{
  "_id": "6a168d8facfb0bcc41d7775c",
  "Package": "HHBayes",
  "Title": "Bayesian Household Transmission Modeling",
  "Version": "0.0.0.9000",
  "Authors@R": "c(\nperson(given = \"Ke\", family = \"Li\",\nemail = \"ke.li.kl662@yale.edu\",\nrole = c(\"aut\",\"cre\")),\nperson(given = \"Yiren\", family = \"Hou\",\nemail = \"yiren.hou@yale.edu\",\nrole = c(\"aut\"))\n)",
  "Description": "Provides a streamlined pipeline to simulate household\ninfection dynamics, estimate transmission parameters, and\nvisualize epidemic timelines. Uses a Bayesian approach with\nStan that models transmission probability as a Function of\nviral load, seasonality and infectivity, multiple infection\nepisodes (reinfections), and waning immunity modeling.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "Funding": "This work was supported by a grant from the National\nInstitutes of Health (R01AI137093). The content is solely the\nresponsibility of the authors and does not necessarily\nrepresent the official views of the National Institutes of\nHealth.",
  "Biarch": "true",
  "SystemRequirements": "GNU make",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/keli5734/HHBayes",
  "BugReports": "https://github.com/keli5734/HHBayes/issues",
  "Config/pak/sysreqs": "cmake make libicu-dev",
  "Repository": "https://keli5734.r-universe.dev",
  "Date/Publication": "2026-04-27 18:30:36 UTC",
  "RemoteUrl": "https://github.com/keli5734/hhbayes",
  "RemoteRef": "HEAD",
  "RemoteSha": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-27 06:11:39 UTC",
    "User": "root"
  },
  "Author": "Ke Li [aut, cre],\nYiren Hou [aut]",
  "Maintainer": "Ke Li <ke.li.kl662@yale.edu>",
  "MD5sum": "c5aa2a88089b5f36d3ceb76c0fb62654",
  "_user": "keli5734",
  "_type": "src",
  "_file": "HHBayes_0.0.0.9000.tar.gz",
  "_fileid": "580a91c4f4896f2e3b3089100c5484ffa261a4ee768eb58666044902914d01b0",
  "_filesize": 500793,
  "_sha256": "580a91c4f4896f2e3b3089100c5484ffa261a4ee768eb58666044902914d01b0",
  "_created": "2026-05-27T06:11:39.000Z",
  "_published": "2026-05-27T06:22:07.742Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78018441016,
      "time": 260,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7233240901"
    },
    {
      "job": 78018440881,
      "time": 295,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7233248854"
    },
    {
      "job": 78018440980,
      "time": 275,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233244291"
    },
    {
      "job": 78018440865,
      "time": 280,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233245312"
    },
    {
      "job": 78018441025,
      "time": 255,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7233233036"
    },
    {
      "job": 78018440962,
      "time": 512,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7233295087"
    },
    {
      "job": 78018441329,
      "time": 211,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233222992"
    },
    {
      "job": 78018440976,
      "time": 438,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233277401"
    },
    {
      "job": 78017723417,
      "time": 372,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233181448"
    },
    {
      "job": 78018440859,
      "time": 170,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78018440868,
      "time": 265,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7233241870"
    },
    {
      "job": 78018441038,
      "time": 271,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7233243288"
    },
    {
      "job": 78018440858,
      "time": 330,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7233257386"
    }
  ],
  "_buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/keli5734/hhbayes",
  "_commit": {
    "id": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
    "author": "Ke Li <48193766+keli5734@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update README to clarify household simulation",
    "time": 1777314636
  },
  "_maintainer": {
    "name": "Ke Li",
    "email": "ke.li.kl662@yale.edu"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "BH",
      "version": ">= 1.66.0",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "version": ">= 0.3.3.3.0",
      "role": "LinkingTo"
    },
    {
      "package": "RcppParallel",
      "version": ">= 5.0.1",
      "role": "LinkingTo"
    },
    {
      "package": "rstan",
      "version": ">= 2.18.1",
      "role": "LinkingTo"
    },
    {
      "package": "StanHeaders",
      "version": ">= 2.18.0",
      "role": "LinkingTo"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "Imports"
    },
    {
      "package": "rstan",
      "version": ">= 2.18.1",
      "role": "Imports"
    },
    {
      "package": "rstantools",
      "version": ">= 2.4.0",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "deSolve",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "RcppParallel",
