R Observatory: Metrics for sommer version 4.4.87

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

sommer

4.4.87Package record

Solving Mixed Model Equations in R

7packages dependsuggested by 2

72.1Kdownloads / year

61.8%test coverage

13/13flavors OK

Overview

About

Maintained by Giovanny Covarrubias-PazaranCRAN page ↗GitHub ↗Issues ↗

Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., unstructured, diagonal, autoregressive, factor analytic, reduced rank, among others) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 doi:10.1371/journal.pone.0156744; Maier et al., 2015 doi:10.1016/j.ajhg.2014.12.006; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate).

Install

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

install.packages("sommer", 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("covaruber/sommer")

Development version from covaruber/sommer. 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-sommer

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-sommer

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-sommer

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: 13.8 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 3 earlier changesHide 3 earlier changes

NOTE12 OK, 2 NOTE2026-04-10
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.4.87

READMEYes · 363 wordsVignettesYes · 10 · dynamicNEWSNoCitation fileYes · cites a publication

Help pages: 71includes a package overview page
Examples that run: 56%36 run in a plain check · 22 never run · 6 hold no code
Exported functions with examples: 91%
Documented parameters: 100%
Return-value docs: 99%
Help pages citing references: 34%

Vignettes (10)

How these are measured

Downloads

72.1K

CRAN downloads in the past year

Rank #1,554 · ~198/day · ~6K/mo

Releases R versions

Daily download trend is not available in this view yet.

5.4K30 days

15.1K90 days

72.1K1 year

Compare downloads with other packages →

Also on1.2K r2u240 autocran167 c2d4u

How downloads are counted

Repository

covaruber/sommer ↗Account: covaruber

65Stars

37Forks

0Open issues

0Open PRs

0Releases

370Commits

17Commit identities

average-informationmixed-modelsrcpparmadillo

370 commits · Last activity 2026-10-18 · +8.3% stars, 30d · Default branch at 4.4.88, ahead of CRAN 4.4.87 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 96%
Median days to close, 50 most recently updated closed issues: 58
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-07-11 · 492026-10-17 · 65

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/covaruber/sommer on 2026-10-11.

Continuous integration (1)

GitHub Actions

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-06 · The repository has a site deploy workflow

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing sommer adds 6 packages (3 with compiled code, 6.8 MB of source tarballs). Heaviest: enhancer 2.3 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB.

Depends (7)

R >= 3.5.0MatrixmethodsstatsMASScrayon enhancer

Imports (1)

Rcpp

LinkingTo (5)

Rcpp RcppArmadillo RcppProgress RcppEigenMatrix

Suggests (10)

rmarkdown knitr plyrparallelorthopolynom RSpectralatticeemmeans estimability testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

7direct

2indirect

Imports 7

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

statgenGWAS gpcp lmDiallel EstimateBreed IPLGP statgenQTLxT pcgen

Suggests, most downloaded first

lucid MoBPS

How these are counted

Code & Tests

People & History

People (1)

Giovanny Covarrubias-Pazaran

Author, Maintainer since 1.1 (2016)

Releases (66)

Pick two releases to compare their code metrics.

4.4.87Latest
record
2026-10-04 · current release · diff ↗ ·
removed 3 exports
AR1, CS, ARMA

added 29 exports
strm, ar1m, ar2m, ar3m, dsumm, mam, fam, antem, corgm, ownm, rrm, maternm, toeplitzm, sar, car, metricm, postPEV, APY, loadings_mmes, scores_mmes, covparams_mmes, covparams_mmes_se, meffects_mmes, wald_mmes, rotate_back_mmes, binm, familym, stackTraits, covmatrix_mmes
4.4.7
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2026-09-11 · diff ↗
4.4.6
record
2026-07-09 · diff ↗
R
R 4.6.0 released · 2026-04-24
4.4.5
record
2026-03-25 · diff ↗
4.4.4
record
2025-11-26 · diff ↗ ·
removed 24 exports
transp, jet.colors, bathy.colors, LD.decay, manhattan, map.plot, atcg1234BackTransform, rrm, overlay, redmm, add.diallel.vars, bbasis, tps, atcg1234, build.HMM, neMarker, adiag1, imputev, propMissing, logspace, stan, leg, wald.test, simGECorMat

