vivaldi

1.0.1

Viral Variant Location and Diversity

0packages depend

2.4Kdownloads / year

62.6%test coverage

13/13checks pass

Overview

About

Maintained by David GreshamFirst published 2022-12-152 releasesCRAN page ↗GitHub ↗

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.

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

Slowest check: 2.7 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.18

62.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 120 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

2.4K

CRAN downloads in the past year

Rank #17,177 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

13030 days

62490 days

2.4K1 year

Compare downloads with other packages →

Also on110 r2u

Repository

GitHub ↗ greshamlab/vivaldi

3Stars

1Forks

0Open issues

0Open PRs

2Releases

378Commits

8Contributors

378 commits · Last activity 2026-06-16

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/greshamlab/vivaldi on 2026-08-02.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (7)

Maintainer (1)

David Gresham

Author, Maintainer, Copyright holder

Authors (7)

David Gresham

Author, Maintainer, Copyright holder

Author

Author

Author

Author

Author

Author

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
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
2023-03-21 · current release · diff ↗
1.0.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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