Package: gllvm 1.4.7

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 appoximations, 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/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:

On CRAN:

44 exports 48 stars 3.73 score 13 dependencies 1 dependents 2 mentions 124 scripts 565 downloads

Last updated 2 days agofrom:2b8495f4ea. Checks:ERROR: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesFAILSep 18 2024
R-4.5-win-x86_64WARNINGAug 13 2024
R-4.5-linux-x86_64WARNINGAug 13 2024
R-4.4-win-x86_64WARNINGAug 13 2024
R-4.4-mac-x86_64WARNINGAug 13 2024
R-4.4-mac-aarch64WARNINGAug 13 2024
R-4.3-win-x86_64WARNINGAug 13 2024
R-4.3-mac-x86_64WARNINGAug 13 2024
R-4.3-mac-aarch64WARNINGAug 13 2024

Exports:AICcAICc.gllvmcoefplotcoefplot.gllvmconfint.gllvmgetEnvironCorgetEnvironCor.gllvmgetEnvironCovgetEnvironCov.gllvmgetLoadingsgetLoadings.gllvmgetLVgetLV.gllvmgetPredictErrgetPredictErr.gllvmgetResidualCorgetResidualCor.gllvmgetResidualCovgetResidualCov.gllvmgllvmlogLik.gllvmnobs.gllvmoptimaoptima.gllvmordiplotordiplot.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 Sep 18 2024.

Last update: 2024-03-19
Started: 2019-07-24

Analysing multivariate abundance data using gllvm

Jenni Niku

Rendered fromvignette1.Rmdusingknitr::rmarkdownon Sep 18 2024.

Last update: 2024-09-06
Started: 2019-07-24

Analysing sparse ecological percent cover data using gllvm

Pekka Korhonen

Rendered fromvignette8.Rmdusingknitr::rmarkdownon Sep 18 2024.

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

How to use the quadratic response model

Bert van der Veen

Rendered fromvignette5.Rmdusingknitr::rmarkdownon Sep 18 2024.

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

Introduction to gllvm Part 1: Ordination

Jenni Niku

Rendered fromvignette3.rmdusingknitr::rmarkdownon Sep 18 2024.

Last update: 2024-09-06
Started: 2020-12-14

Introduction to gllvm Part 2: Species correlations

Jenni Niku

Rendered fromvignette4.rmdusingknitr::rmarkdownon Sep 18 2024.

Last update: 2024-09-06
Started: 2020-12-14

Ordination with predictors

Bert van der Veen

Rendered fromvignette6.Rmdusingknitr::rmarkdownon Sep 18 2024.

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

Phylogenetic random effects

Bert van der Veen

Rendered fromvignette7.Rmdusingknitr::rmarkdownon Sep 18 2024.

Last update: 2024-09-12
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
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 datakelpforest
Log-likelihood of gllvmlogLik logLik.gllvm
Microbial community datamicrobialdata
Plot latent variables from gllvm modelordiplot ordiplot.gllvm
Plot Diagnostics for an gllvm Objectplot.gllvm
Plot variance partitioningplotVarPartitioning plotVP
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
SBC LTER: Reef: Kelp Forest Community Dynamics: Cover of sessile organisms, Uniform Point ContactSBC_LTER
Standard errors for gllvm modelse se.gllvm
Simulate data from gllvm fitsimulate simulate.gllvm
Skabbholmen island dataSkabbholmen
Summarizing gllvm model fitsprint.summary.gllvm summary.gllvm
Calculate variance partitioningvarPartitioning varPartitioning.gllvm VP
Returns variance-covariance matrix of coefficients in a GLLVM.vcov vcov.gllvm