Package: gllvm 1.5.0

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'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • Skabbholmen - Skabbholmen island data
  • 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

On CRAN:

10.32 score 49 stars 1 packages 179 scripts 623 downloads 2 mentions 46 exports 13 dependencies

Last updated 18 hours agofrom:6f2ffc9e50. Checks:OK: 3 WARNING: 4 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-win-x86_64OKNov 22 2024
R-4.5-linux-x86_64OKNov 22 2024
R-4.4-win-x86_64NOTENov 22 2024
R-4.4-mac-x86_64WARNINGNov 22 2024
R-4.4-mac-aarch64WARNINGNov 22 2024
R-4.3-win-x86_64NOTENov 22 2024
R-4.3-mac-x86_64WARNINGNov 22 2024
R-4.3-mac-aarch64WARNINGNov 22 2024

Exports:AICcAICc.gllvmcoefplotcoefplot.gllvmconfint.gllvmgetEnvironCorgetEnvironCor.gllvmgetEnvironCovgetEnvironCov.gllvmgetLoadingsgetLoadings.gllvmgetLVgetLV.gllvmgetPredictErrgetPredictErr.gllvmgetResidualCorgetResidualCor.gllvmgetResidualCovgetResidualCov.gllvmgllvmlogLik.gllvmnobs.gllvmoptimaoptima.gllvmordiplotordiplot.gllvmphyloplotphyloplot.gllvmplotVarPartitioningplotVPpredict.gllvmpredictLVspredictLVs.gllvmprint.summary.gllvmrandomCoefplotrandomCoefplot.gllvmsese.gllvmsimulatesimulate.gllvmtolerancestolerances.gllvmvarPartitioningvarPartitioning.gllvmvcov.gllvmVP

Dependencies:alabamafishModlatticeMASSMatrixmgcvnlmenloptrnumDerivRcppRcppEigenstatmodTMB

Analysing high-dimensional microbial community data using gllvm

Jenni Niku

Rendered fromvignette2.rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-11-20
Started: 2019-07-24

Analysing multivariate abundance data using gllvm

Jenni Niku

Rendered fromvignette1.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-11-20
Started: 2019-07-24

Analysing sparse ecological percent cover data using gllvm

Pekka Korhonen

Rendered fromvignette8.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-09-19
Started: 2024-09-13

Correlation structures for latent variables and row effects

Jenni Niku

Rendered fromvignette9.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-11-20
Started: 2024-09-25

How to use the quadratic response model

Bert van der Veen

Rendered fromvignette5.Rmdusingknitr::rmarkdownon Nov 22 2024.

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

Introduction to gllvm Part 1: Ordination

Jenni Niku

Rendered fromvignette3.rmdusingknitr::rmarkdownon Nov 22 2024.

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

Introduction to gllvm Part 2: Species correlations

Jenni Niku

Rendered fromvignette4.rmdusingknitr::rmarkdownon Nov 22 2024.

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

Ordination with predictors

Bert van der Veen

Rendered fromvignette6.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-11-22
Started: 2021-07-01

Phylogenetic random effects

Bert van der Veen

Rendered fromvignette7.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-11-05
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
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
Plot random slope coefficientsrandomCoefplot randomCoefplot.gllvm
Dunn-Smyth residuals for gllvm modelresiduals.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
Calculate variance partitioningplotVarPartitioning plotVP varPartitioning varPartitioning.gllvm VP
Returns variance-covariance matrix of coefficients in a GLLVM.vcov vcov.gllvm