R Observatory: Metrics for ViroReportR version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ViroReportR

1.0.4

Respiratory Viral Infection Forecast Reporting

0packages depend

1.3Kdownloads / year

84.7%test coverage

13/13checks pass

Overview

About

Maintained by Mike IrvineFirst published 2026-02-122 releasesCRAN page ↗GitHub ↗

Tools for reporting and forecasting viral respiratory infections, using case surveillance data. Report generation tools for short-term forecasts, and validation metrics for an arbitrary number of customizable respiratory viruses. Estimation of the effective reproduction number is based on the 'EpiEstim' framework described in work by 'Cori' and colleagues. (2013) doi:10.1093/aje/kwt133.

Install

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

install.packages("ViroReportR", 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("BCCDC-PHSA/ViroReportR")

Development version from BCCDC-PHSA/ViroReportR. 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-viroreportr

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-ViroReportR

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-ViroReportR

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

Health

CRAN checks

13OK

Slowest check: 5.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.39

84.7%

Coverage · measured lines

100%

Documentation · exports

17

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 341 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 88%
Documented parameters: 96%
Return-value docs: 100%
References docs: 0%

Downloads

1.3K

CRAN downloads in the past year

Rank #22,715 · ~4/day · ~109/mo

Releases R versions

Daily download trend is not available in this view yet.

11230 days

46490 days

1.3K1 year

Compare downloads with other packages →

Also on46 r2u

Repository

GitHub ↗ bccdc-phsa/viroreportr

1Stars

1Forks

0Open issues

0Open PRs

1Releases

334Commits

26Contributors

License GPL-3.0 · 334 commits · Last activity 2026-06-03 · 0% stars, 30d

Stars over time

2026-01-28 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/bccdc-phsa/viroreportr on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Research and citation (1)

JOSS paper

Show all practices

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (17)

data.table dplyr EpiEstim ggplot2 incidence lubridate projections purrr rlang tibblestatsutilstidyr gluemgcvkableExtra cowplot

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Mike Irvine

Author, Maintainer, Copyright holder

Authors (5)

Mike Irvine

Author, Maintainer, Copyright holder

Author

Author

Author

Author

Copyright holders (1)

Mike Irvine

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.4Latest
2026-02-18 · current release · diff ↗
1.0.3
2026-02-12
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-12
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Download size: 110 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ViroReportR")

The authors publish a JOSS paper, so they have said how they want this cited. Run citation() and use what it gives you.

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 ViroReportR version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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