{ "_id": "6ace157ca14063b82c3af67d", "Package": "serosv", "Type": "Package", "Title": "Model Infectious Disease Parameters from Serosurveys", "Version": "1.3.0.9000", "Authors@R": "c(\nperson(\"Anh\", \"Phan Truong Quynh\", email = \"anhptq@oucru.org\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0000-2129-435X\")),\nperson(\"Nguyen\", \"Pham Nguyen The\", email = \"nguyenpnt@oucru.org\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-0356-2776\")),\nperson(\"Long\", \"Bui Thanh\", role = \"aut\"),\nperson(\"Tuyen\", \"Huynh\", email = \"tuyenhn@oucru.org\", role = \"aut\"),\nperson(\"Thinh\", \"Ong\", email = \"thinhop@oucru.org\", role = \"aut\", comment = c(ORCID = \"0000-0001-6772-9291\")),\nperson(\"Marc\", \"Choisy\", email = \"mchoisy@oucru.org\", role = \"aut\", comment = c(ORCID = \"0000-0002-5187-6390\"))\n)", "Description": "An easy-to-use and efficient tool to estimate infectious\ndiseases parameters using serological data. Implemented models\ninclude SIR models (basic_sir_model(), static_sir_model(),\nmseir_model(), sir_subpops_model()), parametric models\n(polynomial_model(), fp_model()), nonparametric models\n(lp_model()), semiparametric models\n(penalized_splines_model()), hierarchical models\n(hierarchical_bayesian_model()). The package is based on the\nbook \"Modeling Infectious Disease Parameters Based on\nSerological and Social Contact Data: A Modern Statistical\nPerspective\" (Hens, Niel & Shkedy, Ziv & Aerts, Marc & Faes,\nChristel & Damme, Pierre & Beutels, Philippe., 2013)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "Collate": "'data.R' 'fractional_polynomial_models.R'\n'polynomial_models.R' 'utils.R' 'compare_models.R'\n'correct_prevalence.R' 'weibull_model.R' 'farrington_model.R'\n'nonparametric.R' 'semiparametric_models.R' 'mixture_model.R'\n'hierarchical_bayesian_model.R' 'to_titer.R' 'serosv.R'\n'stanmodels.R' 'plots.R' 'compute_ci.R' 'age_time_model.R'\n'predict.R' 'print.R'", "Config/testthat/edition": "3", "URL": "https://oucru-modelling.github.io/serosv/,\nhttps://github.com/OUCRU-Modelling/serosv", "VignetteBuilder": "knitr", "Biarch": "true", "SystemRequirements": "GNU make", "BugReports": "https://github.com/OUCRU-Modelling/serosv/issues", "Config/roxygen2/version": "8.0.0", "Repository": "https://oucru-modelling.r-universe.dev", "Date/Publication": "2026-08-14 05:59:11 UTC", "RemoteUrl": "https://github.com/oucru-modelling/serosv", "RemoteRef": "HEAD", "RemoteSha": "75163a6681739d78b8222ce202914eb0d8e132db", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-13 11:04:48 UTC", "User": "root" }, "Author": "Anh Phan Truong Quynh [aut, cre] (ORCID:\n),\nNguyen Pham Nguyen The [aut] (ORCID:\n),\nLong Bui Thanh [aut],\nTuyen Huynh [aut],\nThinh Ong [aut] (ORCID: ),\nMarc Choisy [aut] (ORCID: )", "Maintainer": "Anh Phan Truong Quynh ", "_user": "oucru-modelling", "_type": "src", "_file": "serosv_1.3.0.9000.tar.gz", "_fileid": "https://r2.ropensci.org/89a6ab08ce5f7386379592899cd1b9070455e0594ec408f3ff642ea2199d6567", "_filesize": 8077649, "_sha256": "89a6ab08ce5f7386379592899cd1b9070455e0594ec408f3ff642ea2199d6567", "_expires": "2027-01-21T11:26:49.000Z", "_created": "2026-10-13T11:04:48.000Z", "_published": "2026-10-13T11:26:52.173Z", "_buildurl": "https://github.com/r-universe/oucru-modelling/actions/runs/38386546192", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 115264865089, "time": 392, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11808110120" }, { "job": 115264865083, "time": 486, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11808070357" }, { "job": 115264865110, "time": 367, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11807499546" }, { "job": 115264865177, "time": 477, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11807479731" }, { "job": 115264865353, "time": 495, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11807504802" }, { "job": 115264865270, "time": 637, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11808040729" }, { "job": 115264865024, "time": 492, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11807524125" }, { "job": 115264865463, "time": 1091, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11808606603" }, { "job": 115259769314, "time": 803, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11807313388" }, { "job": 115264865077, "time": 204, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11806519644" }, { "job": 115264865187, "time": 669, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11806814969" }, { "job": 115264865055, "time": 567, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11807139637" }, { "job": 115264865161, "time": 501, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11807950442" }, { "job": 115264865133, "time": 688, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11807815918" }, { "job": 115264865164, "time": 584, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11808600100" } ], "_upstream": "https://github.com/oucru-modelling/serosv", "_commit": { "id": "75163a6681739d78b8222ce202914eb0d8e132db", "author": "Anh Phan <90673616+quingzz@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #56 from OUCRU-Modelling/resolve-issues\n\nThe failed tests are caused by an issue while running boost.ci on Ubuntu. \n\nThe issue has yet to be reproduced on MacOS, but it is likely that, under very specific conditions, the result from `stat_func()` in nonparametric_bootstrap is considered non-numeric. It is unclear if this is a platform-specific issue or an issue in