R Observatory: Metrics for agvgd version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

agvgd

0.1.2Package record

An R Implementation of the 'Align-GVGD' Method

0packages depend

3.8Kdownloads / year

82.6%test coverage

13/13flavors OK

Overview

About

Maintained by Ramiro MagnoCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: CINTESIS

'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/.

Changes in 0.1.2

Fixed a bug with read_substitutions() that would not parse positions correctly.
Added a new substitutions example file lee2010_sub.txt.
Added a new function read_agvgdweb_results() aimed at developers.

From NEWS.md in the release

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. 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-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). 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

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.2

READMEYes · 534 wordsVignettes· In the repository, left out of the releaseNEWSYes · 100% structured · mentions 0.1.2Citation fileNoWebsiteYes · pkgdown

Help pages: 18 (4 internal)includes a package overview page
Examples that run: 100%13 run in a plain check
Exported functions with examples: 81%
Documented parameters: 94%
Return-value docs: 100%
Help pages citing references: 6%

How these are measured

Downloads

3.8K

CRAN downloads in the past year

Rank #7,985 · ~10/day · ~317/mo

Releases R versions

Daily download trend is not available in this view yet.

39030 days

1.2K90 days

3.8K1 year

Compare downloads with other packages →

Also on108 r2u23 autocran72 c2d4u

How downloads are counted

Repository

maialab/agvgd ↗Organization: maialab

3Stars

1Forks

0Open issues

0Open PRs

0Releases

71Commits

2Commit identities

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

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2022-09-12 · 22026-07-07 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/maialab/agvgd on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2023-12-16 · The repository has a site deploy workflow

pkgdown site last built 2023-12-16

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing agvgd adds 29 packages (17 with compiled code, 32 MB of source tarballs). Heaviest: stringi 11 MB, sp 4.3 MB, seqinr 3.4 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Ramiro Magno

Author, Maintainer since 0.1.0 (2022)

Isabel Duarte

Author

Ana-Teresa Maia

Author

CINTESIS

Copyright holder, Funder

Releases (3)

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
0.1.2Latest
record
2022-09-10 · current release · diff ↗ ·
added 4 exports
profile_to_alignment, read_agvgdweb_results, write_alignment, write_substitutions
R
R 4.2.0 released · 2022-04-22
0.1.1
record
2022-02-03 · diff ↗ ·
removed 3 exports
align_gvgd, alignment_pos_to_residue_pos, residue_pos_to_alignment_pos

added 6 exports
cpv_ranges, dev, gd, gv, poi_to_res, res_to_poi
0.1.0
record
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

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 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 agvgd version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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