Package: gllvm 2.0.9

gllvm: Generalized Linear Latent Variable Models

Analysis of multivariate data using generalized linear latent variable models (gllvm). Estimation is performed using either the Laplace method, variational approximations, or extended variational approximations, implemented via TMB (Kristensen et al. (2016), <doi:10.18637/jss.v070.i05>).

Authors:Jenni Niku [aut, cre], Wesley Brooks [aut], Riki Herliansyah [aut], Francis K.C. Hui [aut], Pekka Korhonen [aut], Sara Taskinen [aut], Bert van der Veen [aut], David I. Warton [aut]

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gllvm.pdf |gllvm.html✨
gllvm/json (API)
NEWS

# Install 'gllvm' in R:
install.packages('gllvm', repos = c('https://jenniniku.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jenniniku/gllvm/issues

Pkgdown/docs site:https://jenniniku.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • beetle - Ground beetle assemblages
  • eSpider - Hunting spider data
  • fungi - Wood-decaying fungi data
  • kelpforest - Kelp Forest community Dynamics: Cover of sessile organisms, Uniform Point Contact
  • microbialdata - Microbial community data
  • Skabbholmen - Skabbholmen island data

On CRAN:

Conda:

cppopenmp

10.78 score 61 stars 1 packages 218 scripts 712 downloads 2 mentions 55 exports 12 dependencies

Last updated from:d7f698a641. Checks:11 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR447
linux-devel-x86_64ERROR438
source / vignettesOK597
linux-release-arm64ERROR416
linux-release-x86_64ERROR375
macos-release-arm64ERROR434
macos-release-x86_64ERROR768
macos-oldrel-arm64ERROR288
macos-oldrel-x86_64ERROR687
windows-develERROR577
windows-releaseERROR506
windows-oldrelERROR582
wasm-releaseOK209

Exports:AICcAICc.gllvmcoefplotcoefplot.gllvmconfint.gllvmgetEnvironCorgetEnvironCor.gllvmgetEnvironCovgetEnvironCov.gllvmgetLoadingsgetLoadings.gllvmgetLVgetLV.gllvmgetPredictErrgetPredictErr.gllvmgetResidualCorgetResidualCor.gllvmgetResidualCovgetResidualCov.gllvmgllvmglmmVAgoodnessOfFitlogLik.gllvmnobs.gllvmoptimaoptima.gllvmordiplotordiplot.gllvmphyloplotphyloplot.gllvmplotVarPartitioningplotVPpredict.gllvmpredictLVspredictLVs.gllvmpredictPairwisepredictPairwise.gllvmpredictSRpredictSR.gllvmprint.summary.gllvmprint.VP.gllvmrandomCoefplotrandomCoefplot.gllvmresiduals.predictSR.gllvmsese.gllvmsimulatesimulate.gllvmtolerancestolerances.gllvmupdate.gllvmvarPartitioningvarPartitioning.gllvmvcov.gllvmVP

Dependencies:alabamafishModlatticeMASSMatrixmgcvnlmenloptrnumDerivRcppRcppEigenTMB

Analysing high-dimensional microbial community data using gllvm

Jenni Niku

Rendered fromvignette2.rmdusingknitr::rmarkdownon Apr 15 2026.

Last update: 2025-03-28
Started: 2019-07-24

Analysing multivariate abundance data using gllvm

Jenni Niku

Rendered fromvignette1.Rmdusingknitr::rmarkdownon Apr 15 2026.

Last update: 2026-04-07
Started: 2019-07-24

Analysing sparse ecological percent cover data using gllvm

Pekka Korhonen

Rendered fromvignette8.Rmdusingknitr::rmarkdownon Apr 15 2026.

Last update: 2026-01-21
Started: 2024-09-13

Assessing Convergence in gllvm models

Jenni Niku

Rendered fromvignette10.Rmdusingknitr::rmarkdownon Apr 15 2026.

Last update: 2026-04-01
Started: 2026-04-01

Correlation structures for latent variables and row effects

Jenni Niku

Rendered fromvignette9.Rmdusingknitr::rmarkdownon Apr 15 2026.

