{ "_id": "6acb4496fe5cc25786e8d22e", "Package": "starling", "Title": "Record Linkage for Public Health Surveillance", "Version": "1.1.0", "Description": "Record linkage for public health surveillance datasets\nusing either the Fellegi-Sunter probabilistic framework (via\nreclin2) or deterministic exact-key matching. Provides\npre-linkage data quality auditing (preflight()), Medicare\nnumber checksum validation (check_medicare()), blocking\nvariable construction (flock()), and the murmuration() linkage\nengine. murmuration() expresses linkage as a single\ncohort-to-event concept (linking a linelist of people to a\ndated stream of vaccination, hospitalisation, or case events\nwithin a before/during/after time window), with the historical\nfour-code taxonomy (case-to-hospitalisation,\nvaccination-to-case, vaccination-to-hospitalisation,\nvaccination-to-event) retained as deprecated aliases. Also\nprovides linkage weight distribution visualisation\n(murmuration_plot()) and threshold sensitivity analysis\n(perch()) with annotated AIHW, WA Data Linkage Unit, and PHRN\nreference benchmarks. perch() can be called standalone or\ntriggered automatically mid-linkage via\nmurmuration(perch_before_linking = TRUE). Includes synthetic\ndatasets (cases_notifiable, vax_air) and three vignettes\ndemonstrating the complete linkage workflow. Part of the aviary\npublic health surveillance ecosystem.", "Authors@R": "person(\"Nicolas\", \"Smoll\", email = \"nicolas.smoll@health.qld.gov.au\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6923-9701\"))", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "URL": "https://github.com/nrsmoll/starling", "BugReports": "https://github.com/nrsmoll/starling/issues", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://nrsmoll.r-universe.dev", "Date/Publication": "2026-07-13 03:01:18 UTC", "RemoteUrl": "https://github.com/nrsmoll/starling", "RemoteRef": "HEAD", "RemoteSha": "e2fd02791b2cc110c3cfd88993571ccb852aeea1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-11 07:47:17 UTC", "User": "root" }, "Author": "Nicolas Smoll [aut, cre] (ORCID:\n)", "Maintainer": "Nicolas Smoll ", "_user": "nrsmoll", "_type": "src", "_file": "starling_1.1.0.tar.gz", "_fileid": 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"R", "version": ">= 4.1", "role": "Depends" }, { "package": "reclin2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "lubridate", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "patchwork", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "phonics", "role": "Suggests" }, { "package": "mudnester", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "nrsmoll", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-29", "n": 2 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "nrsmoll", "count": 1, "uuid": 28223011 } ], "_userbio": { "uuid": 28223011, "type": "user", "name": "Nicolas Smoll", "followers": 6, "description": "Medical Doctor\r\nPublic Health Physician\r\nBiostatistics and programming" }, "_downloads": { "count": 306, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/starling" }, "_devurl": "https://github.com/nrsmoll/starling", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "extra/starling.html", "LICENSE" ], "_homeurl": "https://github.com/nrsmoll/starling", "_realowner": "nrsmoll", "_cranurl": true, "_releases": [ { "version": "0.6.5", "date": "2026-01-26" }, { "version": "1.1.0", "date": "2026-07-10" } ], "_exports": [ "check_medicare", "flock", "murmuration", "murmuration_plot", "perch", "preflight" ], "_datasets": [ { "name": "cases_notifiable", "title": "Synthetic Notifiable Disease Case Linelist", "object": "cases_notifiable", "file": "cases_notifiable.rda", "class": [ "data.frame" ], "fields": [ "id_var", "true_link_id", "lettername1", "lettername2", "dob", "gender", "postcode", "medicare10", "onset_date", "pathogen" ], "rows": 300, "table": true, "tojson": true }, { "name": "vax_air", "title": "Synthetic Australian Immunisation Register Extract", "object": "vax_air", "file": "vax_air.rda", "class": [ "data.frame" ], "fields": [ "id_var", "lettername1", "lettername2", "dob", "gender", "postcode", "medicare10", "vax_date_1", "vax_type_1", "vax_date_2", "vax_type_2", "vax_date_3", "vax_type_3", "vax_date_4", "vax_type_4" ], "rows": 400, "table": true, "tojson": true } ], "_help": [ { "page": "cases_notifiable", "title": "Synthetic Notifiable Disease Case Linelist", "topics": [ "cases_notifiable" ] }, { "page": "check_medicare", "title": "Validate Australian Medicare Numbers Using the Modulus 10 Checksum", "topics": [ "check_medicare" ] }, { "page": "flock", "title": "Create Blocking Variables for Probabilistic Record Linkage", "topics": [ "flock" ] }, { "page": "murmuration", "title": "Links case, hospital, outbreak, event linelists, vaccination datasets", "topics": [ "murmuration" ] }, { "page": "murmuration_plot", "title": "Visualise Linkage Weight Distribution with Threshold Overlay", "topics": [ "murmuration_plot" ] }, { "page": "perch", "title": "Threshold Sensitivity Analysis for Linkage Score Cutoff Selection", "topics": [ "perch" ] }, { "page": "preflight", "title": "Pre-Linkage Data Quality Checks", "topics": [ "preflight" ] }, { "page": "vax_air", "title": "Synthetic Australian Immunisation Register Extract", "topics": [ "vax_air" ] } ], "_readme": "https://github.com/nrsmoll/starling/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "data.table", "dplyr", "farver", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "lpSolve", "lubridate", "magrittr", "pillar", "pkgconfig", "R6", "RColorBrewer", "Rcpp", "reclin2", "rlang", "S7", "scales", "stringdist", "stringi", "stringr", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "linked-cohort.Rmd", "filename": "linked-cohort.html", "title": "Linked Cohort Analysis: Linking Case Records to Vaccination History", "author": "Dr Nicolas Smoll, SCPHU, Sunshine Coast Hospital and Health Service", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Step 1: Pre-linkage audit with preflight()", "Step 2: Medicare checksum validation with check_medicare()", "Step 3: Blocking variable construction with flock()", "Step 4: Threshold sensitivity analysis with perch()", "Step 5: Probabilistic linkage with murmuration()", "Step 6: Visualise the score distribution with murmuration_plot()", "Step 7: Post-linkage validation", "Summary: the complete starling workflow", "Session information" ], "created": "2026-07-13 00:36:21", "modified": "2026-07-13 00:36:21", "commits": 1 }, { "source": "pre-linkage-quality.Rmd", "filename": "pre-linkage-quality.html", "title": "Pre-Linkage Data Quality: preflight(), check_medicare(), 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