{
  "_id": "6a2207b5cd65a98ecbd437a7",
  "Package": "mitey",
  "Title": "Serial Interval and Case Reproduction Number Estimation",
  "Version": "0.4.0",
  "Authors@R": "person(\"Kylie\", \"Ainslie\", email = \"ainslie.kylie@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0001-5419-7206\"))",
  "Author": "Kylie Ainslie [aut, cre, cph]\n(<https://orcid.org/0000-0001-5419-7206>)",
  "Maintainer": "Kylie Ainslie <ainslie.kylie@gmail.com>",
  "Description": "Provides methods to estimate serial intervals and\ntime-varying case reproduction numbers from infectious disease\noutbreak data. Serial intervals measure the time between\nsymptom onset in linked transmission pairs, while case\nreproduction numbers quantify how many secondary cases each\ninfected individual generates over time. These parameters are\nessential for understanding transmission dynamics, evaluating\ncontrol measures, and informing public health responses. The\npackage implements the maximum likelihood framework from Vink\net al. (2014) <doi:10.1093/aje/kwu209> for serial interval\nestimation and the retrospective method from Wallinga &\nLipsitch (2007) <doi:10.1098/rspb.2006.3754> for reproduction\nnumber estimation. Originally developed for scabies\ntransmission analysis but applicable to other infectious\ndiseases including influenza, COVID-19, and emerging pathogens.\nDesigned for epidemiologists, public health researchers, and\ninfectious disease modelers working with outbreak surveillance\ndata.",
  "Date": "2026-06-04",
  "License": "EUPL-1.2",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "8.0.0",
  "URL": "https://github.com/kylieainslie/mitey,\nhttps://kylieainslie.github.io/mitey/",
  "BugReports": "https://github.com/kylieainslie/mitey/issues",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Repository": "https://kylieainslie.r-universe.dev",
  "Date/Publication": "2026-06-04 22:36:54 UTC",
  "RemoteUrl": "https://github.com/kylieainslie/mitey",
  "RemoteRef": "HEAD",
  "RemoteSha": "62b60ee9a1ca140daa014d242a64d139eb7a8495",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-04 23:14:13 UTC",
    "User": "root"
  },
  "MD5sum": "aae10b45bdce74d2554f887c584fb226",
  "_user": "kylieainslie",
  "_type": "src",
  "_file": "mitey_0.4.0.tar.gz",
  "_fileid": "9750027da33bbf7c04c9abe045f80ab8289e429343e1abe57cc3b62358b05782",
  "_filesize": 4536465,
  "_sha256": "9750027da33bbf7c04c9abe045f80ab8289e429343e1abe57cc3b62358b05782",
  "_created": "2026-06-04T23:14:13.000Z",
  "_published": "2026-06-04T23:18:13.713Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79633324730,
      "time": 202,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7425216413"
    },
    {
      "job": 79633324770,
      "time": 204,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7425216964"
    },
    {
      "job": 79633324753,
      "time": 127,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7425199903"
    },
    {
      "job": 79633324733,
      "time": 125,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7425199294"
    },
    {
      "job": 79632773682,
      "time": 287,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7425170818"
    },
    {
      "job": 79633324709,
      "time": 163,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7425208286"
    },
    {
      "job": 79633324781,
      "time": 178,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7425210991"
    },
    {
      "job": 79633324769,
      "time": 155,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7425206407"
    },
    {
      "job": 79633324773,
      "time": 164,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7425208307"
    }
  ],
  "_buildurl": "https://github.com/r-universe/kylieainslie/actions/runs/26985055842",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/kylieainslie/mitey",
  "_commit": {
    "id": "62b60ee9a1ca140daa014d242a64d139eb7a8495",
    "author": "Kylie Ainslie <ainslie.kylie@gmail.com>",
    "committer": "Kylie Ainslie <ainslie.kylie@gmail.com>",
    "message": "edits to flexible routes and date uncertainty vignette\n",
    "time": 1780612614
  },
  "_maintainer": {
    "name": "Kylie Ainslie",
    "email": "ainslie.kylie@gmail.com",
    "login": "kylieainslie",
    "bluesky": "@kylieainslie.bsky.social",
    "linkedin": "in/kylieainslie",
    "orcid": "0000-0001-5419-7206",
    "description": "Modelling for Policy Lead at the Peter Doherty Institute for Infection and Immunity and The University of Melbourne",
    "uuid": 9805381
