{
  "_id": "6a1f07acb401979e7341bf40",
  "Package": "cyclomort",
  "Type": "Package",
  "Title": "Survival Modeling with a Periodic Hazard Function",
  "Version": "1.0.3",
  "Date": "2025-05-13",
  "Authors@R": "c(person(\"Eliezer\", \"Gurarie\", role = c(\"aut\", \"cre\"), email = \"egurarie@esf.edu\"), person(\"Thompson\", \"Peter\", role = \"aut\"))",
  "Description": "Modeling periodic mortality (or other time-to event)\nprocesses from right-censored data. Given observations of a\nprocess with a known period (e.g. 365 days, 24 hours),\nfunctions determine the number, intensity, timing, and duration\nof peaks of periods of elevated hazard within a period.  The\nunderlying model is a mixed wrapped Cauchy function fitted\nusing maximum likelihoods (details in Gurarie et al. (2020)\n<doi:10.1111/2041-210X.13305>). The development of these tools\nwas motivated by the strongly seasonal mortality patterns\nobserved in many wild animal populations. Thus, the respective\nperiods of higher mortality can be identified as \"mortality\nseasons\".",
  "License": "GPL (>= 3)",
  "RoxygenNote": "7.3.2",
  "URL": "https://github.com/EliGurarie/cyclomort",
  "BugReports": "https://github.com/EliGurarie/cyclomort/issues",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://eligurarie.r-universe.dev",
  "Date/Publication": "2025-05-23 15:24:20 UTC",
  "RemoteUrl": "https://github.com/eligurarie/cyclomort",
  "RemoteRef": "HEAD",
  "RemoteSha": "1a79e3de44094cc55a4a95f5d3f1a75424477534",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-18 06:42:22 UTC",
    "User": "root"
  },
  "Author": "Eliezer Gurarie [aut, cre],\nThompson Peter [aut]",
  "Maintainer": "Eliezer Gurarie <egurarie@esf.edu>",
  "MD5sum": "717148b9d8f5da2cde28fb3aa661006c",
  "_user": "eligurarie",
  "_type": "src",
  "_file": "cyclomort_1.0.3.tar.gz",
  "_fileid": "bbba6abe61781179dcd240260c3b0588e62480cb327349e3f1853476db0b12c1",
  "_filesize": 1185999,
  "_sha256": "bbba6abe61781179dcd240260c3b0588e62480cb327349e3f1853476db0b12c1",
  "_created": "2026-05-18T06:42:22.000Z",
  "_published": "2026-06-02T16:41:16.506Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79122987736,
      "time": 187,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7051139551"
    },
    {
      "job": 79122987936,
      "time": 161,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051132959"
    },
    {
      "job": 79122987966,
      "time": 158,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7051132321"
    },
    {
      "job": 79122987719,
      "time": 109,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051120821"
    },
    {
      "job": 79122987528,
      "time": 212,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051093463"
    },
    {
      "job": 79122987412,
      "time": 122,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7364046565"
    },
    {
      "job": 79122988205,
      "time": 147,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7051130329"
    },
    {
      "job": 79122988241,
      "time": 159,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7051133082"
    },
    {
      "job": 79122988542,
      "time": 150,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051130573"
    }
  ],
  "_buildurl": "https://github.com/r-universe/eligurarie/actions/runs/26017685869",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/eligurarie/cyclomort",
  "_commit": {
    "id": "1a79e3de44094cc55a4a95f5d3f1a75424477534",
    "author": "Eliezer Gurarie <egurarie@esf.edu>",
    "committer": "Eliezer Gurarie <egurarie@esf.edu>",
    "message": "cran submission\n",
    "time": 1748013860
  },
  "_maintainer": {
    "name": "Eliezer Gurarie",
    "email": "egurarie@esf.edu",
    "login": "eligurarie",
    "description": "Professor of Quantitative Wildlife Ecology\n",
    "uuid": 3239417
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "flexsurv",
      "role": "Imports"
    },
    {
      "package": "lubridate",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "mvtnorm",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "survival",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    }
  ],
  "_owner": "eligurarie",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-20",
      "n": 1
    },
    {
      "week": "2025-21",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "pthompson234",
      "count": 60,
      "uuid": 47431897
    },
    {
      "user": "elieguru",
      "count": 26,
      "uuid": 12075063
    },
    {
      "user": "eligurarie",
      "count": 5,
      "uuid": 3239417
    }
  ],
  "_userbio": {
    "uuid": 3239417,
    "type": "user",
    "name": "Eli(e) Gurarie",
    "description": "Professor of Quantitative Wildlife Ecology\r\n"
  },
  "_downloads": {
