{ "_id": "6a14127bacfb0bcc41d3b9ec", "Package": "npfseir", "Title": "Nested Particle Filter for Stochastic SEIR Epidemic Models", "Version": "0.2.1", "Date": "2026-04-22", "Authors@R": "person(\"Weinan\", \"Wang\",\nemail = \"ww@ou.edu\",\nrole = c(\"aut\", \"cre\"))", "Description": "Implements the online Bayesian inference framework for\njoint state and parameter estimation in a stochastic\nSusceptible-Exposed-Infectious-Recovered (SEIR) epidemic model\nwith a time-varying transmission rate. The log-transmission\nrate is modelled as a latent Ornstein-Uhlenbeck (OU) process\nwith exact Gaussian discrete-time transitions. Inference is\nperformed via the nested particle filter (NPF) of Crisan and\nMiguez (2018) , which maintains an outer\nparticle layer over the OU hyperparameters and, for each outer\nparticle, an inner bootstrap filter over epidemic states. The\nCori-style renewal-equation estimator follows Cori et al.\n(2013) . The package also provides\nutilities for simulation, posterior summarisation, and\nforecasting.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-25 09:09:31 UTC", "User": "root" }, "Author": "Weinan Wang [aut, cre]", "Maintainer": "Weinan Wang ", "Repository": "https://wwang-math.r-universe.dev", "Date/Publication": "2026-04-24 20:05:00 UTC", "RemoteUrl": "https://github.com/cran/npfseir", "RemoteRef": "HEAD", "RemoteSha": "6b776c32d3bb18ba8c28e0670326dffea6914fa5", "MD5sum": "e214886808fc3be0810ad6987b8bb648", "_user": "wwang-math", "_type": "src", "_file": "npfseir_0.2.1.tar.gz", "_fileid": "d8b2e582bdc691d00c9f871006ae6f14354e1e4a1082b9ee8614f102cdc43630", "_filesize": 446414, "_sha256": "d8b2e582bdc691d00c9f871006ae6f14354e1e4a1082b9ee8614f102cdc43630", "_created": "2026-05-25T09:09:31.000Z", "_published": "2026-05-25T09:12:27.247Z", "_distro": "noble", "_jobs": [ { "job": 77686093796, "time": 115, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7195229043" }, { "job": 77686093834, "time": 112, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7195228517" }, { "job": 77686093818, "time": 144, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7195228376" }, { "job": 77686093775, "time": 113, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7195225096" }, { "job": 77685878437, "time": 156, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7195204809" }, { "job": 77686093803, "time": 90, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7195223683" }, { "job": 77686094379, "time": 79, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7195221100" }, { "job": 77686093804, "time": 62, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7195217249" }, { "job": 77686093766, "time": 65, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7195217773" } ], "_buildurl": "https://github.com/r-universe/wwang-math/actions/runs/26392661237", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/npfseir", "_commit": { "id": "6b776c32d3bb18ba8c28e0670326dffea6914fa5", "author": "Weinan Wang ", "committer": "cran-robot ", "message": "version 0.2.1\n", "time": 1777061100 }, "_maintainer": { "name": "Weinan Wang", "email": "ww@ou.edu", "login": "wwang-math", "description": "", "uuid": 25256351 }, "_registered": true, "_dependencies": [ { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-17", "n": 1 } ], "_tags": [ { "name": "0.2.1", "date": "2026-04-24" } ], "_stars": 0, "_contributors": [ { "user": "wwang-math", "count": 1, "uuid": 25256351 } ], "_userbio": { "uuid": 25256351, "type": "user", "name": "Wang" }, "_downloads": { "count": 442, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/npfseir" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/npfseir.