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lme4

Mixed-effects models in R using S4 classes and methods with RcppEigen

https://github.com/lme4/lme4

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 47 committers (8.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (18.3%) to scientific vocabulary

Keywords from Contributors

package-creation visualisation weighted data-manipulation missing-data travis-ci date-time codecov coverage coverage-report
Last synced: 10 months ago · JSON representation

Repository

Mixed-effects models in R using S4 classes and methods with RcppEigen

Basic Info
  • Host: GitHub
  • Owner: lme4
  • License: other
  • Language: HTML
  • Default Branch: master
  • Size: 58.9 MB
Statistics
  • Stars: 664
  • Watchers: 53
  • Forks: 160
  • Open Issues: 232
  • Releases: 2
Created over 13 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License

README.md

lme4: Mixed-effects models in R.

R-CMD-check cran version downloads total downloads <!-- badges: start -->

Recent/release notes

Where to get help

  • r-sig-mixed-models@r-project.org for questions about lme4 usage and more general mixed model questions; please read the info page, and subscribe, before posting ... (note that the mailing list does not support images or large/non-text attachments)
  • https://github.com/lme4/lme4/issues for bug, infelicity, and wishlist reporting
  • The lme4 tag on StackOverflow for programming-related or the lme4-nlme tag on CrossValidated for statistics-related questions
  • maintainer e-mail only for urgent/private communications

Support

If you choose to support lme4 development financially, you can contribute to a fund at McMaster University (home institution of one of the developers) here. The form will say that you are donating to the "Global Coding Fund"; this fund is available for use by the developers, under McMaster's research spending rules. We plan to use the funds, as available, to pay students to do maintenance and development work. There is no way to earmark funds or set up a bounty to direct funding toward particular features, but you can e-mail the maintainers and suggest priorities for your donation.

Features

  • Efficient for large data sets, using algorithms from the Eigen linear algebra package via the RcppEigen interface layer.
  • Allows arbitrarily many nested and crossed random effects.
  • Fits generalized linear mixed models (GLMMs) and nonlinear mixed models (NLMMs) via Laplace approximation or adaptive Gauss-Hermite quadrature; GLMMs allow user-defined families and link functions.
  • Incorporates likelihood profiling and parametric bootstrapping.

Installation

On current R (>= 3.6.0)

  • From CRAN (stable release 1.+)

  • Development version from Github: r library("devtools"); install_github("lme4/lme4",dependencies=TRUE) (This requires devtools >= 1.6.1, and installs the "master" (development) branch.) This approach builds the package from source, i.e. make and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually. Specify build_vignettes=FALSE if you have trouble because your system is missing some of the LaTeX/texi2dvi tools.

  • Development binaries from r-universe: r install.packages('lme4', repos = c('https://lme4.r-universe.dev', getOption("repos")[["CRAN"]]))

Development notes

lme4 is developed in a mixture of

  • traditional R package building tools, as documented in Writing R Extensions
    • NEWS in inst/NEWS.Rd (not a top-level NEWS.md file)
    • documentation as .Rd files (not roxygen2, although some functions have internal roxygen-style documentation [not used])
    • 'classic' tests in the tests/ directory
    • some Sweave (knitr)/Rnw-format vignette, especially vignettes/lmer.Rnw
  • 'tidyverse'-style tools, as documented in R Packages (Wickham and Bryan)
    • testthat tests, in tests/testthat
    • pkgdown web site (via pkgdown.extras, extensions to allow PDF vignettes); trigger manual builds here
  • GitHub
    • primary development repository
    • issues
    • testing on GitHub actions (activated by specifying "[run ci]" at the end of a commit message)
    • pull requests are welcome, but please open a discussion as an issue first

Owner

  • Name: `lme4` R package authors
  • Login: lme4
  • Kind: organization
  • Email: lme4-authors@r-project.org

GitHub Events

Total
  • Create event: 6
  • Commit comment event: 9
  • Issues event: 43
  • Watch event: 42
  • Delete event: 4
  • Member event: 2
  • Issue comment event: 144
  • Push event: 126
  • Pull request review event: 8
  • Pull request review comment event: 5
  • Pull request event: 24
  • Fork event: 18
Last Year
  • Create event: 6
  • Commit comment event: 9
  • Issues event: 43
  • Watch event: 42
  • Delete event: 4
  • Member event: 2
  • Issue comment event: 144
  • Push event: 126
  • Pull request review event: 8
  • Pull request review comment event: 5
  • Pull request event: 24
  • Fork event: 18

