R Observatory: Metrics for EpiSignalDetection version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

EpiSignalDetection

0.1.3Package record

Signal Detection Analysis

0packages depend

3.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Lore MerdrignacCRAN page ↗GitHub ↗Declared funders: Margot Einoder-Moreno, Joana Gomes Dias and 1 more

Exploring time series for signal detection. It is specifically designed to detect possible outbreaks using infectious disease surveillance data at the European Union / European Economic Area or country level. Automatic detection tools used are presented in the paper "Monitoring count time series in R: aberration detection in public health surveillance", by Salmon (2016) doi:10.18637/jss.v070.i10. The package includes: - Signal Detection tool, an interactive 'shiny' application in which the user can import external data and perform basic signal detection analyses; - An automated report in HTML format, presenting the results of the time series analysis in tables and graphs. This report can also be stratified by population characteristics (see 'Population' variable). This project was funded by the European Centre for Disease Prevention and Control.

Changes in 0.1.3

CRAN fixes

Removing underscored 'dplyr' function names, (e.g., group_by_())

From NEWS.md in the release

Install

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

install.packages("EpiSignalDetection", 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("EU-ECDC/EpiSignalDetection")

Development version from EU-ECDC/EpiSignalDetection. 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-episignaldetection

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-EpiSignalDetection

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-EpiSignalDetection

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: 1.3 min · r-oldrel-windows-x86_64

Status changes

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 0.1.3

READMEYes · 144 wordsVignettesYes · 1 · dynamicNEWSYes · 33% structured · mentions 0.1.3Citation fileNoWebsitenot declared in DESCRIPTION

Description cites a JSS article

Help pages: 12
Examples that run: 60%6 run in a plain check · 4 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 90%
Help pages citing references: 0%

Vignettes (1)

The 'Epidemiological Signal Detection' Package

How these are measured

Downloads

3.8K

CRAN downloads in the past year

Rank #10,237 · ~10/day · ~314/mo

Releases R versions

Daily download trend is not available in this view yet.

39530 days

99690 days

3.8K1 year

Compare downloads with other packages →

Also on102 r2u4 autocran

How downloads are counted

Repository

eu-ecdc/episignaldetection ↗Organization: EU-ECDC

20Stars

6Forks

1Open issues

1Open PRs

0Releases

80Commits

6Commit identities

License file reads as EUPL-1.2 · 80 commits · Last activity 2025-07-18 · 0% stars, 30d · The default branch showed an older version (0.1.1) than CRAN on 2026-10-18

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-03-14 · 172026-08-20 · 20

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/eu-ecdc/episignaldetection on 2026-10-18.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing EpiSignalDetection adds 57 packages (35 with compiled code, 55 MB of source tarballs). Heaviest: stringi 11 MB, bslib 5.6 MB, sp 4.3 MB.

Depends (1)

R >= 3.4.0

Imports (7)

dplyrgraphicsISOweek rmarkdown shiny surveillanceutils

LinkingTo (0)

none

Suggests (4)

DT ggplot2 knitr pander

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 (5)

Lore Merdrignac

Author, Contractor, Maintainer since 0.1.2 (2021)

Author of the package and original code

Joana Gomes Dias

Author, Funder

Project manager

Tommi Karki

Author, Funder

Esther Kissling

Author, Contractor

Margot Einoder-Moreno

Contributor, Funder

Previously maintained by Joana Gomes Dias (0.1.0 to 0.1.1).

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.3Latest
record
2026-03-03 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-11-30
0.1.2
record
2021-11-30 · diff ↗
archivedRemoved from CRAN
2021-10-05
check problems were not corrected in time
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.1.1
record
2018-11-15 · diff ↗
0.1.0
record
2018-11-14
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-11-14
Total releases: 4 / 8 yrs
License: EUPL
Minimum R: ≥ 3.4.0
Bundled data: 58 KB / 2 files
Download size: 840 KB

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("EpiSignalDetection")

Format

Merdrignac, L., Einoder-Moreno, M., Gomes Dias, J., Karki, T., & Kissling, E. (2026). EpiSignalDetection: Signal Detection Analysis (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.EpiSignalDetection

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 EpiSignalDetection version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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