R Observatory: Metrics for anovir version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

anovir

0.1.0Package record

Analysis of Virulence

0packages depend

3.1Kdownloads / year

9.0%test coverage

11/13flavors OK

Overview

About

Maintained by Philip AgnewCRAN page ↗

Epidemiological population dynamics models traditionally define a pathogen's virulence as the increase in the per capita rate of mortality of infected hosts due to infection. This package provides functions allowing virulence to be estimated by maximum likelihood techniques. The approach is based on the analysis of relative survival comparing survival in matching cohorts of infected vs. uninfected hosts (Agnew 2019) doi:10.1101/530709.

Install

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

install.packages("anovir", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-anovir

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-anovir

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-anovir

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Philip Agnew <philip.agnew@ird.fr>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘anovir-package.Rd’:
    https://doi.org/10.1101/530709
  File ‘data_blanford.Rd’:
    https://doi.org/10.1186/1475-2875-11-365
  File ‘data_lorenz.Rd’:
    https://doi.org/10.1101/530709
    https://doi.org/10.1111/j.1752-4571.2011.00199.x
    https://doi.org/10.5061/dryad.2s231
  File ‘data_parker.Rd’:
    https://doi.org/10.1111/evo.12418
    https://doi.org/10.5061/dryad.24gq7

Additional issues

donttest

CRAN check page ↗

Slowest check: 5.1 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-08
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-07
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMENoVignettesYes · 11 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 26includes a package overview page
Examples that run: 88%22 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 4%

Vignettes (11)

Show 1 moreHide 1 vignette

Worked examples II HTML

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #12,346 · ~8/day · ~257/mo

Releases R versions

Daily download trend is not available in this view yet.

29030 days

90690 days

3.1K1 year

Compare downloads with other packages →

Also on82 r2u22 autocran

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing anovir adds 4 packages (2 with compiled code, 1.6 MB of source tarballs). Heaviest: mvtnorm 1.0 MB, bbmle 529 KB, numDeriv 74 KB.

Depends (3)

R >= 2.10bbmlestats4

Imports (0)

none

LinkingTo (0)

none

Suggests (4)

knitr rmarkdownstatstestthat

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 (2)

Philip Agnew

Author, Maintainer since 0.1.0 (2020)

Jimmy Lopez

Author

Releases (1)

R
R 4.6.0 released · 2026-04-24
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
R
R 4.1.0 released · 2021-05-18
0.1.0Latest
record
2020-10-24 · current release
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-10-24
Total releases: 1 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 7.1 KB / 5 files
Download size: 390 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("anovir")

Format

Agnew, P., & Lopez, J. (2020). anovir: Analysis of Virulence (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.anovir

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 anovir version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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