{
  "_id": "6a20efbbcd65a98ecbd1b443",
  "Package": "serodynamics",
  "Title": "What the Package Does (One Line, Title Case)",
  "Version": "0.0.0.9055",
  "Authors@R": "c(\nperson(\"Peter\", \"Teunis\", , \"p.teunis@emory.edu\", role = c(\"aut\", \"cph\"),\ncomment = \"Author of the method and original code.\"),\nperson(\"Samuel\", \"Schildhauer\", , \"sschildhauer@ucdavis.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Kwan Ho\", \"Lee\", , \"ksjlee@ucdavis.edu\", role = \"aut\"),\nperson(\"Kristen\", \"Aiemjoy\", , \"kaiemjoy@ucdavis.edu\", role = \"aut\"),\nperson(\"Douglas Ezra\", \"Morrison\", , \"demorrison@ucdavis.edu\", role = \"aut\")\n)",
  "Description": "Modeling longitudinal immune seroresponses to pathogens.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "URL": "https://github.com/UCD-SERG/serodynamics,\nhttps://ucd-serg.github.io/serodynamics/",
  "BugReports": "https://github.com/UCD-SERG/serodynamics/issues",
  "Language": "en-US",
  "Config/testthat/edition": "3",
  "Config/needs/test": "withr, vdiffr, here, readr, magrittr, readr, rlist",
  "Config/needs/check": "commonmark, xml2",
  "Remotes": [
    "ucd-serg/serocalculator"
  ],
  "LazyData": "true",
  "VignetteBuilder": "knitr, quarto",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "make jags libicu-dev libssl-dev libx11-dev\nzlib1g-dev",
  "Repository": "https://ucd-serg.r-universe.dev",
  "Date/Publication": "2026-05-29 18:31:07 UTC",
  "RemoteUrl": "https://github.com/ucd-serg/serodynamics",
  "RemoteRef": "HEAD",
  "RemoteSha": "ba9ae9868709bb0b019067d1304c63f2dd15a4c9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-04 03:14:49 UTC",
    "User": "root"
  },
  "Author": "Peter Teunis [aut, cph] (Author of the method and original code.),\nSamuel Schildhauer [aut, cre],\nKwan Ho Lee [aut],\nKristen Aiemjoy [aut],\nDouglas Ezra Morrison [aut]",
  "Maintainer": "Samuel Schildhauer <sschildhauer@ucdavis.edu>",
  "MD5sum": "8655376c35fd5ac9fea4c4332c8c54a4",
  "_user": "ucd-serg",
  "_type": "src",
  "_file": "serodynamics_0.0.0.9055.tar.gz",
  "_fileid": "046ccaf15ef7224a0f06cbba76fcc489eb91b77deb62906f909b7dd815f028e7",
  "_filesize": 14354652,
  "_sha256": "046ccaf15ef7224a0f06cbba76fcc489eb91b77deb62906f909b7dd815f028e7",
  "_created": "2026-06-04T03:14:49.000Z",
  "_published": "2026-06-04T03:23:39.308Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79442156897,
      "time": 357,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7402217741"
    },
    {
      "job": 79442156881,
      "time": 361,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7402218641"
    },
    {
      "job": 79442156849,
      "time": 324,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7402210333"
    },
    {
      "job": 79442156845,
      "time": 315,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7402208368"
    },
    {
      "job": 79441716203,
      "time": 253,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7402140602"
    },
    {
      "job": 79442156844,
      "time": 160,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7402174660"
    },
    {
      "job": 79442156862,
      "time": 472,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7402244264"
    },
    {
      "job": 79442156872,
      "time": 392,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7402225555"
    },
    {
      "job": 79442156884,
      "time": 391,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7402225136"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ucd-serg/actions/runs/26927932356",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/ucd-serg/serodynamics",
  "_commit": {
    "id": "ba9ae9868709bb0b019067d1304c63f2dd15a4c9",
    "author": "Douglas Ezra Morrison <demorrison@ucdavis.edu>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #242 from UCD-SERG/ci/lint-changed-files-gh-pat\n\nci(lint): fix invalid GitHub PAT format in lint-changed-files",
    "time": 1780079467
  },
  "_maintainer": {
    "name": "Samuel Schildhauer",
    "email": "sschildhauer@ucdavis.edu",
    "login": "sschildhauer",
    "description": "",
    "uuid": 165851188
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "coda",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggmcmc",