      "version": ">= 5.0.1",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    }
  ],
  "_owner": "keli5734",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-08",
      "n": 44
    },
    {
      "week": "2026-09",
      "n": 13
    },
    {
      "week": "2026-11",
      "n": 2
    },
    {
      "week": "2026-12",
      "n": 2
    },
    {
      "week": "2026-14",
      "n": 7
    },
    {
      "week": "2026-17",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 6,
  "_contributors": [
    {
      "user": "keli5734",
      "count": 70,
      "uuid": 48193766
    }
  ],
  "_userbio": {
    "uuid": 48193766,
    "type": "user",
    "name": "Ke Li"
  },
  "_downloads": {
    "count": 499,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/HHBayes"
  },
  "_devurl": "https://github.com/keli5734/hhbayes",
  "_searchresults": 2,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/HHBayes.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/keli5734/hhbayes",
  "_realowner": "keli5734",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.1",
      "date": "2026-04-10"
    }
  ],
  "_exports": [
    "calculate_sar_quick",
    "calculate_sar_robust",
    "fill_missing_viral_data",
    "fit_household_model",
    "plot_covariate_effects",
    "plot_epidemic_curve",
    "plot_household_timeline",
    "plot_posterior_distributions",
    "prepare_stan_data",
    "reconstruct_transmission_chains",
    "simulate_multiple_households_comm",
    "summarize_attack_rates"
  ],
  "_help": [
    {
      "page": "calculate_sar_quick",
      "title": "Quick SAR Calculator (Convenience Wrapper)",
      "topics": [
        "calculate_sar_quick"
      ]
    },
    {
      "page": "calculate_sar_robust",
      "title": "Calculate Secondary Attack Rate (Robust)",
      "topics": [
        "calculate_sar_robust"
      ]
    },
    {
      "page": "fill_missing_viral_data",
      "title": "Fill Missing Viral Data (Ct or Log10) based on Episode Start",
      "topics": [
        "fill_missing_viral_data"
      ]
    },
    {
      "page": "fit_household_model",
      "title": "Fit Household Transmission Model",
      "topics": [
        "fit_household_model"
      ]
    },
    {
      "page": "generate_contact_matrix_from_roles",
      "title": "Generate Household Contact Matrix from Role Rules",
      "topics": [
        "generate_contact_matrix_from_roles"
      ]
    },
    {
      "page": "ode_system_func",
      "title": "ODE System for Within-Host Dynamics",
      "topics": [
        "ode_system_func"
      ]
    },
    {
      "page": "plot_covariate_effects",
      "title": "Plot Covariate Coefficients (Forest Plot)",
      "topics": [
        "plot_covariate_effects"
      ]
    },
    {
      "page": "plot_epidemic_curve",
      "title": "Plot Dual-Axis Epidemic Curve (Binned)",
      "topics": [
        "plot_epidemic_curve"
      ]
    },
    {
      "page": "plot_household_timeline",
      "title": "Plot Household Timeline with Person-Centric Reinfections",
      "topics": [
        "plot_household_timeline"
      ]
    },
    {
      "page": "plot_posterior_distributions",
      "title": "Plot Posterior Distributions (Phi and Kappa)",
      "topics": [
        "plot_posterior_distributions"
      ]
    },
    {
      "page": "prepare_stan_data",
      "title": "Prepare Data for Stan Model",
      "topics": [
        "prepare_stan_data"
      ]
    },
    {
      "page": "reconstruct_transmission_chains",
      "title": "Reconstruct Transmission Chains",
      "topics": [
        "reconstruct_transmission_chains"
      ]
    },
    {
      "page": "simulate_multiple_households_comm",
      "title": "Simulate Household Transmission",
      "topics": [
        "simulate_multiple_households_comm"
      ]
    },
    {
      "page": "summarize_attack_rates",
      "title": "Summarize Attack Rates & Reinfections",
      "topics": [
        "summarize_attack_rates"
      ]
    }
  ],
  "_pkglogo": "https://github.com/keli5734/hhbayes/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/keli5734/hhbayes/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "BH",
    "boot",
    "broom",
    "callr",
    "car",
    "carData",
    "checkmate",
    "cli",
    "colorspace",
    "corrplot",
    "cowplot",
    "cpp11",
    "Deriv",
    "desc",
    "deSolve",
    "distributional",
    "doBy",
    "dplyr",
    "farver",
    "forecast",
    "Formula",
    "fracdiff",
    "generics",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "gridExtra",
    "gtable",
    "inline",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "loo",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "matrixStats",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "pbkrtest",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "polynom",
    "posterior",
    "processx",
    "ps",
