R Observatory: Metrics for grantham version 0.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

grantham

0.1.4

Calculate the Grantham Distance

1packages depend

7.2Kdownloads / year

32.0%test coverage

13/13checks pass

Overview

About

Maintained by Ramiro MagnoFirst published 2021-12-205 releasesCRAN page ↗GitHub ↗

A minimal set of routines to calculate the Grantham distance doi:10.1126/science.185.4154.862. The Grantham distance attempts to provide a proxy for the evolutionary distance between two amino acids based on three key chemical properties: composition, polarity and molecular volume. In turn, evolutionary distance is used as a proxy for the impact of missense mutations. The higher the distance, the more deleterious the substitution is expected to be.

Install

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

install.packages("grantham", 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("patterninstitute/grantham")

Development version from patterninstitute/grantham. 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-grantham

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-grantham

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-grantham

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

Health

CRAN checks

13OK

Slowest check: 1.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.91

32.0%

Coverage · measured lines

100%

Documentation · exports

2

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 · 428 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

7.2K

CRAN downloads in the past year

Rank #6,157 · ~20/day · ~598/mo

Releases R versions

Daily download trend is not available in this view yet.

27530 days

1.3K90 days

7.2K1 year

Compare downloads with other packages →

Also on118 r2u26 autocran18 c2d4u

Repository

GitHub ↗ patterninstitute/grantham

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2025-06-01

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/patterninstitute/grantham on 2026-08-23.

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

Governance and community (1)

Support guide

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

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (2)

tibble dplyr

LinkingTo (0)

none

Suggests (2)

spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

agvgd

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Ramiro Magno

Author, Maintainer

Authors (3)

Ramiro Magno

Author, Maintainer

Isabel Duarte

Author

Ana-Teresa Maia

Author

Copyright holders (1)

Pattern Institute

Copyright holder, Funder · added in 0.1.2

Funders (3)

Pattern Institute

Copyright holder, Funder · added in 0.1.2

CINTESIS

Funder

University of Algarve

Funder · added in 0.1.2

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.4Latest
2025-06-01 · current release · diff ↗
0.1.3
2025-06-01 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.2
2024-07-30 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.1
2022-01-07 · diff ↗
0.1.0
2021-12-20
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-20
Total releases: 5 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.3 KB / 2 files
Download size: 195 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("grantham")

Format

Magno, R., CINTESIS, Pattern Institute, University of Algarve, Duarte, I., & Maia, A. (2025). grantham: Calculate the Grantham Distance (Version 0.1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.grantham

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 grantham version 0.1.4 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →