R Observatory: Metrics for ViroReportR version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ViroReportR

1.0.4Package record

Respiratory Viral Infection Forecast Reporting

0packages depend

1.9Kdownloads / year

84.7%test coverage

13/13flavors OK

Overview

About

Maintained by Mike IrvineCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 1.0.4

Fixed CRAN Debian write-permission issue in report rendering.
Replaced T/F with TRUE/FALSE throughout package.
Improved report rendering environment isolation.

From NEWS.md in the release

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

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
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 1.0.4

READMEYes · 341 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.4Citation fileNo

Help pages: 18 (4 internal)includes a package overview page
Examples that run: 88%7 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Model fitting and producing short-term forecasts using daily data with EpiEstim HTML

How these are measured

Downloads

1.9K

CRAN downloads in the past year

Rank #19,901 · ~5/day · ~157/mo

Releases R versions

Daily download trend is not available in this view yet.

24130 days

66090 days

1.9K1 year

Compare downloads with other packages →

Also on51 r2u5 autocran

How downloads are counted

Repository

bccdc-phsa/viroreportr ↗Organization: BCCDC-PHSA

2Stars

1Forks

0Open issues

0Open PRs

1Releases

338Commits

26Commit identities

License file reads as GPL-3.0 · 338 commits · Last activity 2026-10-06 · 0% stars, 30d · Default branch at 1.0.5, ahead of CRAN 1.0.4 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 93%
Median days to close, 50 most recently updated closed issues: 52
Median days to close, 50 most recently updated closed PRs: 4

Stars over time

2026-01-28 · 12026-08-20 · 2

How these are measured

PracticesBeta

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

Checks run against github.com/bccdc-phsa/viroreportr on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-06 · The repository has a site deploy workflow

CRAN release process (1)

cran-comments.md

Research and citation (1)

JOSS paper

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing ViroReportR adds 76 packages (41 with compiled code, 67 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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.

How these are counted

Code & Tests

People & History

People (5)

Author

Author

Author

Author

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.4Latest
record
2026-02-18 · current release · diff ↗
1.0.3
record
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

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ViroReportR")

Format

Irvine, M., Falcao, R., Tamvada, N., Tang, N., & Wong, C. (2026). ViroReportR: Respiratory Viral Infection Forecast Reporting (Version 1.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.ViroReportR

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 ViroReportR version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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