Last update: 2025-03-31
Started: 2024-09-25

How to use the quadratic response model

Bert van der Veen

Rendered fromvignette5.Rmdusingknitr::rmarkdownon Apr 15 2026.

Last update: 2024-09-06
Started: 2021-07-01

Introduction to gllvm Part 1: Ordination

Jenni Niku

Rendered fromvignette3.rmdusingknitr::rmarkdownon Apr 15 2026.

Last update: 2024-11-20
Started: 2020-12-14

Introduction to gllvm Part 2: Species correlations

Jenni Niku

Rendered fromvignette4.rmdusingknitr::rmarkdownon Apr 15 2026.

Last update: 2024-11-20
Started: 2020-12-14

Ordination with predictors

Bert van der Veen

Rendered fromvignette6.Rmdusingknitr::rmarkdownon Apr 15 2026.

Last update: 2025-02-28
Started: 2021-07-01

Phylogenetic random effects

Bert van der Veen

Rendered fromvignette7.Rmdusingknitr::rmarkdownon Apr 15 2026.

Last update: 2024-11-25
Started: 2024-09-06

Readme and manuals

Help Manual

Help pageTopics
Corrected Akaike information criterion and number of observationsAICc AICc.gllvm nobs nobs.gllvm
Analysis Of Deviance for gllvmanova.gllvm
ground beetle assemblagesbeetle
Plot covariate coefficients and confidence intervalscoefplot coefplot.gllvm
Confidence intervals for model parametersconfint confint.gllvm
Functions to extract ecological quantities of the latent variables from a GLLVM, if species are a quadratic function of the latent variables.ecoCoefs optima optima.gllvm tolerances tolerances.gllvm
Hunting spider dataeSpider
Wood-decaying fungi datafungi
Extract species covariances due to environmental random effects from gllvm objectgetEnvironCor getEnvironCor.gllvm getEnvironCov getEnvironCov.gllvm
Extract loadingsgetLoadings getLoadings.gllvm
Extract latent variablesgetLV getLV.gllvm
Extract prediction errors for latent variables from gllvm objectgetPredictErr getPredictErr.gllvm
Extract residual correlations from gllvm objectgetResidualCor getResidualCor.gllvm
Extract residual covariance matrix from gllvm objectgetResidualCov getResidualCov.gllvm
Generalized Linear Latent Variable Modelsgllvm
Fitting Generalized Linear Mixed-Effects Models with Variational ApproximationglmmVA
Goodness of fit measures for a gllvmgoodnessOfFit
Kelp Forest community Dynamics: Cover of sessile organisms, Uniform Point Contactkelpforest
Log-likelihood of gllvmlogLik logLik.gllvm
Microbial community datamicrobialdata
Plot latent variables from gllvm modelordiplot ordiplot.gllvm
Plot phylogenetic random effects from gllvmphyloplot phyloplot.gllvm
Plot Diagnostics for an gllvm Objectplot.gllvm
Predict Method for gllvm Fitspredict predict.gllvm
Predict latent variables for gllvm FitspredictLVs predictLVs.gllvm
Predict co-occurrence from a gllvm objectpredictPairwise predictPairwise.gllvm
Predict species richness from a gllvm objectpredictSR predictSR.gllvm
Plot random slope coefficientsrandomCoefplot randomCoefplot.gllvm
Dunn-Smyth residuals for gllvm modelresiduals.gllvm
Dunn-Smyth residuals for species richness from a gllvm objectresiduals.predictSR.gllvm
Standard errors for gllvm modelse se.gllvm
Simulate data from gllvm fitsimulate simulate.gllvm
Skabbholmen island dataSkabbholmen
Summarizing gllvm model fitsplot.summary.gllvm print.summary.gllvm summary.gllvm
Update and Re-fit a gllvm Model Callupdate update.gllvm
Returns variance-covariance matrix of coefficients in a GLLVM.vcov vcov.gllvm
Calculate variance partitioningplot.VP.gllvm plotVarPartitioning plotVP print.VP.gllvm varPartitioning varPartitioning.gllvm VP VP.gllvm