    "count": 615,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cyclomort"
  },
  "_devurl": "https://github.com/eligurarie/cyclomort",
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/cyclomort.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/eligurarie/cyclomort",
  "_realowner": "eligurarie",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.2",
      "date": "2020-08-20"
    },
    {
      "version": "1.0.3",
      "date": "2025-05-27"
    }
  ],
  "_exports": [
    "censor_cycloSurv",
    "create_cycloSurv",
    "DeltaToRho",
    "factorfit_cyclomort",
    "findDelta",
    "findRho",
    "fit_cyclomort",
    "guess_initial_parameters",
    "imwc",
    "iwc",
    "loglike",
    "loglike_optim",
    "mwc",
    "select_seasons",
    "simulate_cycloSurv",
    "trim_cycloSurv",
    "wc"
  ],
  "_datasets": [
    {
      "name": "nwt_morts",
      "title": "Mortality data for Northwest territory boreal woodland caribou.",
      "object": "nwt_morts",
      "file": "nwt_morts.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "region",
        "start",
        "end",
        "status"
      ],
      "rows": 370,
      "table": true,
      "tojson": true
    },
    {
      "name": "seasonalsex",
      "title": "Simulated data of seasonal mortality data for two sex groups",
      "object": "seasonalsex",
      "file": "seasonalsex.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "sex",
        "event"
      ],
      "rows": 200,
      "table": false,
      "tojson": false
    },
    {
      "name": "timetoeventprediction",
      "title": "Example fitted time to event prediction",
      "object": "timetoeventprediction",
      "file": "timetoeventprediction.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "wah_morts",
      "title": "Mortality data for Western Arctic Herd Caribou",
      "object": "wah_morts",
      "file": "wah_morts.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "start",
        "end",
        "fate"
      ],
      "rows": 90,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "censor_cycloSurv",
      "title": "Censor and Trim",
      "topics": [
        "censor_cycloSurv",
        "trim_cycloSurv"
      ]
    },
    {
      "page": "create_cycloSurv",
      "title": "Create a cycloSurv object",
      "topics": [
        "create_cycloSurv"
      ]
    },
    {
      "page": "factorfit_cyclomort",
      "title": "Factorial analysis of seasonal survival models",
      "topics": [
        "factorfit_cyclomort"
      ]
    },
    {
      "page": "findDelta",
      "title": "Converting between Rho to Delta",
      "topics": [
        "DeltaToRho",
        "findDelta",
        "findRho"
      ]
    },
    {
      "page": "fit_cyclomort",
      "title": "Estimate periodic hazard function.",
      "topics": [
        "fit_cyclomort"
      ]
    },
    {
      "page": "guess_initial_parameters",
      "title": "Produce initial parameter estimates based on mortality data",
      "topics": [
        "guess_initial_parameters"
      ]
    },
    {
      "page": "loglike",
      "title": "Obtain log-likelihood value from a data set given a set of parameter values",
      "topics": [
        "loglike"
      ]
    },
    {
      "page": "loglike_optim",
      "title": "Log-likelihood function",
      "topics": [
        "loglike_optim"
      ]
    },
    {
      "page": "nwt_morts",
      "title": "Mortality data for Northwest territory boreal woodland caribou.",
      "topics": [
        "nwt_morts"
      ]
    },
    {
      "page": "plot.cmfactorfit",
      "title": "Plot cmfactorfit objects",
      "topics": [
        "plot.cmfactorfit"
      ]
    },
    {
      "page": "plot.cmfit",
      "title": "Plot cmfit objects",
      "topics": [
        "plot.cmfit"
      ]
    },
    {
      "page": "predict.cmfit",
      "title": "Prediction method for cyclomort fits",
      "topics": [
        "predict.cmfit"
      ]
    },
    {
      "page": "seasonalsex",
      "title": "Simulated data of seasonal mortality data for two sex groups",
      "topics": [
        "seasonalsex"
      ]
    },
    {
      "page": "select_seasons",
      "title": "Select the number of mortality seasons",
      "topics": [
        "select_seasons"
      ]
    },
    {
      "page": "simulate_cycloSurv",
      "title": "Simulate periodic mortality process",
      "topics": [
        "simulate_cycloSurv"
      ]
    },
    {
      "page": "summary.cmfactorfit",
      "title": "Summary method for cyclomort factorial fit",
      "topics": [
        "summary.cmfactorfit"
      ]
    },
    {
      "page": "summary.cmfit",
      "title": "Provide a short summary of cmfit (parameter estimates for periodic mortality curves) objects",
      "topics": [
        "summary.cmfit"
      ]
    },
    {
