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baselinenowcast: Baseline Nowcasting for Right-Truncated Epidemiological Data

Nowcasting right-truncated epidemiological data is critical for timely public health decision-making, as reporting delays can create misleading impressions of declining trends in recent data. This package provides nowcasting methods based on using empirical delay distributions and uncertainty from past performance. It is also designed to be used as a baseline method for developers of new nowcasting methods. For more details on the performance of the method(s) in this package applied to case studies of COVID-19 and norovirus, see our recent paper at <https://wellcomeopenresearch.org/articles/10-614>. The package supports standard data frame inputs with reference date, report date, and count columns, as well as the direct use of reporting triangles, and is compatible with 'epinowcast' objects. Alongside an opinionated default workflow, it has a low-level pipe-friendly modular interface, allowing context-specific workflows. It can accommodate a wide spectrum of reporting schedules, including mixed patterns of reference and reporting (daily-weekly, weekly-daily). It also supports sharing delay distributions and uncertainty estimates between strata, as well as custom uncertainty models and delay estimation methods.

Version: 0.2.0
Depends: R (≥ 4.1.0)
Imports: cli, checkmate, stats, utils, rlang, purrr
Suggests: bookdown, ChainLadder, dplyr, tidyr, stringr, lubridate, readr, ggplot2, spelling, rmarkdown, testthat (≥ 3.1.9), usethis, withr, knitr, zoo, glue
Published: 2026-02-03
DOI: 10.32614/CRAN.package.baselinenowcast (may not be active yet)
Author: Kaitlyn Johnson ORCID iD [aut, cre, cph], Emily Tyszka ORCID iD [aut], Johannes Bracher ORCID iD [aut], Sebastian Funk ORCID iD [aut], Sam Abbott ORCID iD [aut], Tim Taylor ORCID iD [ctb]
Maintainer: Kaitlyn Johnson <kaitlyn.johnson at lshtm.ac.uk>
BugReports: https://github.com/epinowcast/baselinenowcast/issues
License: MIT + file LICENSE
URL: https://github.com/epinowcast/baselinenowcast, https://baselinenowcast.epinowcast.org
NeedsCompilation: no
Language: en-GB
Citation: baselinenowcast citation info
Materials: README, NEWS
CRAN checks: baselinenowcast results

Documentation:

Reference manual: baselinenowcast.html , baselinenowcast.pdf
Vignettes: Getting Started with baselinenowcast (source, R code)
Mathematical methods for baselinenowcast (source, R code)
Modular workflow for flexible model development (source, R code)
Nowcasting nomenclature (source)
Nowcasting syndromic surveillance system data: a case study applied to the U.S. National Syndromic Surveillance Program (NSSP) data (source, R code)

Downloads:

Package source: baselinenowcast_0.2.0.tar.gz
Windows binaries: r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

Please use the canonical form https://CRAN.R-project.org/package=baselinenowcast to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.