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gllvm

Generalized Linear Latent Variable Models

https://github.com/jenniniku/gllvm

Science Score: 77.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 13 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: arxiv.org, springer.com, wiley.com, plos.org
  • ✓
    Committers with academic emails
    4 of 9 committers (44.4%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.6%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Generalized Linear Latent Variable Models

Basic Info
Statistics
  • Stars: 59
  • Watchers: 16
  • Forks: 21
  • Open Issues: 16
  • Releases: 2
Created almost 9 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Citation

README.md

gllvm

gllvm is an R package for analysing multivariate ecological data with Generalized Linear Latent Variable Models (GLLVM). Estimation is performed using maximum likelihood estimation, together with either variational approximation (VA) or Laplace approximation (LA) method to approximate the marginal likelihood.

Installation

From CRAN you can install the package using: install.packages("gllvm") Or the development version of gllvm from github with the help of devtools package using: devtools::install_github("JenniNiku/gllvm")

Getting started

For getting started with gllvm we recommend to read vignette Analysing multivariate abundance data using gllvm or introductions for using gllvm for ordination and for analysing species correlations.

Other available vignettes are: Analysing microbial community data, How to use the quadratic response model, Ordination with predictors, Analysing percent cover data and Structured and correlated random effects and latent variables.

Citation

The citation function in R provides information on how to cite the methods in this package. Please remember to cite the software (version) separately from any relevent research articles to provide the appropriate credit to all associated contributors. The reference for the software package is: Niku, J., Brooks, W., Herliansyah, R., Hui, F. K. C., Korhonen, P., Taskinen, S., van der Veen, B., and Warton, D. I. (YYYY). gllvm: Generalized Linear Latent Variable Models.R package version XXX, where YYYY represents the publication date of the used version of the package represented by XXX.

Package references

Hui, F.K.C., Warton, D., Ormerod, J., Haapaniemi, V., & Taskinen, S. (2017). Variational approximations for generalized linear latent variable models. Journal of Computational and Graphical Statistics, 26(1), 35 - 43.

Niku, J., Warton, D., Hui, F.K.C., & Taskinen, S. (2017). Generalized linear latent variable models for multivariate count and biomass data in ecology. Journal of Agricultural, Biological and Environmental Statistics, 22(4), 498 - 522.

Niku, J., Hui, F.K.C., Taskinen, S., & Warton, D. (2019). gllvm: Fast analysis of multivariate abundance data with generalized linear latent variable models in r. Methods in Ecology and Evolution, 10(12), 2173 - 2182.

Niku, J., Brooks, W., Herliansyah, R., Hui, F.K.C., Taskinen, S., & Warton, D. (2019). Efficient estimation of generalized linear latent variable models. PloS one, 14(5), e0216129.

Niku, J., Hui, F. K. C., Taskinen, S., and Warton, D. I. (2021). Analyzing environmental-trait interactions in ecological communities with fourth-corner latent variable models. Environmetrics, 32(6), 1-17.

van der Veen, B., Hui, F.K.C., Hovstad, K.A., Solbu, E.B., & O'Hara, R.B. (2021). Model-based ordination for species with unequal niche widths. Methods in Ecology and Evolution, 12(7), 1288 - 1300.

van der Veen, B., Hui, F. K. C., Hovstad, K.A., and O'Hara, R.B. (2023). Concurrent ordination: simultaneous unconstrained and constrained latent variable modelling. Methods in Ecology and Evolution, 14(2), 683-695.

van der Veen, B. and O'Hara, R.B. (2024). Fast fitting of phylogenetic mixed effects models. arxiv.

Korhonen, P., Hui, F. K. C., Niku, J., and Taskinen, S. (2023). Fast and universal estimation of latent variable models using extended variational approximations. Statistics and Computing, 33(1), 1-16.

Other references

The package references can be quite technical. Here we list some related references that may be more accessible.

Warton, D. I., Blanchet, F. G., OHara, R. B., Ovaskainen, O., Taskinen, S., Walker, S. C., & Hui, F. K. (2015). So many variables: joint modeling in community ecology. Trends in ecology and evolution, 30(12), 766-779.

