{ "_id": "6a2076e6cd65a98ecbd14aff", "Package": "NobBS", "Title": "Nowcasting by Bayesian Smoothing", "Version": "1.1.2", "Authors@R": "c(\nperson(\"Sarah\", \"McGough\", email = \"sfm341@mail.harvard.edu\", role = c(\"aut\", \"ctb\")),\nperson(\"Nicolas\", \"Menzies\", email = \"nmenzies@hsph.harvard.edu\", role = \"aut\"),\nperson(\"Marc\", \"Lipsitch\", email = \"mlipsitc@hsph.harvard.edu\", role = \"aut\"),\nperson(\"Michael\", \"Johansson\", email = \"mjohansson@cdc.gov\", role = \"aut\"),\nperson(\"Rami\", \"Yaari\", email = \"ramiyaari@gmail.com\", role = c(\"aut\",\"ctb\")),\nperson(\"Rodrigo\", \"Zepeda Tello\", email = \"rzepeda17@gmail.com\", role = c(\"cre\",\"aut\",\"ctb\")),\nperson(\"Teresa\", \"Yamana\", email = \"tky2104@climate.columbia.edu\", role = c(\"ctb\")),\nperson(\"Matteo\", \"Perini\", email = \"mperini@climate.columbia.edu\", role = c(\"ctb\"))\n)", "Description": "A Bayesian approach to estimate the number of\noccurred-but-not-yet-reported cases from incomplete,\ntime-stamped reporting data for disease outbreaks. 'NobBS'\nlearns the reporting delay distribution and the time evolution\nof the epidemic curve to produce smoothed nowcasts in both\nstable and time-varying case reporting settings, as described\nin McGough et al. (2020) .", "SystemRequirements": "JAGS (http://mcmc-jags.sourceforge.net/) for\nanalysis of Bayesian hierarchical models", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "jags", "Repository": "https://sarahhbellum.r-universe.dev", "Date/Publication": "2026-06-03 15:58:55 UTC", "RemoteUrl": "https://github.com/sarahhbellum/nobbs", "RemoteRef": "HEAD", "RemoteSha": "f45caee94292f0c4749fd794ee2fd5f224acdfbd", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 18:40:56 UTC", "User": "root" }, "Author": "Sarah McGough [aut, ctb],\nNicolas Menzies [aut],\nMarc Lipsitch [aut],\nMichael Johansson [aut],\nRami Yaari [aut, ctb],\nRodrigo Zepeda Tello [cre, aut, ctb],\nTeresa Yamana [ctb],\nMatteo Perini [ctb]", "Maintainer": "Rodrigo Zepeda Tello ", "MD5sum": "43f575313a14b275d98a9872391a9dc3", "_user": "sarahhbellum", "_type": "src", "_file": "NobBS_1.1.2.tar.gz", "_fileid": "7e391ac098e2a7145919f79c61547c56a0d1d10200b11761452afa3a5e1c419b", "_filesize": 2089219, "_sha256": "7e391ac098e2a7145919f79c61547c56a0d1d10200b11761452afa3a5e1c419b", "_created": "2026-06-03T18:40:56.000Z", "_published": "2026-06-03T18:48:06.466Z", "_distro": "noble", "_jobs": [ { "job": 79369162452, "time": 172, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7393692102" }, { "job": 79369162565, "time": 145, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7393681738" }, { "job": 79369162457, "time": 103, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7393775416" }, { "job": 79369162700, "time": 97, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7393745259" }, { "job": 79368404583, "time": 232, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7393625979" }, { "job": 79369162524, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7393669057" }, { "job": 79369162523, "time": 104, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7393666067" }, { "job": 79369162598, "time": 106, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7393667200" }, { "job": 79369162587, "time": 93, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7393661975" } ], "_buildurl": "https://github.com/r-universe/sarahhbellum/actions/runs/26905276938", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/sarahhbellum/nobbs", "_commit": { "id": "f45caee94292f0c4749fd794ee2fd5f224acdfbd", "author": "ramiyaari ", "committer": "ramiyaari ", "message": "Updates News.Rmd with new changes\n", "time": 1780502335 }, "_maintainer": { "name": "Rodrigo Zepeda Tello", "email": "rzepeda17@gmail.com", "login": "rodrigozepeda", "twitter": "@RodZepeda", "description": "", "uuid": 13838319 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.3.