R Observatory: Metrics for agvgd version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

agvgd

0.1.2

An R Implementation of the 'Align-GVGD' Method

0packages depend

3.5Kdownloads / year

82.6%test coverage

13/13checks pass

Overview

About

Maintained by Ramiro MagnoFirst published 2022-01-173 releasesCRAN page ↗GitHub ↗

'Align-GVGD' ('A-GVGD') is a method to predict the impact of 'missense' substitutions based on the properties of amino acid side chains and protein multiple sequence alignments doi:10.1136/jmg.2005.033878. 'A-GVGD' is an extension of the original 'Grantham' distance to multiple sequence alignments. This package provides an alternative R implementation to the web version found on http://agvgd.hci.utah.edu/.

Install

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

install.packages("agvgd", 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("maialab/agvgd")

Development version from maialab/agvgd. 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-agvgd

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-agvgd

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-agvgd

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

Health

CRAN checks

13OK

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.71

82.6%

Coverage · measured lines

94%

Documentation · exports

12

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 534 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 94%
Return-value docs: 100%
References docs: 6%

Downloads

3.5K

CRAN downloads in the past year

Rank #10,527 · ~10/day · ~296/mo

Releases R versions

Daily download trend is not available in this view yet.

28430 days

91490 days

3.5K1 year

Compare downloads with other packages →

Also on143 r2u43 autocran15 c2d4u

Repository

GitHub ↗ maialab/agvgd

3Stars

1Forks

0Open issues

0Open PRs

0Releases

71Commits

2Contributors

71 commits · Last activity 2023-12-16 · 0% stars, 30d

Stars over time

2022-09-12 · 22026-07-07 · 3

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/maialab/agvgd on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (12)

crayon dplyr glue grantham magrittr purrr rlang seqinr stringr tibble tidyr vctrs

LinkingTo (0)

none

Suggests (3)

rmarkdown covr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Ramiro Magno

Author, Maintainer

Authors (3)

Ramiro Magno

Author, Maintainer

Isabel Duarte

Author

Ana-Teresa Maia

Author

Copyright holders (1)

CINTESIS

Copyright holder, Funder

Funders (1)

CINTESIS

Copyright holder, Funder

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
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.1.2Latest
2022-09-10 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
0.1.1
2022-02-03 · diff ↗
0.1.0
2022-01-17
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-17
Total releases: 3 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Download size: 1.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("agvgd")

Format

Magno, R., CINTESIS, Duarte, I., & Maia, A. (2022). agvgd: An R Implementation of the 'Align-GVGD' Method (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.agvgd

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 agvgd version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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