{ "_id": "6ae5ad7c8d250e7ad09f34c4", "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", "Config/pak/sysreqs": "cmake", "Repository": "https://timktsang.r-universe.dev", "Date/Publication": "2026-03-30 14:58:43 UTC", "RemoteUrl": "https://github.com/timktsang/seroreconstruct", "RemoteRef": "HEAD", "RemoteSha": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-31 08:24:14 UTC", "User": "root" }, "Author": "Tim Tsang [aut, cre] (ORCID: )", "_user": "timktsang", "_type": "src", "_file": "seroreconstruct_1.1.5.tar.gz", "_fileid": "https://r2.ropensci.org/5a672062544f50156a7f1f88dbe8b0fde52dda33d3a8e55c05d917d162c92fbd", "_filesize": 946007, "_sha256": "5a672062544f50156a7f1f88dbe8b0fde52dda33d3a8e55c05d917d162c92fbd", "_expires": "2027-02-08T08:57:31.000Z", "_created": "2026-10-31T08:24:14.000Z", "_published": "2026-10-31T08:57:32.595Z", "_upstream": "https://github.com/timktsang/seroreconstruct", "_status": "success", "_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" }, "_jobs": [ { "job": 124488549328, "time": 154, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "13036497242" }, { "job": 124488549429, "time": 152, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13036920790" }, { "job": 124488549325, "time": 145, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "13036547080" }, { "job": 124488549382, "time": 154, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "13036572062" }, { "job": 124488549321, "time": 119, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13037076057" }, { "job": 124488549492, "time": 302, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13036434095" }, { "job": 124488549367, "time": 151, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13037061473" }, { "job": 124488549354, "time": 381, "config": "macos-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13036023011" }, { "job": 124487726882, "time": 236, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "13036556755" }, { "job": 124488549315, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13036227651" }, { "job": 124488549337, "time": 373, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "13036316813" }, { "job": 124488549355, "time": 193, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13036920871" }, { "job": 124488549350, "time": 150, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13037015324" }, { "job": 124488549345, "time": 373, "config": "windows-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13036422736" }, { "job": 124488549398, "time": 143, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13036846037" } ], "_buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605", "_commit": { "id": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "author": "Tim Tsang ", "committer": "Tim Tsang ", "message": "Bump to v1.1.5 for CRAN resubmission\n", "time": 1774882723 }, "_distro": "resolute", "_host": "GitHub-Actions", "_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": 7 }, { "week": "2026-13", "n": 22 }, { "week": "2026-14", "n": 3 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "timktsang", "count": 34, "uuid": 27651606 } ], "_userbio": { "uuid": 27651606, "type": "user", "name": "Tim Tsang", "followers": 15, "description": "Assistant Professor, School of Public Health, The University of Hong Kong" }, "_downloads": { "count": 248, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/seroreconstruct" }, "_devurl": "https://github.com/timktsang/seroreconstruct", "_searchresults": 5, "_topics": [ "openblas", "cpp" ], "_abi": { "exports": [], "imports": [ { "key": "Rcpp::Rcpp_precious_preserve()", "hash": "33a97ea62b293da6" }, { "key": "Rcpp::Rcpp_precious_remove()", "hash": "63d26947ba7e1377" }, { "key": "Rcpp::dataptr()", "hash": "54e69ad2e6668c83" }, { "key": "Rcpp::demangle()", "hash": "b0cfd6754c5ebc4e" }, { "key": "Rcpp::enterRNGScope()", "hash": "a04a299137cef947" }, { "key": "Rcpp::exitRNGScope()", "hash": "a04a299137cef947" }, { "key": "Rcpp::rcpp_get_stack_trace()", "hash": "c684a9bbe15cdc52" }, { "key": "Rcpp::rcpp_set_stack_trace()", "hash": "33a97ea62b293da6" } ] }, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/seroreconstruct.html" ], "_homeurl": "https://github.com/timktsang/seroreconstruct", "_realowner": "timktsang", "_cranurl": true, "_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/timktsang/seroreconstruct/raw/HEAD/README.md", "_rundeps": [ "Rcpp", "RcppArmadillo", "RcppParallel" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "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": "2026-03-23 08:05:26", "modified": "2026-03-30 14:22:23", "commits": 4 }, { "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": "2026-03-23 08:05:26", "modified": "2026-03-23 08:56:06", "commits": 2 } ], "_score": 4.477121254719663, "_indexed": true, "_nocasepkg": "seroreconstruct", "_universes": [ "timktsang" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.5", "date": "2026-10-31T08:26:44.000Z", "distro": "resolute", "arch": "aarch64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/29f6dd2fdaf85f40731c0f4260c95db56748dcebd495b6b0a187c2b8a69fbf85", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.7.0", "os": "linux", "version": "1.1.5", "date": "2026-10-31T08:26:28.000Z", "distro": "resolute", "arch": "x86_64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/fece63343e9bc7a621b5b23770e9b358ffc2330d87e717ec273d6b46863f95a2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.6.1", "os": "linux", "version": "1.1.5", "date": "2026-10-31T08:26:38.000Z", "distro": "resolute", "arch": "aarch64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/d6f96ecfe81a60625bdded4412097622c371822e7dbe6f54dfca9677a65393d4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.6.1", "os": "linux", "version": "1.1.5", "date": "2026-10-31T08:26:43.000Z", "distro": "resolute", "arch": "x86_64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/c45ac370bc2fadc3418c68822496ac77aa7a1d85ab47106dc9e73c472a74e1bf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.5.3", "os": "mac", "version": "1.1.5", "date": "2026-10-31T08:52:42.000Z", "arch": "aarch64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/507cc156d98cbc63a548af88eacb0c552ec561b68b53697bc6e8db2e90d7bf22", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.5.3", "os": "mac", "version": "1.1.5", "date": "2026-10-31T08:38:55.000Z", "arch": "x86_64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/c2dd339e20585f9e5fe9300e585ca8896d0a6973873df17833dbbde4908a38d8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.6.2", "os": "mac", "version": "1.1.5", "date": "2026-10-31T08:56:10.000Z", "arch": "aarch64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/bae287dd1a4427c1d28668665b66385b81bcfd0db11d1d4741e358d07e7b75fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.6.2", "os": "mac", "version": "1.1.5", "date": "2026-10-31T08:37:51.000Z", "arch": "x86_64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/5589dfa1d6bada365b7fbfbf0f5ac5a938313e70a32dc8062dd57ff5cec47724", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.5", "date": "2026-10-31T08:26:30.000Z", "arch": "emscripten", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/3f1e36dfcfedaeacf76f2120586da2e2399febe570dab7471259e522ba64fc29", "status": "success", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.7.0", "os": "win", "version": "1.1.5", "date": "2026-10-31T08:29:28.000Z", "arch": "aarch64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/782b6852aef7fdf49be98c8d50c73266e47fece482f31a48ca63e63648d9f50d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.7.0", "os": "win", "version": "1.1.5", "date": "2026-10-31T08:25:46.000Z", "arch": "x86_64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/cf194914e3bbf04769c855abd14c9f8291a7c8c9bde553bd70c8935c90bae459", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.5.3", "os": "win", "version": "1.1.5", "date": "2026-10-31T08:25:47.000Z", "arch": "x86_64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/a299e551a9c26055d49855737eba5c3a5a527b23072becff032c2762a078ca20", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.6.2", "os": "win", "version": "1.1.5", "date": "2026-10-31T08:29:38.000Z", "arch": "aarch64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/ccd9032f3ef6aad770d8891bdd21d52aeb55a32cf4ab40931802acc17fd79577", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" }, { "r": "4.6.2", "os": "win", "version": "1.1.5", "date": "2026-10-31T08:25:47.000Z", "arch": "x86_64", "commit": "5bb6441eaa4450489fb61eb116899b5f455dd7b0", "fileid": "https://r2.ropensci.org/489f70ef7918ef59d84334c88bf8893b59c8a871f7074a35182dedbad7e47457", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/timktsang/actions/runs/41184214605" } ] }