      "commit": "361b04dbb0344d4b3e28ff90af14e7c203f33f87",
      "fileid": "9d22b447fbcaff07c539fdb3f0b99351e63d08008a0551f2d7194472d380592c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/27492102910"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.5",
      "date": "2026-06-14T07:42:10.000Z",
      "commit": "361b04dbb0344d4b3e28ff90af14e7c203f33f87",
      "fileid": "1c3284c64e8ad3e4e239a65c7e55edae853600b8711775b9381d7311ba62c4fb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/27492102910"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.5",
      "date": "2026-06-14T07:42:14.000Z",
      "commit": "361b04dbb0344d4b3e28ff90af14e7c203f33f87",
      "fileid": "02ae8e246ec0e8bf705d692dfcf4f93e9bfb5a587d5ae465583cfea4e01d83c2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/27492102910"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.5",
      "date": "2026-06-14T07:41:33.000Z",
      "commit": "361b04dbb0344d4b3e28ff90af14e7c203f33f87",
      "fileid": "6536633b9d5f7f7f84c2b89a6c71888ac872e111c9aa97095aff7fab14735fa3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/27492102910"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.5",
      "date": "2026-06-14T07:41:29.000Z",
      "commit": "361b04dbb0344d4b3e28ff90af14e7c203f33f87",
      "fileid": "0178126c6ab9d52bb9a3b5beafdbb3819ceeb534b48d9e870d45bd36dd2b22d5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/27492102910"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.5",
      "date": "2026-06-14T07:41:30.000Z",
      "commit": "361b04dbb0344d4b3e28ff90af14e7c203f33f87",
      "fileid": "74692a893c0d54c72cd344bfd5bf40ebc84b87cc9813fe0227284956ee73bdd8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/27492102910"
    }
  ]
}