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 2,576
  • Total Committers: 47
  • Avg Commits per committer: 54.809
  • Development Distribution Score (DDS): 0.479
Past Year
  • Commits: 71
  • Committers: 5
  • Avg Commits per committer: 14.2
  • Development Distribution Score (DDS): 0.239
Top Committers
Name Email Commits
Ben Bolker b****r@g****m 1,343
Martin Maechler m****r@r****g 486
dmbates d****s@e****b 271
Steve Walker s****r@m****a 186
bbolker b****r@e****b 94
mmaechler m****r@e****b 70
Douglas Bates d****s@g****m 17
fabian-s f****l@g****m 14
Øystein Sørensen o****n@h****m 10
Peter p****i@g****m 8
Michael Chirico c****m@g****m 7
Ross Boylan on EB-WS-12 r****n@u****u 6
Peter Green G****P@l****z 4
Emi Tanaka d****a@g****m 4
ggrothendieck g****k@g****m 4
Mikael Jagan j****n@m****a 4
singmann h****n@p****e 3
user n****l 3
Vincent Dorie v****t@s****u 3
Anna Ly a****y@a****e 3
pkgdown-bot p****t 3
Steve Walker s****r@u****a 3
Phillip Alday me@p****m 3
mpadge m****m@e****m 2
hadley wickham h****m@g****m 2
Helen Ogden h****2@g****m 2
cfhammill c****l@g****m 1
danstowell d****b@g****m 1
davidkretch d****h@g****m 1
helix123 k****e@g****e 1
and 17 more...
Committer Domains (Top 20 + Academic)
landcareresearch.co.nz: 2 r-project.org: 1 math.mcmaster.ca: 1 google.com: 1 ucsf.edu: 1 mcmaster.ca: 1 psychologie.uni-freiburg.de: 1 stat.columbia.edu: 1 annas-air.home: 1 utoronto.ca: 1 phillipalday.com: 1 email.com: 1 gmx.de: 1 fellstat.com: 1 pobox.com: 1 phsz.ch: 1 donarmstrong.com: 1 debian.org: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 210
  • Total pull requests: 49
  • Average time to close issues: 7 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 126
  • Total pull request authors: 18
  • Average comments per issue: 4.28
  • Average comments per pull request: 1.92
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 33
  • Pull requests: 27
  • Average time to close issues: 3 days
  • Average time to close pull requests: 6 days
  • Issue authors: 19
  • Pull request authors: 7
  • Average comments per issue: 0.88
  • Average comments per pull request: 0.74
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • bbolker (60)
  • covaruber (4)
  • GabrielHoffman (4)
  • jaganmn (4)
  • mmaechler (3)
  • DexterGlass (3)
  • GregForkutza (3)
  • user1212dasdas (2)
  • KushalKC1094 (2)
  • yanminwang576 (2)
  • CamilaDeu (2)
  • strengejacke (2)
  • mckman (2)
  • zoeluo15 (2)
  • iago-pssjd (2)
Pull Request Authors
  • annahuynhly (17)
  • MichaelChirico (5)
  • jaganmn (3)
  • GregForkutza (3)
  • sashahafner (2)
  • osorensen (2)
  • YancyLan (2)
  • klmr (2)
  • emitanaka (2)
  • RossBoylan (2)
  • NikNakk (2)
  • nfultz (1)
  • pablobernabeu (1)
  • danwkenn (1)
  • palday (1)
Top Labels
Issue Labels
enhancement (1) release_critical (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 425,411 last-month
  • Total docker downloads: 835,293
  • Total dependent packages: 547
    (may contain duplicates)
  • Total dependent repositories: 1,396
    (may contain duplicates)
  • Total versions: 147
  • Total maintainers: 1
cran.r-project.org: lme4

Linear Mixed-Effects Models using 'Eigen' and S4

  • Versions: 134
  • Dependent Packages: 500
  • Dependent Repositories: 1,383
  • Downloads: 425,411 Last month
  • Docker Downloads: 835,293
Rankings
Dependent packages count: 0.2%
Dependent repos count: 0.3%
Forks count: 0.4%
Downloads: 0.5%
Stargazers count: 0.6%
Average: 3.2%
Docker downloads count: 17.3%
Maintainers (1)
bbolker+lme4@gmail.com
Last synced: 10 months ago
conda-forge.org: r-lme4
  • Versions: 13
  • Dependent Packages: 47
  • Dependent Repositories: 13
Rankings
Dependent packages count: 1.5%
Dependent repos count: 9.8%
Average: 11.0%
Forks count: 15.8%
Stargazers count: 16.9%
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • Matrix >= 1.2 depends
  • R >= 3.5.0 depends
  • methods * depends
  • stats * depends
  • MASS * imports
  • boot * imports
  • graphics * imports
  • grid * imports
  • lattice * imports
  • minqa >= 1.1.15 imports
  • nlme >= 3.1 imports
  • nloptr >= 1.0.4 imports
  • parallel * imports
  • splines * imports
  • utils * imports
  • HSAUR3 * suggests
  • MEMSS * suggests
  • car * suggests
  • dfoptim * suggests
  • gamm4 * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • merDeriv * suggests
  • mgcv * suggests
  • mlmRev * suggests
  • numDeriv * suggests
  • optimx >= 2013.8.6 suggests
  • pbkrtest * suggests
  • rmarkdown * suggests
  • rr2 * suggests
  • semEff * suggests
  • statmod * suggests
  • testthat >= 0.8.1 suggests
  • tibble * suggests