added 6 exports
MNR, unsm2, usr, dsr, csr, atr
4.4.3
record
2025-07-30 · diff ↗ ·
removed 1 export
stackTrait
4.4.2
record
2025-05-26 · diff ↗ ·
added 1 export
stan
R
R 4.5.0 released · 2025-04-11
4.4.1
record
2025-04-04 · diff ↗ ·
removed 38 exports
mmec, atr, csr, dsr, usr, gvsr, atc, csc, dsc, usc, vsc, isc, rrc, covc, fcm, list2usmat, transformConstraints, bivariateRun, spl2Da, spl2Db, EM, MEMMA, AI, summary.mmer, residuals.mmer, fitted.mmer, coef.mmer, anova.mmer, plot.mmer, predict.mmer and 8 more

added 16 exports
mmes, atm, csm, dsm, usm, vsm, ism, rrm, covm, summary.mmes, residuals.mmes, fitted.mmes, coef.mmes, anova.mmes, plot.mmes, predict.mmes
4.3.7
record
2025-02-03 · diff ↗
4.3.6
record
2024-10-20 · diff ↗
4.3.5
record
2024-07-31 · diff ↗ ·
added 1 export
tps
R
R 4.4.0 released · 2024-04-24
4.3.4
record
2024-03-17 · diff ↗ ·
added 2 exports
atcg1234BackTransform, propMissing
4.3.3
record
2023-11-13 · diff ↗

Show 62 earlier eventsHide 62 earlier events

4.3.2
record
2023-08-11 · diff ↗ ·
added 1 export
covc
4.3.1
record
2023-06-14 · diff ↗ ·
added 1 export
neMarker
4.3.0
record
2023-05-11 · diff ↗ ·
added 3 exports
redmm, stackTrait, corImputation
R
R 4.3.0 released · 2023-04-21
4.2.1.2
record
2023-04-07 · diff ↗ ·
added 3 exports
rrc, logspace, r2
4.2.0.1
record
2023-01-08 · diff ↗
4.2.0
record
2022-09-11 · diff ↗
4.1.9
record
2022-09-09 · diff ↗
4.1.8
record
2022-09-06 · diff ↗ ·
added 1 export
predict.mmec
4.1.7
record
2022-06-16 · diff ↗ ·
removed 9 exports
mmer2, GWAS2, at, cs, ds, us, gvs, uncm, h2.fun

added 22 exports
mmec, atr, csr, dsr, usr, vsr, gvsr, atc, csc, dsc, usc, vsc, isc, spl2Dc, AI, summary.mmec, residuals.mmec, fitted.mmec, coef.mmec, anova.mmec, plot.mmec, pmonitor
R
R 4.2.0 released · 2022-04-22
4.1.6
record
2022-04-17 · diff ↗
4.1.5
record
2021-12-15 · diff ↗ ·
removed 1 export
spl2D

added 5 exports
spl2Da, spl2Db, spl2Dmats, bbasis, tpsmmbwrapper
4.1.4
record
2021-07-29 · diff ↗
R
R 4.1.0 released · 2021-05-18
4.1.3
record
2021-04-05 · diff ↗ ·
added 3 exports
gvs, add.diallel.vars, vpredict.mmer
4.1.2
record
2021-01-06 · diff ↗ ·
removed 4 exports
fill.design, pedtoK, spatPlots, pin

added 4 exports
LD.decay, dfToMatrix, vpredict, H.mat
4.1.1
record
2020-09-30 · diff ↗ ·
removed 1 export
unsBLUP

added 1 export
wald.test
4.1.0
record
2020-06-16 · diff ↗ ·
added 1 export
unsBLUP
R
R 4.0.0 released · 2020-04-24
4.0.9
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2020-02-07 · diff ↗
4.0.8
record
2019-11-01 · diff ↗
4.0.4
record
2019-08-24 · diff ↗
4.0.1
record
2019-07-02 · diff ↗ ·
added 1 export
simGECorMat
R
R 3.6.0 released · 2019-04-26
3.9.3
record
2019-04-04 · diff ↗
3.9.1
record
2019-03-26 · diff ↗
3.8
record
2019-01-02 · diff ↗ ·
added 2 exports
transformConstraints, bivariateRun
3.7.3
record
2018-12-10 · diff ↗
3.7.2
record
2018-12-09 · diff ↗
3.7.1
record
2018-12-07 · diff ↗
3.7
record
2018-12-04 · diff ↗ ·
removed 30 exports
hits, big.peaks.col, blocker, blockerL, blockerT, brewer.pal, design.score, fdr, fdr2, hadamard.prod, hdm, is.diagonal.matrix, is.square.matrix, matrix.trace, maxi.qtl, MNR, nna, phase.F1, score.calcMV, vctable, vctable.help, summary.MMERM, residuals.MMERM, fitted.MMERM, plot.MMERM, variogram, variogram.MMERM, plot.variogram.MMERM, anova.MMERM, coef.MMERM

