R Observatory: Metrics for epiflows version 0.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

epiflows

0.2.2

Predicting Disease Spread from Flow Data

0packages depend

3.1Kdownloads / year

95.9%test coverage

13/13checks pass

Overview

About

Maintained by Pawel PiatkowskiFirst published 2018-08-143 releasesCRAN page ↗GitHub ↗

Provides functions and classes designed to handle and visualise epidemiological flows between locations. Also contains a statistical method for predicting disease spread from flow data initially described in Dorigatti et al. (2017) doi:10.2807/1560-7917.ES.2017.22.28.30572. This package is part of the RECON (https://www.repidemicsconsortium.org/) toolkit for outbreak analysis.

Install

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

install.packages("epiflows", 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("reconhub/epiflows")

Development version from reconhub/epiflows. 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-epiflows

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-epiflows

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-epiflows

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

Health

CRAN checks

13OK

Slowest check: 3.4 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.62

95.9%

Coverage · measured lines

100%

Documentation · exports

10

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

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 92%
Return-value docs: 79%
References docs: 11%

Downloads

3.1K

CRAN downloads in the past year

Rank #12,049 · ~8/day · ~254/mo

Releases R versions

Daily download trend is not available in this view yet.

24930 days

84090 days

3.1K1 year

Compare downloads with other packages →

Also on157 r2u23 autocran48 c2d4u

Repository

GitHub ↗ reconhub/epiflows

19Stars

13Forks

3Open issues

4Open PRs

4Releases

258Commits

10Contributors

r-packageoutbreakr

258 commits · Last activity 2026-03-09 · 0% stars, 30d

Stars over time

2024-04-01 · 182026-07-07 · 19

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/reconhub/epiflows on 2026-08-23.

Continuous integration (2)

Travis CIAppVeyor

Reproducibility and dev environment (1)

Binder

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

lintr

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (10)

epicontacts leaflet ggmap geosphere ggplot2 tibble spstatshtmltools visNetwork

LinkingTo (0)

none

Suggests (7)

testthat roxygen2 knitr outbreaks vdiffr curl rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (7)

Maintainer (1)

Pawel Piatkowski

Author, Maintainer

Authors (6)

Author, Maintainer

Author

Author

Author

Author

Author

Contributors (1)

Isobel Blake

Contributor, Data contributor

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
0.2.2Latest
2026-02-20 · current release · diff ↗
unarchivedReturned to CRAN
2026-02-20
archivedRemoved from CRAN
2025-11-28
issues were not corrected despite reminders
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
0.2.1
2023-04-09 · diff ↗
unarchivedReturned to CRAN
2023-04-09
archivedRemoved from CRAN
2023-04-07
policy violation On Internet access
R
R 4.2.0 released · 2022-04-22
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
0.2.0
2018-08-14
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-08-14
Total releases: 3 / 8 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Bundled data: 6.4 KB / 5 files
Download size: 1.5 MB
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("epiflows")

Format

Piatkowski, P., Blake, I., Jombart, T., Kamvar, Z. N., Moraga, P., Nagraj, V., & Toikkanen, S. E. (2026). epiflows: Predicting Disease Spread from Flow Data (Version 0.2.2) [Computer software]. https://doi.org/10.32614/CRAN.package.epiflows

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 epiflows version 0.2.2 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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