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "fdrtool",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "BH",
      "role": "Suggests"
    },
    {
      "package": "brms",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "broom",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "EpiLPS",
      "role": "Suggests"
    },
    {
      "package": "extraDistr",
      "role": "Suggests"
    },
    {
      "package": "flextable",
      "role": "Suggests"
    },
    {
      "package": "forcats",
      "role": "Suggests"
    },
    {
      "package": "ftExtra",
      "role": "Suggests"
    },
    {
      "package": "ggridges",
      "role": "Suggests"
    },
    {
      "package": "gt",
      "role": "Suggests"
    },
    {
      "package": "here",
      "role": "Suggests"
    },
    {
      "package": "ISOweek",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "lubridate",
      "role": "Suggests"
    },
    {
      "package": "officer",
      "role": "Suggests"
    },
    {
      "package": "openxlsx",
      "role": "Suggests"
    },
    {
      "package": "outbreaks",
      "role": "Suggests"
    },
    {
      "package": "purrr",
      "role": "Suggests"
    },
    {
      "package": "RcppEigen",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "stringr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "tidybayes",
      "role": "Suggests"
    },
    {
      "package": "tidyr",
      "role": "Suggests"
    },
    {
      "package": "viridis",
      "role": "Suggests"
    },
    {
      "package": "zoo",
      "role": "Suggests"
    }
  ],
  "_owner": "kylieainslie",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-25",
      "n": 5
    },
    {
      "week": "2025-32",
      "n": 1
    },
    {
      "week": "2025-33",
      "n": 13
    },
    {
      "week": "2025-34",
      "n": 5
    },
    {
      "week": "2025-35",
      "n": 3
    },
    {
      "week": "2025-37",
      "n": 8
    },
    {
      "week": "2025-40",
      "n": 1
    },
    {
      "week": "2025-45",
      "n": 1
    },
    {
      "week": "2026-02",
      "n": 2
    },
    {
      "week": "2026-05",
      "n": 2
    },
    {
      "week": "2026-09",
      "n": 3
    },
    {
      "week": "2026-22",
      "n": 1
    },
    {
      "week": "2026-23",
      "n": 6
    }
  ],
  "_tags": [
    {
      "name": "v0.2.0",
      "date": "2025-08-16"
    },
    {
      "name": "v0.3.0",
      "date": "2026-01-08"
    },
    {
      "name": "v0.3.1",
      "date": "2026-01-30"
    },
    {
      "name": "v0.4.0",
      "date": "2026-06-04"
    }
  ],
  "_stars": 7,
  "_contributors": [
    {
      "user": "kylieainslie",
      "count": 450,
      "uuid": 9805381
    },
    {
      "user": "simon-carreel",
      "count": 56,
      "uuid": 101939974
    }
  ],
  "_userbio": {
    "uuid": 9805381,
    "type": "user",
    "name": "Kylie Ainslie",
    "description": "Modelling for Policy Lead at the Peter Doherty Institute for Infection and Immunity and The University of Melbourne"
  },
  "_downloads": {
    "count": 148,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mitey"
  },
  "_devurl": "https://github.com/kylieainslie/mitey",
  "_pkgdown": "https://kylieainslie.github.io/mitey/",
  "_searchresults": 8,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/mitey.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/kylieainslie/mitey",
  "_realowner": "kylieainslie",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.2.0",
      "date": "2025-09-02"
    }
  ],
  "_exports": [
    "compare_n_routes",
    "generate_synthetic_epidemic",
    "plot_si_fit",
    "plot_si_fit_result",
    "si_estim",
    "wallinga_lipsitch"
  ],
  "_help": [
    {
      "page": "compare_n_routes",
      "title": "Compare Serial Interval Models Across Different Numbers of Transmission Routes",
      "topics": [
        "compare_n_routes"
      ]
    },
    {
      "page": "generate_synthetic_epidemic",
      "title": "Generate Synthetic Epidemic Data Using the Renewal Equation",
      "topics": [
        "generate_synthetic_epidemic"
      ]
    },
    {
      "page": "plot_si_fit",
      "title": "Visualize Serial Interval Distribution Fit to Outbreak Data",
      "topics": [
        "plot_si_fit"
      ]
    },
    {
      "page": "plot_si_fit_result",
      "title": "Plot Serial Interval Fit from si_estim Result",
      "topics": [
        "plot_si_fit_result"
      ]
    },
    {
      "page": "si_estim",