the re-sampling method.", "time": 1786687151 }, "_maintainer": { "name": "Anh Phan Truong Quynh", "email": "anhptq@oucru.org", "login": "quingzz", "description": "Research Assistant @OUCRU-Modelling ", "uuid": 90673616, "orcid": "0009-0000-2129-435X" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "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": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "janitor", "role": 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"title": "Visualize positive threshold at different dilution factors", "topics": [ "add_thresholds" ] }, { "page": "age_time_model", "title": "Age-time varying seroprevalence", "topics": [ "age_time_model" ] }, { "page": "compare_models", "title": "Generate table of metrics for model comparison", "topics": [ "compare_models" ] }, { "page": "compute_ci.age_time_model", "title": "Compute confidence interval for time age model", "topics": [ "compute_ci.age_time_model" ] }, { "page": "compute_ci.default", "title": "Compute confidence interval for a model of serosv", "topics": [ "compute_ci.default" ] }, { "page": "compute_ci.estimate_from_mixture", "title": "Compute confidence interval for the prevalence estimate from mixture model", "topics": [ "compute_ci.estimate_from_mixture" ] }, { "page": "compute_ci.farrington_model", "title": "Compute confidence interval for Farrington model", "topics": [ "compute_ci.farrington_model" ] }, { "page": "compute_ci.fp_model", "title": "Compute confidence interval for fractional polynomial model", "topics": [ "compute_ci.fp_model" ] }, { "page": "compute_ci.hierarchical_bayesian_model", "title": "Compute 95% credible interval for hierarchical Bayesian model", "topics": [ "compute_ci.hierarchical_bayesian_model" ] }, { "page": "compute_ci.lp_model", "title": "Compute confidence interval for local polynomial model", "topics": [ "compute_ci.lp_model" ] }, { "page": "compute_ci.mixture_model", "title": "Compute confidence interval for mixture model", "topics": [ "compute_ci.mixture_model" ] }, { "page": "compute_ci.penalized_spline_model", "title": "Compute confidence interval for penalized_spline_model", "topics": [ "compute_ci.penalized_spline_model" ] }, { "page": "compute_ci.weibull_model", "title": "Compute confidence interval for Weibull model", "topics": [ "compute_ci.weibull_model" ] }, { "page": "correct_prevalence", "title": "Estimate the true sero prevalence using Frequentist/Bayesian estimation", "topics": [ "correct_prevalence" ] }, { "page": "est_foi", "title": "Estimate force of infection", "topics": [ "est_foi" ] }, { "page": "estimate_from_mixture", "title": "Estimate seroprevalence and FOI from a fixed mixture model", "topics": [ "estimate_from_mixture" ] }, { "page": "farrington_model", "title": "The Farrington (1990) model.", "topics": [ "farrington_model" ] }, { "page": "find_best_fp_powers", "title": "Returns the powers of the fractional polynomial model which has the lowest deviance score.", "topics": [ "find_best_fp_powers" ] }, { "page": "fp_model", "title": "A fractional polynomial model.", "topics": [ "fp_model" ] }, { "page": "hav_be_1993_1994", "title": "Hepatitis A serological data from Belgium in 1993 and 1994 (aggregated)", "topics": [ "hav_be_1993_1994" ] }, { "page": "hav_be_2002", "title": "Hepatitis A serological data from Belgium in 2002 (line listing)", "topics": [ "hav_be_2002" ] }, { "page": "hav_bg_1964", "title": "Hepatitis A serological data from Bulgaria in 1964 (aggregated)", "topics": [ "hav_bg_1964" ] }, { "page": "hbv_ru_1999", "title": "Hepatitis B serological data from Russia in 1999 (aggregated)", "topics": [ "hbv_ru_1999" ] }, { "page": "hcv_be_2006", "title": "Hepatitis C serological data from Belgium in 2006 (line listing)", "topics": [ "hcv_be_2006" ] }, { "page": "hierarchical_bayesian_model", "title": "Hierarchical Bayesian Model", "topics": [ "hierarchical_bayesian_model" ] }, { "page": "lp_model", "title": "A local polynomial model.", "topics": [ "lp_model" ] }, { "page": "mixture_model", "title": "Fit a mixture model to classify serostatus", "topics": [ "mixture_model" ] }, { "page": "mumps_uk_1986_1987", "title": "Mumps serological data from the UK in 1986 and 1987 (aggregated)", "topics": [ "mumps_uk_1986_1987" ] }, { "page": "parvob19_be_2001_2003", "title": "Parvo B19 serological data from Belgium from 2001-2003 (line listing)", "topics": [ "parvob19_be_2001_2003" ] }, { "page": "parvob19_ew_1996", "title": "Parvo B19 serological data from England and Wales in 1996 (line listing)", "topics": [ "parvob19_ew_1996" ] }, { "page": "parvob19_fi_1997_1998", "title": "Parvo B19 serological data from Finland from 1997-1998 (line listing)", "topics": [ "parvob19_fi_1997_1998" ] }, { "page": "parvob19_it_2003_2004", "title": "Parvo B19 serological data from Italy from 2003-2004 (line listing)", "topics": [ "parvob19_it_2003_2004" ] }, { "page": "parvob19_pl_1995_2004", "title": "Parvo B19 serological data from Poland from 1995-2004 (line listing)", "topics": [ "parvob19_pl_1995_2004" ] }, { "page": "pava", "title": "Monotonize seroprevalence", "topics": [ "pava" ] }, { "page": "penalized_spline_model", "title": "Penalized Spline model", "topics": [ "penalized_spline_model" ] }, { "page": "plot_corrected_prev", "title": "Plot output for corrected_prevalence", "topics": [ "plot_corrected_prev" ] }, { "page": "plot_gcv", "title": "Plotting GCV values with respect to different nn-s and h-s parameters.", "topics": 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