R Observatory: Metrics for ATQ version 0.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ATQ

0.2.3

Alert Time Quality - Evaluating Timely Epidemic Metrics

0packages depend

3Kdownloads / year

44.4%test coverage

0/13checks pass

Overview

About

Maintained by Vinay JoshyFirst published 2024-07-273 releasesCRAN page ↗GitHub ↗

Provides tools for evaluating timely epidemic detection models within school absenteeism-based surveillance systems. Introduces the concept of alert time quality as an evaluation metric. Includes functions to simulate populations, epidemics, and alert metrics associated with epidemic spread using population census data. The methods are based on research published in Vanderkruk et al. (2023) doi:10.1186/s12889-023-15747-z and Ward et al. (2019) doi:10.1186/s12889-019-7521-7.

Install

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

install.packages("ATQ", 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("vjoshy/ATQ_Surveillance_Package")

Development version from vjoshy/ATQ_Surveillance_Package. 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-atq

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-ATQ

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-ATQ

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 6.9 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.14

44.4%

Coverage · measured lines

100%

Documentation · exports

7

Dependencies · direct

Check history

NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
3 OK · 11 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 466 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

3K

CRAN downloads in the past year

Rank #13,905 · ~8/day · ~247/mo

Releases R versions

Daily download trend is not available in this view yet.

19930 days

73490 days

3K1 year

Compare downloads with other packages →

Also on125 r2u49 autocran

Repository

GitHub ↗ vjoshy/atq_surveillance_package

2Stars

0Forks

1Open issues

0Open PRs

2Releases

129Commits

1Contributors

License GPL-3.0 · 129 commits · Last activity 2025-12-18 · 0% stars, 30d

Stars over time

2024-07-27 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/vjoshy/atq_surveillance_package on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (7)

dplyr purrr zoo ggplot2 gridExtra rlang scales

LinkingTo (0)

none

Suggests (8)

knitr rmarkdown cli fansi farver utf8 devtools testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Vinay Joshy

Author, Maintainer, Copyright holder

Authors (5)

Vinay Joshy

Author, Maintainer, Copyright holder

Lorna Deeth

Author, Copyright holder, Thesis advisor

Zeny Feng

Author, Copyright holder, Thesis advisor

Justin Slater

Author, Copyright holder, Thesis advisor

Kayla Vanderkruk

Author, Compiler, Contributor

Contributors (1)

Kayla Vanderkruk

Author, Compiler, Contributor

Copyright holders (4)

Vinay Joshy

Author, Maintainer, Copyright holder

Lorna Deeth

Author, Copyright holder, Thesis advisor

Zeny Feng

Author, Copyright holder, Thesis advisor

Justin Slater

Author, Copyright holder, Thesis advisor

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.2.3Latest
2024-08-18 · current release · diff ↗
0.2.2
2024-07-29 · diff ↗
0.2.0
2024-07-27
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-07-27
Total releases: 3 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Download size: 376 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ATQ")

Format

Joshy, V., Deeth, L., Feng, Z., Slater, J., & Vanderkruk, K. (2024). ATQ: Alert Time Quality - Evaluating Timely Epidemic Metrics (Version 0.2.3) [Computer software]. https://doi.org/10.32614/CRAN.package.ATQ

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 ATQ version 0.2.3 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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