{
  "_id": "6a25192a4b233be19838cd13",
  "Package": "hhdynamics",
  "Type": "Package",
  "Title": "Fitting Household Transmission Model to Estimate Household\nTransmission Dynamics of Influenza",
  "Version": "1.3.3",
  "Authors@R": "c(person(given = \"Tim\",\nfamily = \"Tsang\",\nrole = c(\"aut\", \"cre\"),\nemail = \"timkltsang@gmail.com\",\ncomment = c(ORCID = \"0000-0001-5037-6776\")))",
  "Maintainer": "Tim Tsang <timkltsang@gmail.com>",
  "Description": "A Bayesian household transmission model to estimate\nhousehold transmission dynamics, with accounting for infection\nfrom community and tertiary cases.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "LazyData": "TRUE",
  "URL": "https://github.com/timktsang/hhdynamics",
  "BugReports": "https://github.com/timktsang/hhdynamics/issues",
  "SystemRequirements": "GNU make",
  "RoxygenNote": "7.3.3",
  "Config/testthat/edition": "3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make",
  "Repository": "https://timktsang.r-universe.dev",
  "Date/Publication": "2026-04-08 22:51:39 UTC",
  "RemoteUrl": "https://github.com/timktsang/hhdynamics",
  "RemoteRef": "HEAD",
  "RemoteSha": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-07 06:47:21 UTC",
    "User": "root"
  },
  "Author": "Tim Tsang [aut, cre] (ORCID: <https://orcid.org/0000-0001-5037-6776>)",
  "MD5sum": "feece2c2ad6addb007cd5a7495d170f7",
  "_user": "timktsang",
  "_type": "src",
  "_file": "hhdynamics_1.3.3.tar.gz",
  "_fileid": "9eee6d88611e297b3e9e745621a4a87bbf6c253679696716f03c0007082b99f8",
  "_filesize": 571206,
  "_sha256": "9eee6d88611e297b3e9e745621a4a87bbf6c253679696716f03c0007082b99f8",
  "_created": "2026-06-07T06:47:21.000Z",
  "_published": "2026-06-07T07:09:30.401Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79938567390,
      "time": 143,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7461608113"
    },
    {
      "job": 79938567388,
      "time": 157,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7461609418"
    },
    {
      "job": 79938567376,
      "time": 188,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7461613233"
    },
    {
      "job": 79938567386,
      "time": 154,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7461609016"
    },
    {
      "job": 79938567413,
      "time": 138,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7461607042"
    },
    {
      "job": 79938567404,
      "time": 269,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7461622237"
    },
    {
      "job": 79938567392,
      "time": 1277,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7461740413"
    },
    {
      "job": 79938567405,
      "time": 268,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7461622155"
    },
    {
      "job": 79938371575,
      "time": 213,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7461591216"
    },
    {
      "job": 79938567352,
      "time": 113,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7461604484"
    },
    {
      "job": 79938567359,
      "time": 132,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7461606491"
    },
    {
      "job": 79938567371,
      "time": 138,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7461607211"
    },
    {
      "job": 79938567344,
      "time": 118,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7461605092"
    }
  ],
  "_buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/timktsang/hhdynamics",
  "_commit": {
    "id": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
    "author": "Tim Tsang <timtsang@connect.hku.hk>",
    "committer": "Tim Tsang <timtsang@connect.hku.hk>",
    "message": "Fix ESS computation error on constant MCMC chains (v1.3.3)\n\nacf() returns NaN for zero-variance input, causing\n\"missing value where TRUE/FALSE needed\" in .effective_sample_size().\nAdd early return for constant chains and defensive is.na() guard.\nFixes CRAN check ERROR on r-devel-linux-x86_64-fedora-gcc.\n",
    "time": 1775688699
  },
  "_maintainer": {
    "name": "Tim Tsang",
    "email": "timkltsang@gmail.com",
    "login": "timktsang",
    "description": "Assistant Professor, School of Public Health, The University of Hong Kong",
    "uuid": 27651606,
    "orcid": "0000-0001-5037-6776"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "RcppParallel",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.9",
      "role": "Imports"
    },
    {
      "package": "RcppParallel",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "timktsang",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-12",
      "n": 10
    },
    {
      "week": "2026-13",
      "n": 10
    },
    {
      "week": "2026-15",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "timktsang",
      "count": 35,
      "uuid": 27651606
    }
  ],
  "_userbio": {
    "uuid": 27651606,
    "type": "user",
    "name": "Tim Tsang",
    "description": "Assistant Professor, School of Public Health, The University of Hong Kong"
  },
  "_downloads": {
