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# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "mudnester" in publications use:'
type: software
license: MIT
title: 'mudnester: Surveillance Data Cleaning and Preparation for Public Health'
version: 0.7.2
identifiers:
- type: doi
  value: 10.32614/CRAN.package.mudnester
abstract: '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:
- family-names: Smoll
  given-names: Nicolas
  email: nicolas.smoll@health.qld.gov.au
  orcid: https://orcid.org/0000-0002-6923-9701
preferred-citation:
  type: manual
  title: 'mudnester: Surveillance Data Cleaning and Preparation for Public Health'
  authors:
  - family-names: Smoll
    given-names: Nicolas
    email: nicolas.smoll@health.qld.gov.au
    orcid: https://orcid.org/0000-0002-6923-9701
  year: '2026'
  notes: R package version 0.7.2
  url: https://github.com/nrsmoll/mudnester
repository: https://nrsmoll.r-universe.dev
repository-code: https://github.com/nrsmoll/mudnester
commit: e12e64a456bf7cb071a947fa8e04878ccd249e07
url: https://github.com/nrsmoll/mudnester
date-released: '2026-07-14'
contact:
- family-names: Smoll
  given-names: Nicolas
  email: nicolas.smoll@health.qld.gov.au
  orcid: https://orcid.org/0000-0002-6923-9701