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "rjags", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "scoringutils", "version": ">= 2.0.0", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" } ], "_owner": "sarahhbellum", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-22", "n": 2 }, { "week": "2026-23", "n": 2 } ], "_tags": [], "_stars": 19, "_contributors": [ { "user": "sarahhbellum", "count": 58, "uuid": 11428423 }, { "user": "ramiyaari", "count": 7, "uuid": 41739638 }, { "user": "mariabnd", "count": 3, "uuid": 33788128 } ], "_userbio": { "uuid": 11428423, "type": "user", "name": "Sarah McGough" }, "_downloads": { "count": 585, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/NobBS" }, "_mentions": 4, "_devurl": "https://github.com/sarahhbellum/nobbs", "_searchresults": 45, "_topics": [ "jags", "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/NobBS.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/sarahhbellum/nobbs", "_realowner": "sarahhbellum", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2020-03-03" }, { "version": "1.0.0", "date": "2024-01-08" }, { "version": "1.1.0", "date": "2025-05-07" }, { "version": "1.1.1", "date": "2026-06-01" } ], "_exports": [ "NobBS", "NobBS.strat" ], "_datasets": [ { "name": "denguedat", "title": "denguedat: Dengue fever reporting data from Puerto Rico", "object": "denguedat", "class": [ "data.frame" ], "fields": [ "onset_week", "report_week", "gender" ], "rows": 52987, "table": true, "tojson": true }, { "name": "mpoxdat", "title": "mpoxdat: Mpox reporting data from the 2022 New York City Outbreak", "object": "mpoxdat", "class": [ "data.frame" ], "fields": [ "dx_date", "dx_report_date", "onset_date", "onset_report_date" ], "rows": 3323, "table": true, "tojson": true } ], "_help": [ { "page": "denguedat", "title": "denguedat: Dengue fever reporting data from Puerto Rico", "topics": [ "denguedat" ] }, { "page": "mpoxdat", "title": "mpoxdat: Mpox reporting data from the 2022 New York City Outbreak", "topics": [ "mpoxdat" ] }, { "page": "NobBS", "title": "Produce smooth Bayesian nowcasts of incomplete, time-stamped reporting data.", "topics": [ "NobBS" ] }, { "page": "NobBS.strat", "title": "Stratified nowcasts of incomplete, time-stamped reporting data.", "topics": [ "NobBS.strat" ] } ], "_readme": "https://github.com/sarahhbellum/nobbs/raw/HEAD/README.md", "_rundeps": [ "cli", "coda", "dplyr", "generics", "glue", "lattice", "lifecycle", "magrittr", "pillar", "pkgconfig", "R6", "rjags", "rlang", "tibble", "tidyselect", "utf8", "vctrs", "withr" ], "_sysdeps": [ { "shlib": "libjags", "package": "jags", "headers": "jags", "source": "jags", "version": "4.3.2-2.2404.0", "name": "jags", "homepage": "https://mcmc-jags.sourceforge.io", "description": "Just Another Gibbs Sampler for Bayesian MCMC - binary\nJAGS is Just Another Gibbs Sampler. It is a program for analysis of\nBayesian hierarchical models using Markov Chain Monte Carlo (MCMC)\nsimulation not wholly unlike BUGS.\n\nJAGS was written with three aims in mind:\n* To have an engine for the BUGS language that runs on Unix\n* To be extensible, allowing users to write their own functions,\ndistributions and samplers.