{ "_id": "6a1ea2aab25058d4daad744d", "Package": "seroreconstruct", "Type": "Package", "Title": "Reconstructing Antibody Dynamics to Estimate the Risk of\nInfluenza Virus Infection", "Version": "1.1.5", "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 ", "Description": "A Bayesian framework for inferring influenza infection\nstatus from serial antibody measurements. Jointly estimates\nseason-specific infection probabilities, antibody boosting and\nwaning after infection, and baseline hemagglutination\ninhibition (HAI) titer distributions via Markov chain Monte\nCarlo (MCMC). Supports multi-season analysis and subgroup\ncomparisons via a group_by interface. See Tsang et al. (2022)\n for methodological details.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "TRUE", "URL": "https://github.com/timktsang/seroreconstruct", "BugReports": "https://github.com/timktsang/seroreconstruct/issues", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "SystemRequirements": "TBB", "RoxygenNote": "7.3.3", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-02 09:25:45 UTC", "User": "root" }, "Author": "Tim Tsang [aut, cre] (ORCID:\n)", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-04-03 09:13:30 UTC", "RemoteUrl": "https://github.com/cran/seroreconstruct", "RemoteRef": "HEAD", "RemoteSha": "f4c8171b1bf8a99811a084feb5bc96e36c295575", "MD5sum": "aa6d774114ec1f58dc6b531645446337", "_user": "cran", "_type": "src", "_file": "seroreconstruct_1.1.5.tar.gz", "_fileid": "946ffa298ddf4d412ca9fdadd6d5d40d0d59cc9e8c1509c8c83e89b2ed7acef0", "_filesize": 947237, "_sha256": "946ffa298ddf4d412ca9fdadd6d5d40d0d59cc9e8c1509c8c83e89b2ed7acef0", "_created": "2026-06-02T09:25:45.000Z", "_published": "2026-06-02T09:30:18.398Z", "_distro": "noble", "_jobs": [ { "job": 79040176988, "time": 152, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7353973268" }, { "job": 79040176969, "time": 214, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7353994126" }, { "job": 79040176914, "time": 150, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7353972665" }, { "job": 79040176936, "time": 206, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7353991070" }, { "job": 79039368758, "time": 278, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7353917346" }, { "job": 79040176924, "time": 117, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7353960530" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26810610006", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/seroreconstruct", "_commit": { "id": "f4c8171b1bf8a99811a084feb5bc96e36c295575", "author": "Tim Tsang ", "committer": "cran-robot ", "message": "version 1.1.5\n", "time": 1775207610 }, "_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": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-14", "n": 1 } ], "_tags": [ { "name": "1.1.5", "date": "2026-04-03" } ], "_stars": 0, "_contributors": [ { "user": "timktsang", "count": 1, "uuid": 27651606 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 140, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/seroreconstruct" }, "_devurl": "https://github.com/timktsang/seroreconstruct", "_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/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/seroreconstruct.html", "manual.pdf" ], "_homeurl": "https://github.com/timktsang/seroreconstruct", "_realowner": "timktsang", "_cranurl": false, "_releases": [ { "version": "1.1.5", "date": "2026-04-03" } ], "_exports": [ "output_model_estimate", "plot_boosting", "plot_diagnostics", "plot_infection_prob", "plot_trajectory", "plot_waning", "sero_reconstruct", "simulate_data", "table_infections", "table_parameters" ], "_datasets": [ { "name": "flu_activity", "title": "Example of flu activity data", "object": "flu_activity", "class": [ "data.frame" ], "fields": [ "h1.activity" ], "rows": 2738, "table": true, "tojson": true }, { "name": "inputdata", "title": "Example of input data", "object": "inputdata", "class": [ "data.frame" ], "fields": [ "age_group", "start_time", "end_time", "time1", "time2", "time3", "HAI_titer_1", "HAI_titer_2", "HAI_titer3" ], "rows": 1753, "table": true, "tojson": true }, { "name": "para1", "title": "Example of parameter vector for the main model", "object": "para1", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "para2", "title": "Example of parameter vector for the baseline HAI titer for the main model", "object": "para2", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "sub-sub-.seroreconstruct_multi", "title": "Subset a seroreconstruct_multi object", "topics": [ "[[.seroreconstruct_multi" ] }, { "page": "flu_activity", "title": "Example of flu activity data", "concept": [ "example_data" ], "topics": [ "flu_activity" ] }, { "page": "inputdata", "title": "Example of input data", "concept": [ "inputdata" ], "topics": [ "inputdata" ] }, { "page": "output_model_estimate", "title": "Extract the model estimates from the fitted MCMC", "topics": [ "output_model_estimate" ] }, { "page": "para1", "title": "Example of parameter vector for the main model", "concept": [ "example_data" ], "topics": [ "para1" ] }, { "page": "para2", "title": "Example of parameter vector for the baseline HAI titer for the main model", "concept": [ "example_data" ], "topics": [ "para2" ] }, { "page": "plot_boosting", "title": "Plot posterior boosting distributions", "topics": [ "plot_boosting" ] }, { "page": "plot_diagnostics", "title": "MCMC diagnostic plots", "topics": [ "plot_diagnostics" ] }, { "page": "plot_infection_prob", "title": "Plot infection probabilities (forest plot)", "topics": [ "plot_infection_prob" ] }, { "page": "plot_trajectory", "title": "Plot antibody trajectory with model fit", "topics": [ "plot_trajectory" ] }, { "page": "plot_waning", "title": "Plot posterior waning curves", "topics": [ "plot_waning" ] }, { "page": "print.seroreconstruct_fit", "title": "Print method for seroreconstruct_fit", "topics": [ "print.seroreconstruct_fit" ] }, { "page": "print.seroreconstruct_joint", "title": "Print method for seroreconstruct_joint", "topics": [ "print.seroreconstruct_joint" ] }, { "page": "print.seroreconstruct_multi", "title": "Print method for seroreconstruct_multi", "topics": [ "print.seroreconstruct_multi" ] }, { "page": "print.summary.seroreconstruct_fit", "title": "Print method for summary.seroreconstruct_fit", "topics": [ "print.summary.seroreconstruct_fit" ] }, { "page": "print.summary.seroreconstruct_joint", "title": "Print method for summary.seroreconstruct_joint", "topics": [ "print.summary.seroreconstruct_joint" ] }, { "page": "print.summary.seroreconstruct_multi", "title": "Print method for summary.seroreconstruct_multi", "topics": [ "print.summary.seroreconstruct_multi" ] }, { "page": "sero_reconstruct", "title": "Run the MCMC for the Bayesian model", "topics": [ "sero_reconstruct" ] }, { "page": "simulate_data", "title": "Simulation of the dataset of the Bayesian model", "topics": [ "simulate_data" ] }, { "page": "summary.seroreconstruct_fit", "title": "Summary method for seroreconstruct_fit", "topics": [ "summary.seroreconstruct_fit" ] }, { "page": "summary.seroreconstruct_joint", "title": "Summary method for seroreconstruct_joint", "topics": [ "summary.seroreconstruct_joint" ] }, { "page": "summary.seroreconstruct_multi", "title": "Summary method for seroreconstruct_multi", "topics": [ "summary.seroreconstruct_multi" ] }, { "page": "table_infections", "title": "Per-individual infection estimates", "topics": [ "table_infections" ] }, { "page": "table_parameters", "title": "Summary table of model parameters with credible intervals", "topics": [ "table_parameters" ] } ], "_readme": "https://github.com/cran/seroreconstruct/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": "introduction.Rmd", "filename": "introduction.html", "title": "Getting Started with seroreconstruct", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Input data", "Fitting the model", "Viewing results", "Visualization", "MCMC diagnostics", "Antibody trajectories", "Boosting and waning", "Infection probabilities", "Tables", "Subgroup analysis", "Joint model with shared parameters", "Simulation", "Citation" ], "created": "2026-04-03 09:13:30", "modified": "2026-04-03 09:13:30", "commits": 1 }, { "source": "methodology.Rmd", "filename": "methodology.html", "title": "Statistical Methodology", "engine": "knitr::rmarkdown", "headings": [ "Model overview", "Notation", "Antibody dynamics model", "Measurement error model", "Infection risk model", "Prior distributions", "MCMC implementation", "Convergence diagnostics", "Recommendations for production analyses", "Parameter layout", "Shared parameter models", "References" ], "created": "2026-04-03 09:13:30", "modified": "2026-04-03 09:13:30", "commits": 1 } ], "_score": 3, "_indexed": false, "_nocasepkg": "seroreconstruct", "_universes": [ "cran" ], "_indexurl": "https://timktsang.r-universe.dev/seroreconstruct", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.5", "date": "2026-06-02T09:28:09.000Z", "distro": "noble", "arch": "aarch64", "commit": "f4c8171b1bf8a99811a084feb5bc96e36c295575", "fileid": "3cce046fe31dceb7033405feb4b74bffebd2bc9307da3b42185448c5bec710a1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/26810610006" }, { "r": "4.7.0", "os": "linux", "version": "1.1.5", "date": "2026-06-02T09:28:55.000Z", "distro": "noble", "arch": "x86_64", "commit": "f4c8171b1bf8a99811a084feb5bc96e36c295575", "fileid": "cf84ca46f0671a68d9eb33169b067ac937e739d9bdcbcf5a7ea9caac8f0fcd8e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/26810610006" }, { "r": "4.6.0", "os": "linux", "version": "1.1.5", "date": "2026-06-02T09:28:09.000Z", "distro": "noble", "arch": "aarch64", "commit": "f4c8171b1bf8a99811a084feb5bc96e36c295575", "fileid": "b22e716b4b90893a1bd7480fcdfdb06bbf1b3104eede4eaabe5469718da7f795", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/26810610006" }, { "r": "4.6.0", "os": "linux", "version": "1.1.5", "date": "2026-06-02T09:28:49.000Z", "distro": "noble", "arch": "x86_64", "commit": "f4c8171b1bf8a99811a084feb5bc96e36c295575", "fileid": "e7a646995261ed6635a0f2ae671a74904438685b5778bf3f47b952677d996bca", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/26810610006" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.5", "date": "2026-06-02T09:28:08.000Z", "arch": "emscripten", "commit": "f4c8171b1bf8a99811a084feb5bc96e36c295575", "fileid": "99462c19f7f7a151c8cb033e56dbf769726085c6507d00f203337ab7e17e0045", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26810610006" } ] }