Package: mudnester
Title: Surveillance Data Cleaning and Preparation for Public Health
Version: 0.7.2
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 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. 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 its reference rate's own bounds.
        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
LazyData: true
Roxygen: list(markdown = 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>
Config/pak/sysreqs: libicu-dev
Repository: https://nrsmoll.r-universe.dev
Date/Publication: 2026-07-14 05:43:38 UTC
RemoteUrl: https://github.com/nrsmoll/mudnester
RemoteRef: HEAD
RemoteSha: e12e64a456bf7cb071a947fa8e04878ccd249e07
Packaged: 2026-10-03 14:12:16 UTC; root