    "purrr",
    "quantreg",
    "QuickJSR",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RcppParallel",
    "Rdpack",
    "reformulas",
    "rlang",
    "rstan",
    "rstantools",
    "rstatix",
    "S7",
    "scales",
    "SparseM",
    "StanHeaders",
    "stringi",
    "stringr",
    "survival",
    "tensorA",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "zoo"
  ],
  "_sysdeps": [
    {
      "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": "HHBayes-tutorial.Rmd",
      "filename": "HHBayes-tutorial.html",
      "title": "Getting Started with HHBayes",
      "author": "Ke Li",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Part 1: Study Setup",
        "1.1 Study Timeline",
        "1.2 Surveillance Data (Community Forcing)",
        "1.3 Contact Matrix (Role Mixing Weights)",
        "1.4 Household Composition",
        "1.5 Intervention Strategies (Covariates)",
        "Part 2: Simulation",
        "2.1 Run the Simulator",
        "2.2 Inspect the Output",
        "2.3 Summarize Attack Rates",
        "2.4 Plot the Epidemic Curve",
        "Part 3: Preparing Data for Stan",
        "3.1 Join Covariates to Diagnostic Data",
        "3.2 Define Priors",
        "3.3 Viral Load Imputation Parameters",
        "3.4 Build the Stan Input",
        "Part 4: Fitting the Bayesian Model",
        "4.1 Run HMC Sampling",
        "4.2 View Summary",
        "4.3 Convergence Diagnostics",
        "Part 5: Visualization",
        "5.1 Posterior Distributions",
        "5.2 Covariate Effects (Forest Plot)",
        "5.3 Transmission Chain Reconstruction",
        "5.4 Household Timeline",
        "Appendix A: Complete Script",
        "Session Info"
      ],
      "created": "2026-02-17 17:14:30",
      "modified": "2026-02-17 17:14:30",
      "commits": 1
    }
  ],
  "_score": 5.3222192947339195,
  "_indexed": true,
  "_nocasepkg": "hhbayes",
  "_universes": [
    "keli5734"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.0.9000",
      "date": "2026-05-27T06:15:18.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
      "fileid": "aa6df725ceacc31d48529a9820410c02d3dc7612c8a6628bcf960fc2a24d0b75",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.0.0.9000",
      "date": "2026-05-27T06:15:41.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
      "fileid": "cb9beea8e9a89e59a42837ebe68708e2efba8799cb025042e2fd0e24607b4ae4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.0.0.9000",
      "date": "2026-05-27T06:15:27.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
      "fileid": "841e0efb4e04355922d05318e5d19e7b471faec800cd531af417cb1ccf187f1a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.0.0.9000",
      "date": "2026-05-27T06:15:28.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
      "fileid": "1499df582d593716275aea3fed47ecffd45917d0237a76761f65ab9f11ac7f60",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.0.9000",
      "date": "2026-05-27T06:15:16.000Z",
      "arch": "aarch64",
      "commit": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
      "fileid": "db8a716373a1e3462d8de6f06a3ead843ad74974cdaa8d45d94cf821cd4ec6f5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.0.0.9000",
      "date": "2026-05-27T06:17:23.000Z",
      "arch": "x86_64",
      "commit": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
      "fileid": "d2f8996b7a91fcf07c1bcb9962690cbd8394adf91e504febde1b15da31794326",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.0.0.9000",
      "date": "2026-05-27T06:14:40.000Z",
      "arch": "aarch64",
      "commit": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
      "fileid": "420ede7f66b4cf78c5eb4befb75dcdb90b0545e48b16142cbd2c3df1cc0339ba",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.0.0.9000",
      "date": "2026-05-27T06:16:18.000Z",
      "arch": "x86_64",
      "commit": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
      "fileid": "50dd431f5704a7dd68c4c9f83c0b4589f9a695a8d72cf72ae3d14d5260bf999a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-05-27T06:14:42.000Z",
      "arch": "x86_64",
      "commit": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
      "fileid": "67fcfad55f1d2c191ea8e822150c4f42c46f8e89754ac83158cdc4ddbb29f2b9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-05-27T06:14:13.000Z",
      "arch": "x86_64",
      "commit": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
      "fileid": "c9048c1d8cd5d57b81628e5d220d4ccb7ca4136c6efa00735f467d00de7a2911",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.0.0.9000",
      "date": "2026-05-27T06:15:04.000Z",
      "arch": "x86_64",
      "commit": "0bb4c18e6cf251d916951bdb4d3cabb6fae2c10e",
      "fileid": "01ac0e2e69b0d0db9a01485ed2f1a9ab9999d2284d89fa87c4c3763f47ecd2a9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/keli5734/actions/runs/26493988313"
    }
  ]
}