R Observatory: Metrics for vivaldi version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

vivaldi

1.0.1Package record

Viral Variant Location and Diversity

0packages depend

2.5Kdownloads / year

62.6%test coverage

13/13flavors OK

Overview

About

Maintained by David GreshamCRAN page ↗GitHub ↗Issues ↗

Analysis of minor alleles in Illumina sequencing data of viral genomes. Functions in 'vivaldi' primarily operate on vcf files.

Install

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

install.packages("vivaldi", 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("GreshamLab/vivaldi")

Development version from GreshamLab/vivaldi. 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-vivaldi

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-vivaldi

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 120 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 21
Examples that run: 100%18 run in a plain check
Exported functions with examples: 90%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

vignette

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #19,827 · ~7/day · ~206/mo

Releases R versions

Daily download trend is not available in this view yet.

26930 days

67190 days

2.5K1 year

Compare downloads with other packages →

Also on74 r2u

How downloads are counted

Repository

greshamlab/vivaldi ↗Organization: GreshamLab

3Stars

1Forks

0Open issues

0Open PRs

2Releases

378Commits

8Commit identities

378 commits · Last activity 2026-06-16

Responsiveness

How these are sampled

PRs merged (all time): 79%
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/greshamlab/vivaldi on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2026-06-16
Pull request: opened by its own account
Commits: 2 by its own account

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing vivaldi adds 76 packages (43 with compiled code, 83 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 2.10

Imports (9)

dplyr ggplot2 glue magrittr plotly seqinr tidyr tidyselect vcfR

LinkingTo (0)

none

Suggests (4)

kableExtra knitr rmarkdown testthat

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)

Author

Author

Author

Author

Author

Author

Releases (2)

Pick two releases to compare their code metrics.

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
1.0.1Latest
record
2023-03-21 · current release · diff ↗
1.0.0
record
2022-12-15
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-12-15
Total releases: 2 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 76 KB / 1 file
Download size: 2.0 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("vivaldi")

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

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 vivaldi version 1.0.1 [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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