Package: gllvm 2.0.12

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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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gllvm/json (API)

# 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

11.01 score 62 stars 1 packages 297 scripts 1.3k downloads 2 mentions 56 exports 12 dependencies

Last updated from:b113221fca. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK616
linux-devel-x86_64OK665
source / vignettesOK694
linux-release-arm64OK609
linux-release-x86_64OK692
macos-release-arm64OK565
macos-release-x86_64OK972
macos-oldrel-arm64OK465
macos-oldrel-x86_64OK1251
windows-develOK801
windows-releaseOK856
windows-oldrelOK777
wasm-releaseOK248

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.gllvmranefresiduals.predictSR.gllvmsese.gllvmsimulatesimulate.gllvmtolerancestolerances.gllvmupdate.gllvmvarPartitioningvarPartitioning.gllvmvcov.gllvmVP

Dependencies:alabamafishModlatticeMASSMatrixmgcvnlmenloptrnumDerivRcppRcppEigenTMB

Phylogenetic random effects
Phylogenetically structured environmental responses | Species ordering | Fit the model | Phylogenetic fourth corner model | References
Rendered fromvignette7.Rmdusingknitr::rmarkdown

Last update: 2026-05-08
Started: 2024-09-06

Analysing sparse ecological percent cover data using gllvm
Hurdle beta GLLVM | Example | Ordered beta GLLVM | Adjusting ordered beta to data without ones | Setting shape parameter to common across species | Model fit | References
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Last update: 2026-04-24
Started: 2024-09-13

Analysing multivariate abundance data using gllvm
Generalized linear latent variable models | Data input | Model-based ordination | Model with environmental variables | Studying co-occurrence patterns | Incorporating functional traits into fourth corner models | Example: Model-based inference | References
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Last update: 2026-04-23
Started: 2019-07-24

Assessing Convergence in gllvm models
How Convergence Is Assessed in Maximum Likelihood Estimation | Assessing Convergence for a GLLVM | What to Do If the Model Did Not Converge | Relative convergence, maximum number of iterations and optimization Algorithm | Modify Starting Values and many starting points | Approximation method: Variational, Extended Variational or Laplace approximation | Simplify variational covariance structure and two-step iteration for variance covariance estimation | Profiling the problematic parameter(s) | Modify or Simplify the Model
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Last update: 2026-04-01
Started: 2026-04-01

Correlation structures for latent variables and row effects
Structured and correlated community level random row effects | Structured and correlated latent variables | Structured latent variables | Correlated latent variables | References
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Last update: 2025-03-31
Started: 2024-09-25

Analysing high-dimensional microbial community data using gllvm
References
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Last update: 2025-03-28
Started: 2019-07-24

Ordination with predictors
Constrained ordination | Random slopes | Group-level unconstrained ordination | Fixed effects unconstrained ordination | Concurrent ordination | Partial constrained or concurrent ordination | References
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Last update: 2025-02-28
Started: 2021-07-01

Introduction to gllvm Part 1: Ordination
Introduction to gllvm | R package gllvm | Distributions | Data input | Example: Spiders | Data fitting | Residual analysis | Model selection | Exercises | Ordination | GLLVM as a model based ordination method | Ordination plot | Biplot | Environmental gradients
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Last update: 2024-11-20
Started: 2020-12-14

Introduction to gllvm Part 2: Species correlations
Introduction to gllvm | R package gllvm | Distributions | Data input | Example: Spiders | Data fitting | Model selection | Residual analysis | Exercises | Studying species correlations | Species correlations | Visualizing species correlations | Studying effects of covariates | Studying effects of environmental variables | Coefficient plot | Correlation matrix | Fourth corner models
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Last update: 2024-11-20
Started: 2020-12-14

How to use the quadratic response model
References
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Last update: 2024-09-06
Started: 2021-07-01

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 method for glmmVA objectspredict.glmmVA
Predict latent variables for gllvm FitspredictLVs predictLVs.gllvm
Predict co-occurrence from a gllvm objectpredictPairwise predictPairwise.gllvm
Predict species richness from a gllvm objectplot.predictSR.gllvm predictSR predictSR.gllvm
Plot random slope coefficientsrandomCoefplot randomCoefplot.gllvm
Generic function for extracting random effectsranef
Extract random effects from a glmmVA objectranef.glmmVA
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