      "version": ">= 1.5.1.2",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "runjags",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "serocalculator",
      "version": ">= 1.3.0.9037",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "Hmisc",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "readr",
      "role": "Suggests"
    },
    {
      "package": "rlist",
      "role": "Suggests"
    },
    {
      "package": "sessioninfo",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "stringr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    },
    {
      "package": "withr",
      "role": "Suggests"
    },
    {
      "package": "vdiffr",
      "role": "Suggests"
    },
    {
      "package": "fs",
      "role": "Suggests"
    },
    {
      "package": "here",
      "role": "Suggests"
    },
    {
      "package": "rjags",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "magrittr",
      "role": "Suggests"
    },
    {
      "package": "rex",
      "role": "Suggests"
    },
    {
      "package": "quarto",
      "role": "Suggests"
    }
  ],
  "_owner": "ucd-serg",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-26",
      "n": 4
    },
    {
      "week": "2025-27",
      "n": 1
    },
    {
      "week": "2025-29",
      "n": 2
    },
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-32",
      "n": 2
    },
    {
      "week": "2025-33",
      "n": 2
    },
    {
      "week": "2025-35",
      "n": 1
    },
    {
      "week": "2025-39",
      "n": 1
    },
    {
      "week": "2025-40",
      "n": 1
    },
    {
      "week": "2025-41",
      "n": 1
    },
    {
      "week": "2025-51",
      "n": 1
    },
    {
      "week": "2026-02",
      "n": 16
    },
    {
      "week": "2026-19",
      "n": 3
    },
    {
      "week": "2026-20",
      "n": 7
    },
    {
      "week": "2026-21",
      "n": 7
    },
    {
      "week": "2026-22",
      "n": 3
    }
  ],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "sschildhauer",
      "count": 832,
      "uuid": 165851188
    },
    {
      "user": "d-morrison",
      "count": 677,
      "uuid": 2474437
    },
    {
      "user": "kwan-jenny",
      "count": 176,
      "uuid": 68584166
    },
    {
      "user": "copilot",
      "count": 124,
      "uuid": 198982749
    },
    {
      "user": "kaiemjoy",
      "count": 38,
      "uuid": 16113030
    },
    {
      "user": "dem-ucdh",
      "count": 3,
      "uuid": 253661458
    }
  ],
  "_userbio": {
    "uuid": 102623664,
    "type": "organization",
    "name": "UC Davis Seroepidemiology Research Group (SeRG)"
  },
  "_downloads": {
    "count": 16,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/serodynamics"
  },
  "_devurl": "https://github.com/ucd-serg/serodynamics",
  "_pkgdown": "https://ucd-serg.github.io/serodynamics/",
  "_topics": [
    "jags",
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "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",
    "extra/serodynamics.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ucd-serg/serodynamics",
  "_realowner": "ucd-serg",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2026-06-02"
    }
  ],
  "_exports": [
    "as_case_data",
    "autoplot",
    "expect_snapshot_data",
    "get_biomarker_levels",
    "get_biomarker_names_var",
    "initsfunction",
    "load_data",
    "plot_jags_dens",
    "plot_jags_effect",
    "plot_jags_Rhat",
    "plot_jags_trace",
    "plot_predicted_curve",
    "post_summ",
    "postprocess_jags_output",
    "prep_data",
    "prep_priors",
    "run_mod",
    "serodynamics_example",
    "sim_case_data",
    "sim_n_obs"
  ],
  "_datasets": [
    {
      "name": "nepal_sees",
      "title": "SEES Typhoid data",
      "object": "nepal_sees",
      "class": [
        "case_data",
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Country",
        "id",
        "sample_id",
        "bldculres",
        "antigen_iso",
        "studyvisit",
        "dayssincefeveronset",
        "result",
        "visit_num"
      ],
      "rows": 904,
      "table": true,
      "tojson": true
    },
    {
      "name": "nepal_sees_jags_output",
      "title": "SEES Typhoid run_mod jags output",
      "object": "nepal_sees_jags_output",
      "class": [
        "sr_model",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Iteration",
        "Chain",
        "Parameter",
        "Iso_type",
