R Observatory: Metrics for nadiv version 2.18.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nadiv

2.18.0Package record

(Non)Additive Genetic Relatedness Matrices

2packages dependsuggested by 2

12.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Matthew WolakCRAN page ↗GitHub ↗Issues ↗

Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (https://vsni.co.uk/software/asreml).

Changes in 2.18.0

NEW

makeDiiF() can now be given coefficients of inbreeding. Facilitates either:
calculating f in a new generation of the pedigree if f has already been calculated for previous generations
creating a "phantom parent" to all founders to specify an average coefficient of inbreeding in the base population.
can be used to speed up simulations where breeding values are calculated based on mid-parent value plus Mendelian sampling deviation (that needs to account for inbreeding of parents).

Major changes

proLik() (and proLik4()) __REMOVED__ from the package.
these functions were _only_ to facilitate advanced use of the asreml R package (which requires purchasing an expensive license) and due to the __unstable__ behavior of asreml discovered when revising proLik() it was decided that nadiv should no longer support this other package in this way.
Instead, time will be spent improving the gremlin R package for a replacement to asreml.
makeA() was affected by a bug in Matrix <1.6-0
Matrix::chol2inv() bug highlighted a messy order of operations in nadiv
now perfected the order of operations and explicitly use tcrossprod() and

Show all changes in 2.18.0Hide the rest of the changes in 2.18.0

solve() which are just what chol2inv() uses

done to be more explicit in nadiv and take 1 step away from future bugs like this
checked speed and memory profiling for several options of types of matrices
dtCMatrix is best for time (tried "dtrMatrix" and "dtpMatrix", but these

were __much__ slower.

chol2inv() and tcrossprod(solve()) allocated same amount of memory according to profmem package
bug in makeAinv(), makeGGAinv(), and makeDiiF() caused coefficients of inbreeding (f) and Mendelian sampling variances (dii) to be ordered incorrectly
this did _not_ cause matrices from these functions to be incorrect (e.g., __Ainv__, __Tinv__, and their related matrices), but did cause matrices built directly from dii to be incorrect - namely the __A__ matrix from makeA() and so consequently anything built from __A__ (i.e., dominance and epistatic relatedness matrices through makeD() etc.)
__this was FIXED__ with details in the commit

Small changes

nadiv version 2.17.2 caused CRAN to archive due to error induced by Matrix updates
Mikael Jagan (Matrix author) helpfully provided excellent explanations and patches
errors in nadiv code caused by new methods for all.equal() and rbind2()
removed methods is.numPed() and is.proLik()
hardly use first and never second plus they just call inherits()

From NEWS.md in the release

Install

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

install.packages("nadiv", 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("matthewwolak/nadiv")

Development version from matthewwolak/nadiv. 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-nadiv

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-nadiv

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-nadiv

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: 3.4 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.18.0

READMEYes · 182 wordsVignettesNoNEWSYes · 100% structured · mentions 2.18.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 45 (2 internal)includes a package overview page
Examples that run: 89%34 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran) · 2 never run
Exported functions with examples: 85%
Documented parameters: 93%
Return-value docs: 97%
Help pages citing references: 33%

How these are measured

Downloads

12.9K

CRAN downloads in the past year

Rank #3,998 · ~35/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

91130 days

2.3K90 days

12.9K1 year

Compare downloads with other packages →

Also on432 r2u236 autocran

How downloads are counted

Repository

matthewwolak/nadiv ↗Account: matthewwolak

23Stars

8Forks

2Open issues

0Open PRs

11Releases

761Commits

1Commit identities

761 commits · Last activity 2024-05-28 · 0% stars, 30d · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-02 · 232026-07-07 · 23

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/matthewwolak/nadiv on 2026-10-21.

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Installing nadiv adds no packages beyond those that come with R.

Depends (2)

R >= 4.2.0Matrix

Imports (3)

graphicsmethodsstats

LinkingTo (0)

none

Suggests (1)

parallel

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Depends 1 · Imports 1

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

dmm pedtricks

Suggests, most downloaded first

visPedigree hsquared

How these are counted

Code & Tests

Datasets

People & History

People (1)

Matthew Wolak

Maintainer since 2.7 (2011), Author

Releases (22)

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
unarchivedReturned to CRAN
2024-05-23
2.18.0Latest
record
2024-05-23 · current release · diff ↗ ·
removed 4 exports
is.numPed, parConstrainFun, proLik, proLik4
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-12-06
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
2.17.2
record
2022-12-08 · diff ↗ ·
added 2 exports
makeM, proLik4
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
2.17.1
record
2021-04-06 · diff ↗
2.17.0
record
2021-01-14 · diff ↗ ·
added 4 exports
makeMinv, makeMinvML, makeT, simPedMCN
R
R 4.0.0 released · 2020-04-24
2.16.2.0
record
2019-10-20 · diff ↗ ·
added 4 exports
geneDrop, makeDiiF, makeGGAinv, makeTinv
R
R 3.6.0 released · 2019-04-26
2.16.0.0
record
2018-05-10 · diff ↗ ·
removed 4 exports
is.proLik, plot.proLik, makeAinv.default, makeAinv.fuzzy

added 3 exports
makeSd, makeSdsim, pin

Show 24 earlier eventsHide 24 earlier events

R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
2.15.2
record
2012-07-16 · diff ↗ ·
removed 8 exports
IBD, IBD2, vchoose, chooser, SEfun, DFC, findBetween, wrap_dij

added 6 exports
aic, drfx, grfx, makeS, simPedDFC, simPedHS
R
R 2.15.0 released · 2012-03-30
2.15.0
record
2012-03-22 · diff ↗ ·
added 10 exports
IBD, IBD2, vchoose, chooser, SEfun, constrainFun, parConstrainFun, wrap_dij, aiCI, varTrans
2.14.3.1
record
2016-09-22 · diff ↗
2.14.3
record
2016-04-19 · diff ↗ ·
added 5 exports
LRTest, makeAstarMult, simGG, makeAinv.default, makeAinv.fuzzy
2.14.2
record
2016-02-05 · diff ↗
2.14.1
record
2015-07-22 · diff ↗
2.14.0
record
2015-07-03 · diff ↗ ·
added 1 export
ronPed
2.13.3
record
2015-06-03 · diff ↗ ·
added 3 exports
founderLine, is.proLik, is.numPed
2.13.2
record
2014-06-20 · diff ↗
2.13
record
2014-06-16 · diff ↗ ·
added 5 exports
ggcontrib, makeAinv, pcc, prepPed, prunePed
2.12
record
2013-07-17 · diff ↗ ·
removed 1 export
DFC

added 5 exports
aic, drfx, grfx, simPedDFC, simPedHS
2.11
record
2013-02-26 · diff ↗
2.10
record
2012-10-17 · diff ↗ ·
removed 5 exports
aic, drfx, grfx, simPedDFC, simPedHS

added 1 export
DFC
2.9
record
2012-03-28 · diff ↗
2.8
record
2012-02-07 · diff ↗ ·
removed 1 export
FindDFC

added 4 exports
findDFC, proLik, plot.proLik, findBetween
2.7
record
2011-12-18
R
R 2.14.0 released · 2011-10-31

Package metadata

First published: 2011-12-18
Total releases: 22 / 15 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Bundled data: 624 KB / 9 files
Download size: 719 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("nadiv")

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 nadiv version 2.18.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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