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "wwang-math", "_cranurl": false, "_releases": [ { "version": "0.2.1", "date": "2026-04-24" } ], "_exports": [ "cori_rt", "npf_seir", "ou_params", "seir_simulate" ], "_help": [ { "page": "npfseir-package", "title": "npfseir: Nested Particle Filter for Stochastic SEIR Epidemic Models", "topics": [ "npfseir-package", "npfseir" ] }, { "page": "cori_rt", "title": "Cori-style renewal-equation R_t estimator", "topics": [ "cori_rt" ] }, { "page": "npf_seir", "title": "Run the Nested Particle Filter for a stochastic SEIR model", "topics": [ "npf_seir" ] }, { "page": "ou_params", "title": "Compute exact Ornstein-Uhlenbeck discrete-time transition parameters", "topics": [ "ou_params" ] }, { "page": "plot.npf_seir", "title": "Plot method for npf_seir", "topics": [ "plot.npf_seir" ] }, { "page": "predict.npf_seir", "title": "Posterior predictive forecasts from an npf_seir object", "topics": [ "predict.npf_seir" ] }, { "page": "print.npf_seir", "title": "Print method for npf_seir", "topics": [ "print.npf_seir" ] }, { "page": "seir_simulate", "title": "Simulate a stochastic SEIR epidemic with latent OU transmission", "topics": [ "seir_simulate" ] }, { "page": "summary.npf_seir", "title": "Summary method for npf_seir", "topics": [ "summary.npf_seir" ] } ], "_readme": "https://github.com/cran/npfseir/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "getting-started.Rmd", "filename": "getting-started.html", "title": "Getting started with npfseir", "engine": "knitr::rmarkdown", "headings": [ "Overview", "1. Simulate a synthetic epidemic", "2. Run the nested particle filter", "3. Inspect results", "4. Plot the R_t trajectory", "5. Forecast", "6. Cori-style R_t comparison (illustrative only)", "References" ], "created": "2026-04-24 20:05:00", "modified": "2026-04-24 20:05:00", "commits": 1 } ], "_score": 2.6989700043360187, "_indexed": true, "_nocasepkg": "npfseir", "_universes": [ "wwang-math" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.1", "date": "2026-05-25T09:11:26.000Z", "distro": "noble", "commit": "6b776c32d3bb18ba8c28e0670326dffea6914fa5", "fileid": "b1261499305c2f6f6c7fb313a550d2ae68867e9b204ed013082d760e53390323", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wwang-math/actions/runs/26392661237" }, { "r": "4.6.0", "os": "linux", "version": "0.2.1", "date": "2026-05-25T09:11:24.000Z", "distro": "noble", "commit": "6b776c32d3bb18ba8c28e0670326dffea6914fa5", "fileid": "421cc8a91b7ea66b3b6b1fca7d76b59ef6344419f57febf5a56f59f8d220bfa2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wwang-math/actions/runs/26392661237" }, { "r": "4.5.3", "os": "mac", "version": "0.2.1", "date": "2026-05-25T09:11:26.000Z", "commit": "6b776c32d3bb18ba8c28e0670326dffea6914fa5", "fileid": "5ecf882854e05729adb1525ad0c046f247d346320ed88a53f294f2270f6b22fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wwang-math/actions/runs/26392661237" }, { "r": "4.6.0", "os": "mac", "version": "0.2.1", "date": "2026-05-25T09:11:14.000Z", "commit": "6b776c32d3bb18ba8c28e0670326dffea6914fa5", "fileid": "93dfce08b29c4ee390abec3c601af0a40b5d16f2e75e2d66db43b44befb0b735", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wwang-math/actions/runs/26392661237" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.1", "date": "2026-05-25T09:11:15.000Z", "commit": "6b776c32d3bb18ba8c28e0670326dffea6914fa5", "fileid": "bb8c189f3952b70b105e8735e6d08c2b143991d962bd79d55c0ee23c33418f07", "status": "success", "buildurl": "https://github.com/r-universe/wwang-math/actions/runs/26392661237" }, { "r": "4.7.0", "os": "win", "version": "0.2.1", "date": "2026-05-25T09:10:47.000Z", "commit": "6b776c32d3bb18ba8c28e0670326dffea6914fa5", "fileid": "b5383d8ff0527e2519e6ebd2e7b34f8027e54a1bb7e001cac7b5ea403d075415", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wwang-math/actions/runs/26392661237" }, { "r": "4.5.3", "os": "win", "version": "0.2.1", "date": "2026-05-25T09:10:31.000Z", "commit": "6b776c32d3bb18ba8c28e0670326dffea6914fa5", "fileid": "d081ace64de7472a0a1b965e11b5a9aa28791a9e3dc6b2a99382534cc2137f88", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wwang-math/actions/runs/26392661237" }, { "r": "4.6.0", "os": "win", "version": "0.2.1", "date": "2026-05-25T09:10:33.000Z", "commit": "6b776c32d3bb18ba8c28e0670326dffea6914fa5", "fileid": "f41abdfa367c994521fa6aed5234ff8d710ca4d3a08c92debabaefd2aef3a865", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wwang-math/actions/runs/26392661237" } ] }