Zuur, A. F., & Ieno, E. N. (2025). The World of Zero-Inflated Models Volume 3: Using GLLVM

Owner

  • Name: Jenni Niku
  • Login: JenniNiku
  • Kind: user
  • Location: Finland
  • Company: University of Jyväskylä

Postdoctoral Researcher in Statistics at University of Jyväskylä. My reseach focus on generalized linear latent variable models. Developer of R package gllvm.

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "Citation for github release."
authors:
- family-names: "Niku"
  given-names: "Jenni"
- family-names: "van der Veen"
  given-names: "Bert"
- family-names: "Hui"
  given-names: "Francis K.C."
- family-names: "Korhonen"
  given-names: "Pekka"
- family-names: "Taskinen"
  given-names: "Sara"
- family-names: "Brooks"
  given-names: "Wesley"
- family-names: "Warton"
  given-names: "David I."
title: "gllvm: Generalized Linear Latent Variable Models. R package"
version: 1.4.8
date-released: 2024-10-02

GitHub Events

Total
  • Issues event: 30
  • Watch event: 7
  • Delete event: 2
  • Issue comment event: 44
  • Push event: 168
  • Pull request event: 5
  • Fork event: 2
Last Year
  • Issues event: 30
  • Watch event: 7
  • Delete event: 2
  • Issue comment event: 44
  • Push event: 168
  • Pull request event: 5
  • Fork event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 937
  • Total Committers: 9
  • Avg Commits per committer: 104.111
  • Development Distribution Score (DDS): 0.565
Past Year
  • Commits: 189
  • Committers: 2
  • Avg Commits per committer: 94.5
  • Development Distribution Score (DDS): 0.27
Top Committers
Name Email Commits
bertv b****n@h****m 408
Bert van der Veen b****n@n****o 251
Niku j****i@j****i 136
JenniNiku j****u@j****i 119
Bert van der Veen b****v@b****o 9
Jenni Niku j****u@s****i 7
David Warton d****n@u****u 4
David Warton D****n@u****u 2
Jarrett Byrnes j****s@u****u 1
Committer Domains (Top 20 + Academic)
unsw.edu.au: 2 jyu.fi: 2 umb.edu: 1 student.jyu.fi: 1 bertv-laptop.math.ntnu.no: 1 nibio.no: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 92
  • Total pull requests: 63
  • Average time to close issues: 10 months
  • Average time to close pull requests: 20 days
  • Total issue authors: 41
  • Total pull request authors: 5
  • Average comments per issue: 3.66
  • Average comments per pull request: 1.08
  • Merged pull requests: 54
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 21
  • Pull requests: 8
  • Average time to close issues: 1 day
  • Average time to close pull requests: 12 days
  • Issue authors: 10
  • Pull request authors: 2
  • Average comments per issue: 0.67
  • Average comments per pull request: 1.0
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • BertvanderVeen (17)
  • hrlai (8)
  • AlainZuur (7)
  • dougwyu (5)
  • RodolfoPelinson (4)
  • jebyrnes (4)
  • mike-kratz (3)
  • SethMusker (3)
  • stouffer (3)
  • adhamab (2)
  • KwnLi (2)
  • wlangera (2)
  • dwarton (2)
  • gooner255 (2)
  • clementviolet (2)
Pull Request Authors
  • BertvanderVeen (58)
  • olivroy (4)
  • pekolako (3)
  • JenniNiku (1)
  • dwarton (1)
Top Labels
Issue Labels
enhancement (20) bug (13) question (11) help wanted (3)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 844 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 3
  • Total versions: 20
  • Total maintainers: 1
cran.r-project.org: gllvm

Generalized Linear Latent Variable Models

  • Versions: 20
  • Dependent Packages: 1
  • Dependent Repositories: 3
  • Downloads: 844 Last month
Rankings
Forks count: 4.1%
Stargazers count: 8.2%
Average: 14.1%
Dependent repos count: 16.5%
Dependent packages count: 18.2%
Downloads: 23.5%
Maintainers (1)
jenni.m.e.niku@jyu.fi
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • TMB * depends
  • mvabund * depends
  • MASS * imports
  • Matrix * imports
  • fishMod * imports
  • mgcv * imports
  • statmod * imports
  • corrplot * suggests
  • gclus * suggests
  • knitr * suggests
  • lattice * suggests
  • rmarkdown * suggests
  • testthat * suggests