      "page": "summary.cmfitlist",
      "title": "Summary method for cmfitlist objects",
      "topics": [
        "summary.cmfitlist"
      ]
    },
    {
      "page": "timetoeventprediction",
      "title": "Example fitted time to event prediction",
      "topics": [
        "timetoeventprediction"
      ]
    },
    {
      "page": "wah_morts",
      "title": "Mortality data for Western Arctic Herd Caribou",
      "topics": [
        "wah_morts"
      ]
    },
    {
      "page": "wc",
      "title": "Wrapped Cauchy and Integrated Wrapped Cauchy functions",
      "topics": [
        "imwc",
        "iwc",
        "mwc",
        "wc"
      ]
    }
  ],
  "_readme": "https://github.com/eligurarie/cyclomort/raw/HEAD/README.md",
  "_rundeps": [
    "assertthat",
    "bbmle",
    "bdsmatrix",
    "cli",
    "cpp11",
    "data.table",
    "deSolve",
    "dplyr",
    "farver",
    "fastGHQuad",
    "flexsurv",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "lsoda",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "mgcv",
    "mstate",
    "muhaz",
    "mvtnorm",
    "nlme",
    "numDeriv",
    "pillar",
    "pkgconfig",
    "plyr",
    "purrr",
    "quadprog",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "rstpm2",
    "S7",
    "scales",
    "statmod",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "cyclomort.Rmd",
      "filename": "cyclomort.html",
      "title": "Using cyclomort: A tool for estimating seasonal mortality patterns",
      "author": "Elie Gurarie and Peter Thompson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Underlying wrapped Cauchy hazard model",
        "Simulating periodic mortality processes",
        "Fitting a periodic hazard process",
        "Identifying the number of mortality seasons within a system using select_seasons",
        "Simple factor analyses",
        "Data",
        "Northwest Territory woodland caribou",
        "Western Arctic herd caribou",
        "References"
      ],
      "created": "2019-02-22 20:52:39",
      "modified": "2025-04-01 20:33:52",
      "commits": 18
    }
  ],
  "_score": 4.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "cyclomort",
  "_universes": [
    "eligurarie"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-05-18T06:44:46.000Z",
      "distro": "noble",
      "commit": "1a79e3de44094cc55a4a95f5d3f1a75424477534",
      "fileid": "c1d9cd10396b8a03c76ffb24ffea4bf34d2a3e489768abfdb4ff47d601fa499d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eligurarie/actions/runs/26017685869"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-05-18T06:44:26.000Z",
      "distro": "noble",
      "commit": "1a79e3de44094cc55a4a95f5d3f1a75424477534",
      "fileid": "273b8bd198b4cf5decc3469c45a15fbd0d980f728d9242b369740c575f1cbfea",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eligurarie/actions/runs/26017685869"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-05-18T06:44:21.000Z",
      "commit": "1a79e3de44094cc55a4a95f5d3f1a75424477534",
      "fileid": "13255118928f46074ca5cb28d3ccca1be1fd5144dc6753f7a688c0a570751a5d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eligurarie/actions/runs/26017685869"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-05-18T06:43:52.000Z",
      "commit": "1a79e3de44094cc55a4a95f5d3f1a75424477534",
      "fileid": "cf1bd02cfc85c80068d520f24fe7a3379cd052707ee019d66d1188cd45df6860",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eligurarie/actions/runs/26017685869"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-05-18T06:43:57.000Z",
      "commit": "1a79e3de44094cc55a4a95f5d3f1a75424477534",
      "fileid": "36d694dd65679697d1bf178efc56ea1ba4d91bab6e049e420c09f64212a53489",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eligurarie/actions/runs/26017685869"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-05-18T06:44:24.000Z",
      "commit": "1a79e3de44094cc55a4a95f5d3f1a75424477534",
      "fileid": "797f40c1240dd6b3f53f8da2a068a15aad5c13ac3f3370326a5308077128cf41",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eligurarie/actions/runs/26017685869"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-05-18T06:44:05.000Z",
      "commit": "1a79e3de44094cc55a4a95f5d3f1a75424477534",
      "fileid": "4a9aba792348442db28cb520db3985dd232ca1db517765e2ea7a8f306ef03f53",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eligurarie/actions/runs/26017685869"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.3",
      "date": "2026-06-02T16:40:51.000Z",
      "commit": "1a79e3de44094cc55a4a95f5d3f1a75424477534",
      "fileid": "bd257ca49a841a790a18251f2473be01060cd34629f33d58e0fc45684cb523fb",
      "status": "success",
      "buildurl": "https://github.com/r-universe/eligurarie/actions/runs/26017685869"
    }
  ]
}