        "Stratification",
        "Subject",
        "value"
      ],
      "rows": 70000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "as_case_data",
      "title": "Convert data into 'case_data'",
      "topics": [
        "as_case_data"
      ]
    },
    {
      "page": "autoplot.case_data",
      "title": "Plot case data",
      "topics": [
        "autoplot.case_data"
      ]
    },
    {
      "page": "initsfunction",
      "title": "JAGS chain initialization function",
      "topics": [
        "initsfunction"
      ]
    },
    {
      "page": "load_data",
      "title": "load and format data",
      "topics": [
        "load_data"
      ]
    },
    {
      "page": "nepal_sees",
      "title": "SEES Typhoid data",
      "topics": [
        "nepal_sees"
      ]
    },
    {
      "page": "nepal_sees_jags_output",
      "title": "SEES Typhoid run_mod jags output",
      "topics": [
        "nepal_sees_jags_output"
      ]
    },
    {
      "page": "plot_jags_dens",
      "title": "Density Plot Diagnostics",
      "topics": [
        "plot_jags_dens"
      ]
    },
    {
      "page": "plot_jags_effect",
      "title": "Plot Effective Sample Size Diagnostics",
      "topics": [
        "plot_jags_effect"
      ]
    },
    {
      "page": "plot_jags_Rhat",
      "title": "Rhat Plot Diagnostics",
      "topics": [
        "plot_jags_Rhat"
      ]
    },
    {
      "page": "plot_jags_trace",
      "title": "Trace Plot Diagnostics",
      "topics": [
        "plot_jags_trace"
      ]
    },
    {
      "page": "plot_predicted_curve",
      "title": "Generate Predicted Antibody Response Curves (Median + 95% CI)",
      "topics": [
        "plot_predicted_curve"
      ]
    },
    {
      "page": "post_summ",
      "title": "Summary Table of Jags Posterior Estimates",
      "topics": [
        "post_summ"
      ]
    },
    {
      "page": "postprocess_jags_output",
      "title": "Postprocess JAGS output",
      "topics": [
        "postprocess_jags_output"
      ]
    },
    {
      "page": "prep_data",
      "title": "prepare data for JAGs",
      "topics": [
        "prep_data"
      ]
    },
    {
      "page": "prep_priors",
      "title": "Prepare priors",
      "topics": [
        "prep_priors"
      ]
    },
    {
      "page": "run_mod",
      "title": "Run Jags Model",
      "topics": [
        "run_mod"
      ]
    },
    {
      "page": "serodynamics_example",
      "title": "Get path to an example file",
      "topics": [
        "serodynamics_example"
      ]
    },
    {
      "page": "sim_case_data",
      "title": "Simulate longitudinal case follow-up data from a homogeneous population",
      "topics": [
        "sim_case_data"
      ]
    }
  ],
  "_readme": "https://github.com/ucd-serg/serodynamics/raw/HEAD/README.md",
  "_rundeps": [
    "and",
    "bit",
    "bit64",
    "cli",
    "clipr",
    "coda",
    "codetools",
    "cpp11",
    "crayon",
    "digest",
    "doParallel",
    "dplyr",
    "farver",
    "forcats",
    "foreach",
    "generics",
    "GGally",
    "ggmcmc",
    "ggplot2",
    "ggstats",
    "glue",
    "gtable",
    "haven",
    "hms",
    "isoband",
    "iterators",
    "labeling",
    "labelled",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "patchwork",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "readr",
    "rlang",
    "rngtools",
    "runjags",
    "S7",
    "scales",
    "serocalculator",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "libjags",
      "package": "jags",
      "headers": "jags",
      "source": "jags",
      "version": "4.3.2-2.2404.0",
      "name": "jags",
      "homepage": "https://mcmc-jags.sourceforge.io",
      "description": "Just Another Gibbs Sampler for Bayesian MCMC - binary\nJAGS is Just Another Gibbs Sampler.  It is a program for analysis of\nBayesian hierarchical models using Markov Chain Monte Carlo (MCMC)\nsimulation not wholly unlike BUGS.\n\nJAGS was written with three aims in mind:\n* To have an engine for the BUGS language that runs on Unix\n* To be extensible, allowing users to write their own functions,\ndistributions and samplers.\n* To be a plaftorm for experimentation with ideas in Bayesian modelling\n\nThis package contains the 'jags' binary as well as the associated\nshared library modules loaded by the binary."
