Package: mudnester
Title: Surveillance Data Cleaning and Preparation for Public Health
Version: 0.7.8
Description: Clean, prepare, and aggregate surveillance data for public
        health analysis. Provides structural data cleaning and
        standardisation (clean_the_nest()), age categorisation against
        ~50 published schemes with publication-ready labelling
        (preening()), time-unit aggregation with zero-filling and
        seasonal awareness (roost()), joint aggregation of several
        linked event dates (e.g. onset, admission, ICU, complication,
        fatality) into one table of comparable rate columns (flyway()),
        under-ascertainment correction via a stratified, time-varying
        multiplier factor supplied directly, derived by the ratio
        (multiplier) method, or derived by inverting an externally
        sourced severity rate (e.g. an infection-fatality-rate anchor)
        against an observed severity ratio (corncrake()), comorbidity
        detection from ICD-10-AM clinical coding (plumage()), vaccine
        coverage data construction (brood()), hash-based
        de-identification (molting()), and relinking of previously
        de-identified data (homing()). brood() produces a brood_df
        object supporting two population models: pre-aggregated
        denominators (population_model = "pre_aggregated") and
        record-level cohort designs (population_model = "cohort"). The
        cohort model handles single time-point coverage snapshots,
        interrupted time series analysis via a built-in sweep returning
        monthly coverage rates (time_series = TRUE), and birth cohort
        designs with person-time computation. This cohort/time-series
        coverage model was applied in Roughan et al. (2026)
        <doi:10.33321/cdi.2026.50.031> to estimate infant immunisation
        coverage against respiratory syncytial virus over an 18-month
        period. Both wide format (one row per person with dose columns,
        from 'starling'::murmuration()) and long format (one row per
        dose) are accepted. corncrake() returns both a point-corrected
        count and uncertainty bounds wherever they can be derived,
        including the inverse relationship between a severity-anchored
        factor and the bounds of its own reference rate. Built for
        Australian public health surveillance practice but not specific
        to it -- see individual function documentation for notes on
        non-Australian use (e.g. Northern Hemisphere season
        boundaries).
Authors@R: c(
    person("Nicolas", "Smoll", email = "nicolas.smoll@health.qld.gov.au",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-6923-9701")),
    person("Moderna", role = "fnd",
        comment = "Support for this package's development was provided via the Moderna Global Research Fellowship")
    )
License: MIT + file LICENSE
Depends: R (>= 4.1)
Imports: dplyr (>= 1.1.0), tidyr (>= 1.3.0), lubridate (>= 1.9.0),
        stringr (>= 1.5.0), rlang (>= 1.1.0), tibble (>= 3.2.0), digest
        (>= 0.6.30), janitor (>= 2.2.0), utils, stats
Suggests: testthat (>= 3.0.0), knitr (>= 1.42), rmarkdown (>= 2.20),
        usethis (>= 2.1.0), gtsummary, ggplot2
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:
        <https://orcid.org/0000-0002-6923-9701>), Moderna [fnd]
        (Support for this package's development was provided via the
        Moderna Global Research Fellowship)
Maintainer: Nicolas Smoll <nicolas.smoll@health.qld.gov.au>
Packaged: 2026-10-02 13:10:15 UTC; 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
