Package: AGHmatrix 3.0.0

AGHmatrix: Relationship Matrices for Diploid and Autopolyploid Species

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.

Authors:Rodrigo Amadeu [aut, cre], Luis Ferrao [aut, ctb], Thiago Oliveira [aut, ctb], Catherine Cellon [ctb], Leticia Lara [ctb], Marcio Resende [ctb], Ivone Oliveira [ctb], Patricio Munoz [ctb], Augusto Garcia [ctb]

AGHmatrix_3.0.0.tar.gz
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AGHmatrix_3.0.0.tar.gz(r-4.7-arm64)AGHmatrix_3.0.0.tar.gz(r-4.7-x86_64)AGHmatrix_3.0.0.tar.gz(r-4.6-arm64)AGHmatrix_3.0.0.tar.gz(r-4.6-x86_64)
AGHmatrix_3.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
AGHmatrix/json (API)

# Install 'AGHmatrix' in R:

install.packages('AGHmatrix', repos = c('https://rramadeu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rramadeu/aghmatrix/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

ped.mrode - Pedigree Data
ped.sol - Pedigree data for autopolyploid examples
snp.pine - Molecular data for diploid examples
snp.sol - Molecular data for autopolyploid examples

On CRAN:

openblas cpp openmp

8.56 score 11 stars 2 packages 211 scripts 1.3k downloads 11 mentions 11 exports 3 dependencies

Last updated from:ab5c4388ec. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	243
linux-devel-x86_64	OK	227
source / vignettes	OK	305
linux-release-arm64	OK	235
linux-release-x86_64	OK	226
macos-release-arm64	OK	512
macos-release-x86_64	OK	550
macos-oldrel-arm64	OK	338
macos-oldrel-x86_64	OK	547
windows-devel	OK	336
windows-release	OK	396
windows-oldrel	OK	302
wasm-release	OK	179

Exports:Amatrix AmatrixPolyCross asciitonumber datatreat expandAmatrix filterpedigree formatmatrix Gmatrix Hmatrix Mcheck missingdata

Dependencies:matrixStats Rcpp RcppArmadillo

AGHmatrix Tutorial

Rodrigo Amadeu

Rendered fromTutorial_AGHmatrix.Rmdusingknitr::rmarkdownon May 11 2026.

Last update: 2023-08-16
Started: 2017-07-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Construction of Relationship Matrix A	Amatrix
Construction of pedigree-based relationship matrix with parental guessing possibility	AmatrixPolyCross
Convert pedigree names to numeric indices using C++	asciitonumber
Organizes pedigree data in a chronological way using C++	datatreat
Add new crosses to a current A matrix	expandAmatrix
Filter the pedigree to keep only the genealogy of a subset of individuals	filterpedigree
Transform a matrix in 3 columns	formatmatrix
Construction of Relationship Matrix G	Gmatrix
Compute Martini block corrections (H11, H12, H21, H22 - A22)	H_martini_blocks
Construction of Combined Relationship Matrix H	Hmatrix
Check and filter markers	Mcheck
Survying on missing data	missingdata
Compute var/mean of G by classes of rounded A, and fill varA/meanG	munoz_var_mean_by_Aclass
Pedigree Data	ped.mrode
Pedigree data for autopolyploid examples	ped.sol
Molecular data for diploid examples	snp.pine
Molecular data for autopolyploid examples	snp.sol