\n* To be a plaftorm for experimentation with ideas in Bayesian modelling\n\nThis package contains the 'jags' binary as well as the associated\nshared library modules loaded by the binary." }, { "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": "dow_effect.Rmd", "filename": "dow_effect.html", "title": "Accounting for Day-of-the-Week Effect in Nowcast Models", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Comparing the Performance with and without DoW Effect", "DoW Coefficients Estimates", "Employing DoW Estimates as Priors for Future Nowcasts", "Conclusion" ], "created": "2025-04-29 19:27:24", "modified": "2025-04-29 19:27:24", "commits": 1 }, { "source": "wis_calc.Rmd", "filename": "wis_calc.html", "title": "Calculating Weighted Interval Score for Nowcast Models", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Nowcasting Scenarios", "Comparing the Nowcast Estimates of the Poisson and negative binomial Models", "Extracting Quantile Estimates", "Calculating and Plotting the Weighted Interval Score", "Conclusion" ], "created": "2025-04-29 19:27:24", "modified": "2025-04-29 19:27:24", "commits": 1 }, { "source": "batched_reports.Rmd", "filename": "batched_reports.html", "title": "Handling Batched Reporting in Nowcast Models", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Data Preparation", "Nowcasting Scenarios", "Delay Distribution Estimates", "Incidence Estimates", "Conclusion" ], "created": "2025-04-29 19:27:24", "modified": "2025-04-29 19:27:24", "commits": 1 } ], "_score": 7.312177356439779, "_indexed": true, "_nocasepkg": "nobbs", "_universes": [ "sarahhbellum", "rodrigozepeda" ], "_previous": "1.1.1", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.2", "date": "2026-06-03T18:43:44.000Z", "distro": "noble", "commit": "f45caee94292f0c4749fd794ee2fd5f224acdfbd", "fileid": "b6c9c3b52a489cafed3c8279816b34c570221b08289c81029508f26fe49d3166", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarahhbellum/actions/runs/26905276938" }, { "r": "4.6.0", "os": "linux", "version": "1.1.2", "date": "2026-06-03T18:43:16.000Z", "distro": "noble", "commit": "f45caee94292f0c4749fd794ee2fd5f224acdfbd", "fileid": "e9cf933c9f0543c56d4eaefe0bf711fa56e473ac6dd737d072179fbffd689774", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarahhbellum/actions/runs/26905276938" }, { "r": "4.5.3", "os": "mac", "version": "1.1.2", "date": "2026-06-03T18:47:30.000Z", "commit": "f45caee94292f0c4749fd794ee2fd5f224acdfbd", "fileid": "b04b5cfdc9a45b134975ccdf6aee53c950ca52138ce402194b2561415208d530", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarahhbellum/actions/runs/26905276938" }, { "r": "4.6.0", "os": "mac", "version": "1.1.2", "date": "2026-06-03T18:46:11.000Z", "commit": "f45caee94292f0c4749fd794ee2fd5f224acdfbd", "fileid": "f19d3f67edf3520f3e52d370e3bbeb78dca290191f239a560979449860d50db7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarahhbellum/actions/runs/26905276938" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.2", "date": "2026-06-03T18:43:08.000Z", "commit": "f45caee94292f0c4749fd794ee2fd5f224acdfbd", "fileid": "2f1d0c1a504e8073adef31c08e39b9a0d7e9cec3ef535bf5082a43ac8d64f6cd", "status": "success", "buildurl": "https://github.com/r-universe/sarahhbellum/actions/runs/26905276938" }, { "r": "4.7.0", "os": "win", "version": "1.1.2", "date": "2026-06-03T18:42:29.000Z", "commit": "f45caee94292f0c4749fd794ee2fd5f224acdfbd", "fileid": "8827444fe37391c70c93a890ce1ec48623e77fdfb0a2e07044ce87bd190d5c8d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarahhbellum/actions/runs/26905276938" }, { "r": "4.5.3", "os": "win", "version": "1.1.2", "date": "2026-06-03T18:42:33.000Z", "commit": "f45caee94292f0c4749fd794ee2fd5f224acdfbd", "fileid": "3a61f2a8e17ebbfb00c2133c76b61bbb6d57439c59571c050b51153bf0a4a247", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarahhbellum/actions/runs/26905276938" }, { "r": "4.6.0", "os": "win", "version": "1.1.2", "date": "2026-06-03T18:42:23.000Z", "commit": "f45caee94292f0c4749fd794ee2fd5f224acdfbd", "fileid": "04d2419e907a029f61e64e211d2bfb6b0c83c19985ec7117f7790eb4f80b09f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sarahhbellum/actions/runs/26905276938" } ] }