baselinenowcast

0.2.0

Baseline Nowcasting for Right-Truncated Epidemiological Data

0packages depend

1.6Kdownloads / year

90.7%test coverage

12/13checks pass

Overview

About

Maintained by Kaitlyn JohnsonFirst published 2026-02-031 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("baselinenowcast", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("epinowcast/baselinenowcast")

Development version from epinowcast/baselinenowcast. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-baselinenowcast

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-baselinenowcast

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-baselinenowcast

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 9.7 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 1.61

90.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 728 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 96%
Return-value docs: 100%
References docs: 0%

Downloads

1.6K

CRAN downloads in the past year

Rank #16,278 · ~4/day · ~134/mo

Releases R versions

Daily download trend is not available in this view yet.

21930 days

65790 days

1.6K1 year

Compare downloads with other packages →

Also on76 r2u4 autocran

Repository

GitHub ↗ epinowcast/baselinenowcast

10Stars

2Forks

59Open issues

2Open PRs

4Releases

1,639Commits

9Contributors

1,639 commits · Last activity 2026-07-22 · 0% stars, 30d

Stars over time

2025-02-04 · 62026-07-07 · 10

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/epinowcast/baselinenowcast on 2026-07-31.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Research and citation (2)

CITATION.cffcodemeta.json

Automation and maintenance (1)

pre-commit

Lint, format, editor (1)

lintr

How this is detected·Detection ruleset v1 (2026-07-18)

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2025-05-19

claude

Most recent: claude on 2025-05-19

Evidence

claude: on 2025-05-19 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (6)

cli checkmatestatsutilsrlang purrr

LinkingTo (0)

none

Suggests (16)

bookdown ChainLadder dplyr tidyr stringr lubridate readr ggplot2 spelling rmarkdown testthat usethis withr knitr zoo glue

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Kaitlyn Johnson

Author, Maintainer, Copyright holder

Authors (5)

Kaitlyn Johnson

Author, Maintainer, Copyright holder

Author

Author

Author

Author

Contributors (1)

Tim Taylor

Contributor

Kaitlyn Johnson

Author, Maintainer, Copyright holder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.2.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-03
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 34 KB / 5 files
Download size: 2.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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