R Observatory: Metrics for WarnEpi version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

WarnEpi

1.0.1Package record

A Comprehensive Tool for Early Warning in Infectious Disease

0packages depend

1.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Mingyue PanCRAN page ↗GitHub ↗Issues ↗

Infectious disease surveillance requires early outbreak detection. This package provides statistical tools for analyzing time-series monitoring data through three core methods: a) EWMA (Exponentially Weighted Moving Average) b) Modified-CUSUM (Modified Cumulative Sum) c) Adjusted-Serfling models Methodologies are based on: - Wang et al. (2010) doi:10.1016/j.jbi.2009.08.003 - Wang et al. (2015) doi:10.1371/journal.pone.0119923 Designed for epidemiologists and public health researchers working with disease surveillance systems.

Install

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

install.packages("WarnEpi", 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("pan-mingyue/WarnEpi")

Development version from pan-mingyue/WarnEpi. 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-warnepi

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-WarnEpi

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-WarnEpi

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 43 s · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 65 wordsVignettesNoNEWSYes · 100% structured · mentions 1.0.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 5
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 80%

How these are measured

Downloads

1.8K

CRAN downloads in the past year

Rank #25,210 · ~5/day · ~151/mo

Releases R versions

Daily download trend is not available in this view yet.

15830 days

39490 days

1.8K1 year

Compare downloads with other packages →

Also on57 r2u2 autocran

How downloads are counted

Repository

pan-mingyue/warnepi ↗Account: pan-mingyue

0Stars

0Forks

2Open issues

0Open PRs

0Releases

License file reads as GPL-3.0 · Last activity 2025-08-21 · The default branch showed an older version (1.0.0) than CRAN on 2026-10-21

Responsiveness

not measured

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/pan-mingyue/warnepi on 2026-10-21.

Reproducibility and dev environment (2)

renvdata-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Installing WarnEpi adds no packages beyond those that come with R.

Depends (1)

R >= 3.5

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Mingyue Pan

Author, Maintainer since 1.0.1 (2025)

Xiaoli Wang

Author

Releases (1)

R
R 4.6.0 released · 2026-04-24
1.0.1Latest
record
2025-08-26 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-08-26
Total releases: 1 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5
Bundled data: 0.7 KB / 1 file
Download size: 8.5 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("WarnEpi")

Format

Pan, M., & Wang, X. (2025). WarnEpi: A Comprehensive Tool for Early Warning in Infectious Disease (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.WarnEpi

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for WarnEpi version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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