{ "_id": "6abfae1d99f7aa8c6aa59349", "Package": "mudnester", "Title": "Surveillance Data Cleaning and Preparation for Public Health", "Version": "0.7.8", "Description": "Clean, prepare, and aggregate surveillance data for public\nhealth analysis. Provides structural data cleaning and\nstandardisation (clean_the_nest()), age categorisation against\n~50 published schemes with publication-ready labelling\n(preening()), time-unit aggregation with zero-filling and\nseasonal awareness (roost()), joint aggregation of several\nlinked event dates (e.g. onset, admission, ICU, complication,\nfatality) into one table of comparable rate columns (flyway()),\nunder-ascertainment correction via a stratified, time-varying\nmultiplier factor supplied directly, derived by the ratio\n(multiplier) method, or derived by inverting an externally\nsourced severity rate (e.g. an infection-fatality-rate anchor)\nagainst an observed severity ratio (corncrake()), comorbidity\ndetection from ICD-10-AM clinical coding (plumage()), vaccine\ncoverage data construction (brood()), hash-based\nde-identification (molting()), and relinking of previously\nde-identified data (homing()). brood() produces a brood_df\nobject supporting two population models: pre-aggregated\ndenominators (population_model = \"pre_aggregated\") and\nrecord-level cohort designs (population_model = \"cohort\"). The\ncohort model handles single time-point coverage snapshots,\ninterrupted time series analysis via a built-in sweep returning\nmonthly coverage rates (time_series = TRUE), and birth cohort\ndesigns with person-time computation. This cohort/time-series\ncoverage model was applied in Roughan et al. (2026)\n to estimate infant immunisation\ncoverage against respiratory syncytial virus over an 18-month\nperiod. Both wide format (one row per person with dose columns,\nfrom 'starling'::murmuration()) and long format (one row per\ndose) are accepted. corncrake() returns both a point-corrected\ncount and uncertainty bounds wherever they can be derived,\nincluding the inverse relationship between a severity-anchored\nfactor and the bounds of its own reference rate. Built for\nAustralian public health surveillance practice but not specific\nto it -- see individual function documentation for notes on\nnon-Australian use (e.g. Northern Hemisphere season\nboundaries).", "Authors@R": "c(\nperson(\"Nicolas\", \"Smoll\", email = \"nicolas.smoll@health.qld.gov.au\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6923-9701\")),\nperson(\"Moderna\", role = \"fnd\",\ncomment = \"Support for this package's development was provided via the Moderna Global Research Fellowship\")\n)", "License": "MIT + file LICENSE", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Language": "en-GB", "LazyData": "true", "RoxygenNote": "8.0.0", "VignetteBuilder": "knitr", "URL": "https://github.com/nrsmoll/mudnester", "BugReports": "https://github.com/nrsmoll/mudnester/issues", "NeedsCompilation": "no", "Author": "Nicolas Smoll [aut, cre] (ORCID:\n), Moderna [fnd]\n(Support for this package's development was provided via the\nModerna Global Research Fellowship)", "Maintainer": "Nicolas Smoll ", "Packaged": { "Date": "2026-10-02 13:10:15 UTC", "User": "root" }, "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-10-02 12:52:35 UTC", "RemoteUrl": "https://github.com/cran/mudnester", "RemoteRef": "HEAD", "RemoteSha": "f7d9bb56bde2a1a502fd8e0c9a8080ab0044f216", "_user": "cran", "_type": "src", "_file": "mudnester_0.7.8.tar.gz", "_fileid": "https://r2.ropensci.org/6a626d7a796bf8ca27a323b9d751562f18d085decadead06d4fa4bb79b837ef1", "_filesize": 605263, "_sha256": "6a626d7a796bf8ca27a323b9d751562f18d085decadead06d4fa4bb79b837ef1", "_expires": "2027-01-10T13:14:03.000Z", "_created": "2026-10-02T13:10:15.000Z", "_published": "2026-10-02T13:14:05.207Z", "_jobs": [ { "job": 110851324703, "time": 182, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11228665157" }, { "job": 110851324731, "time": 131, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11228326319" }, { "job": 110849116296, "time": 371, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11227499268" }, { "job": 110851324784, "time": 156, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11227474954" }, { "job": 110851324788, "time": 103, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11227623428" }, { "job": 110851324793, "time": 94, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11227871681" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/37010553279", "_status": "success", "_upstream": "https://github.com/cran/mudnester", "_commit": { "id": "f7d9bb56bde2a1a502fd8e0c9a8080ab0044f216", "author": "Nicolas Smoll ", "committer": "cran-robot ", "message": "version 0.7.8\n", "time": 1790945555 }, "_maintainer": { "name": "Nicolas Smoll", "email": "nicolas.smoll@health.qld.gov.au", "orcid": "0000-0002-6923-9701" }, "_distro": "resolute", "_registered": true, 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Definitions", "object": "age_schemes", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "scheme", "family", "focus_tags", "n_bands", "breaks", "labels", "age_unit", "source", "source_url", "last_checked", "is_illustrative" ], "rows": 50, "table": true, "tojson": true } ], "_help": [ { "page": "age_schemes", "title": "Age Banding Scheme Definitions", "topics": [ "age_schemes" ] }, { "page": "brood", "title": "Construct a Vaccine Coverage Data Object", "topics": [ "brood" ] }, { "page": "clean_the_nest", "title": "Clean and Standardise Surveillance Data", "topics": [ "clean_the_nest" ] }, { "page": "corncrake", "title": "Correct Surveillance Counts for Under-Ascertainment", "topics": [ "corncrake" ] }, { "page": "flyway", "title": "Aggregate Multiple Sequential Event Dates in One Table", "topics": [ "flyway" ] }, { "page": "homing", "title": "Relink De-identified Data Using the molting() Lookup Table", "topics": [ "homing" ] }, { "page": "list_age_schemes", "title": "List 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"withr" ], "_vignettes": [ { "source": "age-schemes.Rmd", "filename": "age-schemes.html", "title": "Age Scheme Catalogue", "author": "Dr Nicolas Smoll, SCPHU, Sunshine Coast Hospital and Health Service", "engine": "knitr::rmarkdown", "headings": [ "Using this catalogue", "Design rules that apply to every scheme", "Family A — National statistical standards (Australia)", "Family B — International statistical standards", "Family C — Vaccination & immunisation guidance", "Family D — Surveillance-system conventions", "Family E — Clinical & developmental staging", "Family F — Disease- and research-specific bands", "Verifying illustrative schemes" ], "created": "2026-10-02 12:52:35", "modified": "2026-10-02 12:52:35", "commits": 1 }, { "source": "brood.Rmd", "filename": "brood.html", "title": "brood(): Vaccine Coverage Data Structures for All Study Designs", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Why \"brood\"?", "Two population models", "Model 1: Pre-aggregated 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