    },
    {
      "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": "dobson.Rmd",
      "filename": "dobson.html",
      "title": "dobson",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2025-02-17 08:36:04",
      "modified": "2025-02-18 06:37:22",
      "commits": 2
    }
  ],
  "_score": 6.079181246047625,
  "_indexed": true,
  "_nocasepkg": "serodynamics",
  "_universes": [
    "ucd-serg",
    "sschildhauer"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.0.9055",
      "date": "2026-06-04T03:17:53.000Z",
      "distro": "noble",
      "commit": "ba9ae9868709bb0b019067d1304c63f2dd15a4c9",
      "fileid": "c4e9e4a4d33f32fd9bbf30360b546a9bfb77841f1dc29927b9c8b13e6309ceda",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ucd-serg/actions/runs/26927932356"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.0.0.9055",
      "date": "2026-06-04T03:17:55.000Z",
      "distro": "noble",
      "commit": "ba9ae9868709bb0b019067d1304c63f2dd15a4c9",
      "fileid": "ecb75b811fba79af8d3547a955612d132e37e2b7904c743f62db3f29e0613a0a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ucd-serg/actions/runs/26927932356"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.0.9055",
      "date": "2026-06-04T03:17:18.000Z",
      "commit": "ba9ae9868709bb0b019067d1304c63f2dd15a4c9",
      "fileid": "e717818f884985c7d9aef36789dc89b12d1065897efabeeadfe8b5ad4bde0c46",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ucd-serg/actions/runs/26927932356"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.0.0.9055",
      "date": "2026-06-04T03:17:00.000Z",
      "commit": "ba9ae9868709bb0b019067d1304c63f2dd15a4c9",
      "fileid": "d66b2323d222a5fb080b8018aaa9c857758f4c15cbe4602030e17931e6fff811",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ucd-serg/actions/runs/26927932356"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.0.0.9055",
      "date": "2026-06-04T03:18:09.000Z",
      "commit": "ba9ae9868709bb0b019067d1304c63f2dd15a4c9",
      "fileid": "2fad3823fd2a208822762f3ec0178e622107a3daa8a1d4023c13ee46f436aeeb",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ucd-serg/actions/runs/26927932356"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.0.9055",
      "date": "2026-06-04T03:16:54.000Z",
      "commit": "ba9ae9868709bb0b019067d1304c63f2dd15a4c9",
      "fileid": "e78569d8338936f79d8afe9672332a7136c9374572c3d604ab12b9d921615d0b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ucd-serg/actions/runs/26927932356"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.0.0.9055",
      "date": "2026-06-04T03:16:44.000Z",
      "commit": "ba9ae9868709bb0b019067d1304c63f2dd15a4c9",
      "fileid": "983a9241c2a47971e90765a52b1ce2bbeb559eddfca4162c4060dfbd172e4106",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ucd-serg/actions/runs/26927932356"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.0.0.9055",
      "date": "2026-06-04T03:16:52.000Z",
      "commit": "ba9ae9868709bb0b019067d1304c63f2dd15a4c9",
      "fileid": "c1b1e0c0693fadc754dc304eea99150e78c95b624119ae376a9f600a145d9746",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ucd-serg/actions/runs/26927932356"
    }
  ]
}