    "count": 423,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hhdynamics"
  },
  "_devurl": "https://github.com/timktsang/hhdynamics",
  "_searchresults": 5,
  "_topics": [
    "openblas",
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/hhdynamics.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/timktsang/hhdynamics",
  "_realowner": "timktsang",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.3.2",
      "date": "2026-03-26"
    },
    {
      "version": "1.3.3",
      "date": "2026-04-09"
    }
  ],
  "_exports": [
    "create_wide_data",
    "household_dynamics",
    "plot_attack_rate",
    "plot_covariates",
    "plot_diagnostics",
    "plot_household",
    "plot_transmission",
    "run_MCMC",
    "simulate_data",
    "table_attack_rates",
    "table_covariates",
    "table_parameters"
  ],
  "_datasets": [
    {
      "name": "inputdata",
      "title": "Example of input data",
      "object": "inputdata",
      "class": [
        "data.frame"
      ],
      "fields": [
        "hhID",
        "member",
        "size",
        "end",
        "inf",
        "onset",
        "age",
        "sex"
      ],
      "rows": 1533,
      "table": true,
      "tojson": true
    },
    {
      "name": "para",
      "title": "Example of parameter vector for the main model",
      "object": "para",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "SI",
      "title": "Example of serial interval distribution of influenza",
      "object": "SI",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "coef.hhdynamics_fit",
      "title": "Extract model coefficients from hhdynamics_fit",
      "topics": [
        "coef.hhdynamics_fit"
      ]
    },
    {
      "page": "create_wide_data",
      "title": "Create a wide format of household data",
      "topics": [
        "create_wide_data"
      ]
    },
    {
      "page": "household_dynamics",
      "title": "Fit a household transmission model via MCMC",
      "topics": [
        "household_dynamics"
      ]
    },
    {
      "page": "inputdata",
      "title": "Example of input data",
      "concept": [
        "inputdata"
      ],
      "topics": [
        "inputdata"
      ]
    },
    {
      "page": "para",
      "title": "Example of parameter vector for the main model",
      "concept": [
        "example_data"
      ],
      "topics": [
        "para"
      ]
    },
    {
      "page": "plot_attack_rate",
      "title": "Plot secondary attack rates",
      "topics": [
        "plot_attack_rate"
      ]
    },
    {
      "page": "plot_covariates",
      "title": "Forest plot of covariate effects",
      "topics": [
        "plot_covariates"
      ]
    },
    {
      "page": "plot_diagnostics",
      "title": "MCMC diagnostic plots",
      "topics": [
        "plot_diagnostics"
      ]
    },
    {
      "page": "plot_household",
      "title": "Plot household infection timeline",
      "topics": [
        "plot_household"
      ]
    },
    {
      "page": "plot_transmission",
      "title": "Plot transmission probability over time since onset",
      "topics": [
        "plot_transmission"
      ]
    },
    {
      "page": "plot.hhdynamics_fit",
      "title": "Plot method for hhdynamics_fit objects",
      "topics": [
        "plot.hhdynamics_fit"
      ]
    },
    {
      "page": "print.hhdynamics_fit",
      "title": "Print method for hhdynamics_fit",
      "topics": [
        "print.hhdynamics_fit"
      ]
    },
    {
      "page": "print.summary.hhdynamics_fit",
      "title": "Print method for summary.hhdynamics_fit",
      "topics": [
        "print.summary.hhdynamics_fit"
      ]
    },
    {
      "page": "run_MCMC",
      "title": "Run the MCMC for the household transmission model",
      "topics": [
        "run_MCMC"
      ]
    },
    {
      "page": "SI",
      "title": "Example of serial interval distribution of influenza",
      "concept": [
        "example_data"
      ],
      "topics": [
        "SI"
      ]
    },
    {
      "page": "simulate_data",
      "title": "Simulate household transmission data",
      "topics": [
        "simulate_data"
      ]
    },
    {
      "page": "summary.hhdynamics_fit",
      "title": "Summary method for hhdynamics_fit",
      "topics": [
        "summary.hhdynamics_fit"
      ]
    },
    {
      "page": "table_attack_rates",
      "title": "Table of secondary attack rates",
      "topics": [
        "table_attack_rates"
      ]
    },
    {
      "page": "table_covariates",
      "title": "Table of covariate effects (odds ratios)",
      "topics": [
        "table_covariates"
      ]
    },
    {
      "page": "table_parameters",
      "title": "Table of transmission parameter estimates",
      "topics": [
        "table_parameters"
      ]
    }
  ],
  "_readme": "https://github.com/timktsang/hhdynamics/raw/HEAD/README.md",
  "_rundeps": [
    "Rcpp",
    "RcppArmadillo",
    "RcppParallel"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "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": "hhdynamics-intro.Rmd",