      "title": "Estimate Serial Interval Distribution Using the Vink Method",
      "topics": [
        "si_estim"
      ]
    },
    {
      "page": "smooth_estimates",
      "title": "Apply Moving Average Smoothing to R Estimates",
      "topics": [
        "smooth_estimates"
      ]
    },
    {
      "page": "wallinga_lipsitch",
      "title": "Estimate Time-Varying Case Reproduction Number Using Wallinga-Lipsitch Method",
      "topics": [
        "wallinga_lipsitch"
      ]
    }
  ],
  "_pkglogo": "https://github.com/kylieainslie/mitey/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/kylieainslie/mitey/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "farver",
    "fdrtool",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "quick_start_guide.Rmd",
      "filename": "quick_start_guide.html",
      "title": "Quick Start Guide: Estimating Epidemiological Parameters with mitey",
      "author": "Kylie Ainslie",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup",
        "Introduction",
        "Estimating the Serial Interval",
        "Simulated Data Example",
        "Advanced Features: Convergence Diagnostics and Multiple Restarts",
        "Convergence Diagnostics",
        "Multiple Restarts for Robust Estimation",
        "Real Data Example: Scabies Outbreaks",
        "Estimating Time-Varying Reproduction Number (Rt)",
        "Method details",
        "Understanding the 'shift' Parameter",
        "Real Data Example",
        "Zika outbreak in Giradot, Colombia (2015)",
        "References"
      ],
      "created": "2025-04-29 17:15:34",
      "modified": "2026-05-28 05:36:07",
      "commits": 6
    }
  ],
  "_score": 5.658011396657113,
  "_indexed": true,
  "_nocasepkg": "mitey",
  "_universes": [
    "kylieainslie"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.4.0",
      "date": "2026-06-04T23:16:49.000Z",
      "distro": "noble",
      "commit": "62b60ee9a1ca140daa014d242a64d139eb7a8495",
      "fileid": "76afd026c86663e57ad91bca8515d04f86ede215db9a7dd8309a7a1f142d2a3f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kylieainslie/actions/runs/26985055842"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.4.0",
      "date": "2026-06-04T23:16:54.000Z",
      "distro": "noble",
      "commit": "62b60ee9a1ca140daa014d242a64d139eb7a8495",
      "fileid": "4816552d2812c1ca793a00ab00d70f3ac5457507b48c93364621de0ff3b51bf0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kylieainslie/actions/runs/26985055842"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.4.0",
      "date": "2026-06-04T23:15:56.000Z",
      "commit": "62b60ee9a1ca140daa014d242a64d139eb7a8495",
      "fileid": "d9be20b46be942f94b838ccfc3f617244a337932fde8ed9b76936dd745c850d6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kylieainslie/actions/runs/26985055842"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.4.0",
      "date": "2026-06-04T23:15:57.000Z",
      "commit": "62b60ee9a1ca140daa014d242a64d139eb7a8495",
      "fileid": "3dadbc31dd733726ab8c2ff58fc2f9e98d01c7c70cc11118f9d3d09d51b2042a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kylieainslie/actions/runs/26985055842"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.4.0",
      "date": "2026-06-04T23:17:12.000Z",
      "commit": "62b60ee9a1ca140daa014d242a64d139eb7a8495",
      "fileid": "217010d6557de6e1cf5ce9281174def9fa6cfc97b30d69a623e5d1aa0214dda3",
      "status": "success",
      "buildurl": "https://github.com/r-universe/kylieainslie/actions/runs/26985055842"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.4.0",
      "date": "2026-06-04T23:16:12.000Z",
      "commit": "62b60ee9a1ca140daa014d242a64d139eb7a8495",
      "fileid": "6d26884c311719bef5f6a1d0776642d169878ddaea2d13d5e90f649131f2200d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kylieainslie/actions/runs/26985055842"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.4.0",
      "date": "2026-06-04T23:15:50.000Z",
      "commit": "62b60ee9a1ca140daa014d242a64d139eb7a8495",
      "fileid": "ea87122099df265cfe93ba720fbd42790930581ed5849651f8cee46a98079801",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kylieainslie/actions/runs/26985055842"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.4.0",
      "date": "2026-06-04T23:16:01.000Z",
      "commit": "62b60ee9a1ca140daa014d242a64d139eb7a8495",
      "fileid": "bec03a6e6f8e1d79fbc9fde4437a500c3fba790f2e2a11b67dd43a260e62269f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/kylieainslie/actions/runs/26985055842"
    }
  ]
}