added 22 exports
at, cs, ds, us, vs, unsm, uncm, fixm, fcm, list2usmat, spl2D, leg, AR1, CS, ARMA, summary.mmer, residuals.mmer, fitted.mmer, plot.mmer, predict.mmer, anova.mmer, coef.mmer
3.6
record
2018-10-08 · diff ↗
3.5
record
2018-07-02 · diff ↗ ·
removed 1 export
AI
R
R 3.5.0 released · 2018-04-23
3.4
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2018-04-06 · diff ↗
3.3
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2018-03-05 · diff ↗ ·
removed 6 exports
and, at, eig, g, grp, us

added 1 export
spatPlots
3.2
record
2018-01-09 · diff ↗ ·
added 7 exports
AI, build.HMM, EM, h2.fun, variogram, variogram.MMERM, plot.variogram.MMERM
3.1
record
2017-10-29 · diff ↗ ·
added 1 export
pedtoK
3.0
record
2017-08-24 · diff ↗ ·
removed 31 exports
AI, AImme, ai2help, eigenGWAS, EM, EM2, EMMA, LD.decay, mmerSNOW, MMERM, MAI, MAI2, name.change, NR, NR22, PEV, poe, score.calc, TP.prep, summary.mmer, summary.mmerM, residuals.mmer, residuals.mmerM, fitted.mmer, fitted.mmerM, plot.mmer, plot.mmerM, anova.mmer, anova.mmerM, coef.mmer and 1 more

added 9 exports
blockerL, blockerT, eig, grp, GWAS, GWAS2, score.calcMV, vctable, vctable.help
2.9
record
2017-07-08 · diff ↗
2.8
record
2017-06-07 · diff ↗ ·
added 4 exports
AImme, blocker, fill.design, pin
R
R 3.4.0 released · 2017-04-21
2.7
record
2017-04-15 · diff ↗ ·
added 5 exports
and, at, g, overlay, us
2.6
record
2017-03-02 · diff ↗ ·
removed 4 exports
AR1.mat, ARMA.mat, CS.mat, NRR
2.5
record
2017-01-03 · diff ↗ ·
added 1 export
fdr2
2.4
record
2016-12-01 · diff ↗
2.3
record
2016-11-01 · diff ↗ ·
added 3 exports
imputev, name.change, nna
2.2
record
2016-10-02 · diff ↗ ·
added 1 export
LD.decay
2.1
record
2016-08-31 · diff ↗ ·
removed 1 export
S.mat

added 4 exports
AR1.mat, ARMA.mat, CS.mat, NRR
2.0
record
2016-07-29 · diff ↗ ·
removed 3 exports
AI2, AI3, EMMAM

added 5 exports
ai2help, MEMMA, MAI, MAI2, MNR
1.9
record
2016-07-01 · diff ↗ ·
removed 1 export
bag

added 12 exports
hits, eigenGWAS, EMMAM, manhattan, MMERM, PEV, summary.MMERM, residuals.MMERM, fitted.MMERM, plot.MMERM, anova.MMERM, coef.MMERM
1.8
record
2016-06-06 · diff ↗ ·
removed 1 export
R.mat

added 14 exports
hadamard.prod, is.diagonal.matrix, is.square.matrix, matrix.trace, maxi.qtl, mmerSNOW, phase.F1, S.mat, summary.mmerM, residuals.mmerM, fitted.mmerM, plot.mmerM, anova.mmerM, coef.mmerM
1.7
record
2016-05-24 · diff ↗ ·
added 2 exports
NR22, R.mat
1.6
record
2016-05-19 · diff ↗ ·
removed 1 export
map.plot2

added 2 exports
map.plot, NR
1.5
record
2016-05-03 · diff ↗ ·
added 1 export
TP.prep
R
R 3.3.0 released · 2016-05-03
1.4
record
2016-03-25 · diff ↗ ·
added 3 exports
big.peaks.col, brewer.pal, EM2
1.3
record
2016-03-10 · diff ↗ ·
added 3 exports
bag, bathy.colors, jet.colors
1.2
record
2016-02-07 · diff ↗ ·
added 5 exports
AI2, AI3, atcg1234, design.score, randef
1.1
record
2016-01-24
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-01-24
Total releases: 66 / 10 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 1.2 MB

Appears in task views

Agricultural Science Mixed, Multilevel, and Hierarchical Models in R

Cite

Cite this package

Run in R for the authors' entry:

citation("sommer")

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 sommer version 4.4.87 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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