      "filename": "hhdynamics-intro.html",
      "title": "Getting Started with hhdynamics",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Data format",
        "Serial interval",
        "Fitting the model",
        "Inspecting results",
        "Quick overview",
        "Parameter estimates",
        "Posterior means",
        "Accessing MCMC output",
        "Visualization",
        "MCMC diagnostics",
        "Transmission probability over time",
        "Covariate effects (forest plot)",
        "Secondary attack rates",
        "Household timeline",
        "Summary tables",
        "Covariate effects",
        "Input validation",
        "Missing data handling",
        "Missing onset times",
        "Missing covariates",
        "Estimating the serial interval",
        "Simulation"
      ],
      "created": "2026-03-19 08:52:55",
      "modified": "2026-03-23 05:23:54",
      "commits": 6
    },
    {
      "source": "hhdynamics-methodology.Rmd",
      "filename": "hhdynamics-methodology.html",
      "title": "Statistical Methodology",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Model",
        "Study design",
        "Infection hazard",
        "Covariates",
        "Likelihood",
        "Individual likelihood",
        "Full likelihood",
        "Prior distributions",
        "MCMC algorithm",
        "Metropolis-Hastings sampler",
        "Adaptive proposal tuning",
        "Data augmentation",
        "Serial interval estimation",
        "Convergence diagnostics",
        "Recommended MCMC settings",
        "Interpretation of parameters",
        "Base parameters",
        "Covariate effects",
        "Serial interval parameters",
        "Computational details",
        "References"
      ],
      "created": "2026-03-23 05:23:54",
      "modified": "2026-03-23 05:23:54",
      "commits": 1
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": true,
  "_nocasepkg": "hhdynamics",
  "_universes": [
    "timktsang"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.3",
      "date": "2026-06-07T06:49:44.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "d2d5eb7b2ca22c91b8d7af24009039960f2b5076362ede115d00e170ea942c74",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.3",
      "date": "2026-06-07T06:49:50.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "ffedb65437ec26eeeb8c8a2b19b8a1b226d3450fbfe31d3121fe31c107b935e2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.3",
      "date": "2026-06-07T06:50:28.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "37846958884bf87bdd37f16023c4a9b13e89aece8e2d172c2048345b8574a576",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.3",
      "date": "2026-06-07T06:49:44.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "5f48a7f6b3d1d0bc6c9cad022350b33d139f3342639e7cae4fa8541127826e67",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.3",
      "date": "2026-06-07T06:49:28.000Z",
      "arch": "aarch64",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "4d03d8642899388e18a53db0f06a5b6c8f8479bb923e0537375a393f930ca486",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.3",
      "date": "2026-06-07T06:50:23.000Z",
      "arch": "x86_64",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "9fb167732df7d8111ef4fd8e447813d6e6258324e2e8b56d1a75ac529f88354a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.3.3",
      "date": "2026-06-07T06:49:30.000Z",
      "arch": "aarch64",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "e0f5b4327780e8a7dc6b9216ff7308c6f07d37a333bd5ad6a4d7f4b9c70f35eb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.3.3",
      "date": "2026-06-07T06:49:53.000Z",
      "arch": "x86_64",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "70cdadc40ac4fe93f6d125f82ee7dfc8d4f74bed38f528e2d9305c7cfb369873",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.3",
      "date": "2026-06-07T06:49:37.000Z",
      "arch": "emscripten",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "7b1219316470cebc932ba6eb7a83f520047aa9c6a5648fd3b9c9ba6539737931",
      "status": "success",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.3",
      "date": "2026-06-07T06:48:57.000Z",
      "arch": "x86_64",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "d6194b583cd33008eebf0d1ed71600413b1a242fb56e7e4540953b113ea38fff",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3.3",
      "date": "2026-06-07T06:48:53.000Z",
      "arch": "x86_64",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "b7b873cdba6185226f22c9e0171cde88d09aaea33ab4c12559402d554e3e4f8a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.3.3",
      "date": "2026-06-07T06:48:47.000Z",
      "arch": "x86_64",
      "commit": "4e3a02544387e83ffc31adda373d8dfe5e9dc37f",
      "fileid": "068fa158cc75b654c6a673bb222d6d604184188bcb3d6a02460c08ef5edb7468",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/timktsang/actions/runs/27085238567"
    }
  ]
}