R Observatory: Metrics for AGHmatrix version 3.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AGHmatrix

3.0.3Package record

Relationship Matrices for Diploid and Autopolyploid Species

2packages dependsuggested by 1

17.8Kdownloads / year

63.4%test coverage

13/13flavors OK

Overview

About

Maintained by Rodrigo AmadeuCRAN page ↗GitHub ↗

Fast computation of A (pedigree), G (genomic-base), and H (A corrected by G) relationship matrices for diploid and autopolyploid species. Several methods are implemented considering additive and non-additive models.

Install

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

install.packages("AGHmatrix", 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("rramadeu/AGHmatrix")

Development version from rramadeu/AGHmatrix. 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-aghmatrix

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-AGHmatrix

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-AGHmatrix

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: 12.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-13
ERROR13 OK, 1 ERROR2026-03-12
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.0.3

READMEYes · 2,403 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publication

Help pages: 17
Examples that run: 79%11 run in a plain check · 2 never run · 1 hold no code
Exported functions with examples: 91%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 41%

Vignettes (1)

AGHmatrix Tutorial HTML

How these are measured

Downloads

17.8K

CRAN downloads in the past year

Rank #2,908 · ~49/day · ~1.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.2K30 days

4.9K90 days

17.8K1 year

Compare downloads with other packages →

Also on342 r2u49 autocran112 c2d4u

How downloads are counted

Repository

rramadeu/aghmatrix ↗Account: rramadeuFork of prmunoz/AGHmatrix

12Stars

3Forks

0Open issues

0Open PRs

8Releases

466Commits

3Commit identities

466 commits · Last activity 2026-09-30 · +9.1% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-04-10 · 112026-10-23 · 12

How these are measured

PracticesBeta

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

Checks run against github.com/rramadeu/aghmatrix on 2026-10-25.

Docs source (1)

GitHub Pages site last deployed 2026-09-30

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen on or before 2026-09-28
Commits: some crediting it in the message, count not recorded

Review tools

Copilot code review
Commits: some accepting its review suggestions, count not recorded

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing AGHmatrix adds 3 packages (3 with compiled code, 3.0 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppArmadillo 1.0 MB, matrixStats 207 KB.

Depends (1)

R >= 3.6.0

Imports (2)

Rcpp matrixStats

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (5)

knitrMASSrmarkdown testthat zoo

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

ASRgenomics gpcp

Suggests, most downloaded first

mappoly

How these are counted

Code & Tests

Datasets

People & History

People (9)

Rodrigo Amadeu

Author, Maintainer since 0.0.4 (2018)

Luis Ferrao

Author, Contributor

Thiago Oliveira

Author, Contributor · added in 3.0.1

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Releases (12)

Pick two releases to compare their code metrics.

3.0.3Latest
record
2026-10-01 · current release · diff ↗
3.0.1
record
2026-07-22 · diff ↗ ·
added 1 export
asciitonumber
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
2.1.4
record
2023-10-03 · diff ↗
2.1.3
record
2023-08-16 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.1.0
record
2023-04-03 · diff ↗ ·
added 2 exports
expandAmatrix, Mcheck
R
R 4.2.0 released · 2022-04-22
2.0.4
record
2021-09-14 · diff ↗ ·
added 2 exports
AmatrixPolyCross, filterpedigree
R
R 4.1.0 released · 2021-05-18
2.0.0
record
2020-09-21 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.2
record
2019-07-30 · diff ↗
1.0.1
record
2019-07-23 · diff ↗

Show 5 earlier eventsHide 5 earlier events

1.0.0
record
2019-07-12 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.0.5
record
2019-03-26 · diff ↗
0.0.4
record
2018-06-06
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-06-06
Total releases: 12 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6.0
Bundled data: 1.9 MB / 5 files
Download size: 2.0 MB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' entry:

citation("AGHmatrix")

The package provides a citation file, so citation() returns the authors' own entry.

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 AGHmatrix version 3.0.3 [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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