R Observatory: Metrics for aedseo version 1.1.0

Balamuta, James Joseph

aedseo

1.1.0

Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels

0packages depend

3.8Kdownloads / year

93.4%test coverage

13/13checks pass

Overview

About

Maintained by Lasse Engbo ChristiansenFirst published 2023-11-077 releasesCRAN page ↗GitHub ↗

A powerful tool for automating the early detection of seasonal epidemic onsets in time series data. It offers the ability to estimate growth rates across consecutive time intervals, calculate the sum of cases (SoC) within those intervals, and estimate seasonal onsets within user defined seasons. With use of a disease-specific threshold it also offers the possibility to estimate seasonal onset of epidemics. Additionally it offers the ability to estimate burden levels for seasons based on historical data. It is aimed towards epidemiologists, public health professionals, and researchers seeking to identify and respond to seasonal epidemics in a timely fashion.

Install

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

install.packages("aedseo", 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("ssi-dk/aedseo")

Development version from ssi-dk/aedseo. 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-aedseo

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-aedseo

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-aedseo

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

Health

CRAN checks

13OK

Slowest check: 10.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.67

93.4%

Coverage · measured lines

100%

Documentation · exports

15

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 250 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 86%
Return-value docs: 100%
References docs: 0%

Downloads

3.8K

CRAN downloads in the past year

Rank #12,509 · ~10/day · ~318/mo

Releases R versions

Daily download trend is not available in this view yet.

20530 days

79190 days

3.8K1 year

Compare downloads with other packages →

Also on169 r2u13 autocran

Repository

GitHub ↗ ssi-dk/aedseo

1Stars

1Forks

1Open issues

1Open PRs

7Releases

622Commits

8Contributors

burden-of-diseaseepidemic-modelepidemic-modellingonset-detectionsurveillance-systems

622 commits · Last activity 2026-07-29

Stars over time

2024-10-29 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/ssi-dk/aedseo on 2026-08-03.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (2)

lintrRStudio project

Show all practices

Coverage (1)

Codecov

Governance and community (2)

Issue templatesPR template

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (15)

base checkmate dplyr ggplot2 lifecycle lubridate plyr purrr pracma rlang scalesstatsstringr tibble tidyr

LinkingTo (0)

none

Suggests (8)

gridISOweek kableExtra knitr mem rmarkdown testthat withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Lasse Engbo Christiansen

Author, Maintainer · added in 0.1.1

Authors (3)

Lasse Engbo Christiansen

Author, Maintainer · added in 0.1.1

Sofia Myrup Otero

Author · added in 0.3.0

Kasper Schou Telkamp

Author

Copyright holders (1)

Statens Serum Institut, SSI

Copyright holder, Funder

Funders (1)

Statens Serum Institut, SSI

Copyright holder, Funder

Reviewers (1)

Rasmus Skytte Randløv

Reviewer

Listed in earlier versions (1)

Rasmus Skytte Randl\u00F8v

no longer listed · 0.3.0 to 1.1.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
2026-01-23 · current release · diff ↗
1.0.1
2025-11-20 · diff ↗
1.0.0
2025-11-17 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.3.0
2025-04-09 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.2
2023-11-27 · diff ↗
0.1.1
2023-11-16 · diff ↗
0.1.0
2023-11-07
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-11-07
Total releases: 7 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.2.0
Download size: 800 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

Cite

Cite this package

Start here. This is the citation for the package itself.

citation("aedseo")

CRAN DOI

https://doi.org/10.32614/CRAN.package.aedseo

BibTeX, derived from DESCRIPTION

@Manual{aedseo,
  title  = {aedseo: Automated and Early Detection of Seasonal Epidemic Onset and
Burden Levels},
  author = {Christiansen, Lasse Engbo and Statens Serum Institut, SSI and Myrup Otero, Sofia and Randløv, Rasmus Skytte and Schou Telkamp, Kasper},
  year   = {2026},
  note   = {R package version 1.1.0},
  doi    = {10.32614/CRAN.package.aedseo},
  url    = {https://CRAN.R-project.org/package=aedseo}
}

Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.

This is the citation for the package. It is not a citation for the R Observatory.

Cite this page

Use this when the claim is about a measurement on this page.

BibTeX

@misc{robservatoryaedseo,
  author    = {Balamuta, James Joseph},
  title     = {{R} {Observatory}: Metrics for {aedseo} version 1.1.0},
  year      = {2026},
  publisher = {HJJB, LLC},
  url       = {https://r-observatory.thecoatlessprofessor.com/packages/aedseo},
  note      = {Data set. Data release v2026-08-05}
}

APA

Balamuta, J. J. (2026). R Observatory: Metrics for aedseo version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/packages/aedseo

RIS

TY  - DATA
AU  - Balamuta, James Joseph
TI  - R Observatory: Metrics for aedseo version 1.1.0
PY  - 2026
PB  - HJJB, LLC
N1  - Data release v2026-08-05
UR  - https://r-observatory.thecoatlessprofessor.com/packages/aedseo
ER  -

In prose

These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/packages/aedseo.

Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.

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