R Observatory: Metrics for VLF version 1.1-3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

VLF

1.1-3

Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records

1packages depend

3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Taryn B. T. AtheyFirst published 2013-11-193 releasesCRAN page ↗

Using frequency matrices, very low frequency variants (VLFs) are assessed for amino acid and nucleotide sequences. The VLFs are then compared to see if they occur in only one member of a species, singleton VLFs, or if they occur in multiple members of a species, shared VLFs. The amino acid and nucleotide VLFs are then compared to see if they are concordant with one another. Amino acid VLFs are also assessed to determine if they lead to a change in amino acid residue type, and potential changes to protein structures. Based on Stoeckle and Kerr (2012) doi:10.1371/journal.pone.0043992 and Phillips et al. (2023) doi:10.3897/BDJ.11.e96480.

Install

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

install.packages("VLF", 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-vlf

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-VLF

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-VLF

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

Health

CRAN checks

13OK

Slowest check: 1.9 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

0

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 · 30 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 0%

Downloads

3K

CRAN downloads in the past year

Rank #18,088 · ~8/day · ~252/mo

Releases R versions

Daily download trend is not available in this view yet.

11030 days

59990 days

3K1 year

Compare downloads with other packages →

Also on96 r2u16 autocran

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

ClusTCR2

Code & Tests

People & History

People (3)

Maintainer (1)

Taryn B. T. Athey

Maintainer

Authors (1)

Paul D. McNicholas

Author

Contributors (1)

Jarrett D. Phillips

Contributor · added in 1.1

Listed in earlier versions (3)

Athey

no longer listed · 1.1-3

McNicholas

no longer listed · 1.1-3

Phillips

no longer listed · 1.1-3

Package Timeline

3 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
1.1-3Latest
2025-04-10 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.1
2022-08-18 · diff ↗
unarchivedReturned to CRAN
2022-08-18
archivedRemoved from CRAN
2022-06-20
check problems were not corrected despite reminders
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16

Show 3 earlier events

R
R 3.1.0 released · 2014-04-10
1.0
2013-11-19
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-11-19
Total releases: 3 / 13 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 477 KB / 2 files
Download size: 485 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("VLF")

Format

Athey, T. B. T., McNicholas, P. D., & Phillips, J. D. (2025). VLF: Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records (Version 1.1-3) [Computer software]. https://doi.org/10.32614/CRAN.package.VLF

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 VLF version 1.1-3 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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