mudnester: Surveillance Data Cleaning and Preparation for Public Health

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).

Version:	0.7.8
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
Published:	2026-10-02
DOI:	10.32614/CRAN.package.mudnester (may not be active yet)
Author:	Nicolas Smoll [aut, cre], Moderna [fnd] (Support for this package's development was provided via the Moderna Global Research Fellowship)
Maintainer:	Nicolas Smoll <nicolas.smoll at health.qld.gov.au>
BugReports:	https://github.com/nrsmoll/mudnester/issues
License:	MIT + file LICENSE
URL:	https://github.com/nrsmoll/mudnester
NeedsCompilation:	no
Language:	en-GB
Citation:	mudnester citation info
CRAN checks:	mudnester results

Documentation:

Reference manual:

mudnester.html , mudnester.pdf

Vignettes:

Age Scheme Catalogue (source, R code) brood(): Vaccine Coverage Data Structures (source, R code) clean_the_nest(): Standardising Surveillance Data (source, R code) corncrake(): Correcting Surveillance Counts for Under-Ascertainment (source, R code) flyway(): Aggregating Several Linked Event Dates in One Table (source, R code) homing(): Relinking De-identified Data (source, R code) molting(): Hash-Based De-identification (source, R code) Getting Started with mudnester (source, R code) plumage(): Comorbidity Detection from ICD-10-AM Coding (source, R code) preening(): Age Categorisation Against ~50 Named Schemes (source, R code) roost(): Time-Unit Aggregation for Surveillance Data (source, R code)

Downloads:

Package source:	mudnester_0.7.8.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: mudnester_0.7.8.zip
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): mudnester_0.7.8.tgz, r-oldrel (x86_64): mudnester_0.7.8.tgz

Reverse dependencies:

Reverse suggests:

starling

Linking:

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