R Observatory: Metrics for epiflows version 0.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

epiflows

0.2.2Package record

Predicting Disease Spread from Flow Data

0packages depend

3.3Kdownloads / year

95.9%test coverage

13/13flavors OK

Overview

About

Maintained by Pawel PiatkowskiCRAN page ↗GitHub ↗Website ↗Issues ↗

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. 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-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). 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: 3.4 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.2

README· In the repository, left out of the releaseVignettesYes · 2 · dynamicNEWSYes · 100% structured · does not mention 0.2.2Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 19includes a package overview page
Examples that run: 100%16 run in a plain check
Exported functions with examples: 86%
Documented parameters: 92%
Return-value docs: 79%
Help pages citing references: 11%

Also includes 1 demo script (run with demo())

Vignettes (2)

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #8,751 · ~9/day · ~276/mo

Releases R versions

Daily download trend is not available in this view yet.

35430 days

1.1K90 days

3.3K1 year

Compare downloads with other packages →

Also on114 r2u2 autocran96 c2d4u

How downloads are counted

Repository

reconhub/epiflows ↗Organization: reconhub

19Stars

13Forks

3Open issues

4Open PRs

4Releases

258Commits

10Commit identities

r-packageoutbreakr

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

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 26
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-14 · 192026-07-07 · 19

How these are measured

PracticesBeta

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

Checks run against github.com/reconhub/epiflows on 2026-10-22.

Continuous integration (2)

Travis CI (config file)AppVeyor

Governance and community (1)

Code of conduct

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-03-09

Reproducibility and dev environment (1)

Binder

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

lintr

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing epiflows adds 82 packages (49 with compiled code, 89 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (7)

Pawel Piatkowski

Author, Maintainer since 0.2.0 (2018)

Author

Author

Author

Author

Author

Contributor, Data contributor

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-02-20
0.2.2Latest
record
2026-02-20 · current release · diff ↗
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
unarchivedReturned to CRAN
2023-04-09
0.2.1
record
2023-04-09 · diff ↗
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
record
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

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' entry:

citation("epiflows")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.12688/f1000research.16032.1.

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 v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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