# Generalized Linear Latent Variable Models

## Documentation for package ‘gllvm’ version 2.0.13

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

AICc | Corrected Akaike information criterion and number of observations
AICc.gllvm | Corrected Akaike information criterion and number of observations
anova.gllvm | Analysis Of Deviance for gllvm
beetle | ground beetle assemblages
coefplot | Plot covariate coefficients and confidence intervals
coefplot.gllvm | Plot covariate coefficients and confidence intervals
confint | Confidence intervals for model parameters
confint.gllvm | Confidence intervals for model parameters
ecoCoefs | Functions to extract ecological quantities of the latent variables from a GLLVM, if species are a quadratic function of the latent variables.
eSpider | Hunting spider data
fungi | Wood-decaying fungi data
getEnvironCor | Extract species covariances due to environmental random effects from gllvm object
getEnvironCor.gllvm | Extract species covariances due to environmental random effects from gllvm object
getEnvironCov | Extract species covariances due to environmental random effects from gllvm object
getEnvironCov.gllvm | Extract species covariances due to environmental random effects from gllvm object
getLoadings | Extract loadings
getLoadings.gllvm | Extract loadings
getLV | Extract latent variables
getLV.gllvm | Extract latent variables
getPredictErr | Extract prediction errors for latent variables from gllvm object
getPredictErr.gllvm | Extract prediction errors for latent variables from gllvm object
getResidualCor | Extract residual correlations from gllvm object
getResidualCor.gllvm | Extract residual correlations from gllvm object
getResidualCov | Extract residual covariance matrix from gllvm object
getResidualCov.gllvm | Extract residual covariance matrix from gllvm object
gllvm | Generalized Linear Latent Variable Models
glmmVA | Fitting Generalized Linear Mixed-Effects Models with Variational Approximation
goodnessOfFit | Goodness of fit measures for a gllvm
kelpforest | Kelp Forest community Dynamics: Cover of sessile organisms, Uniform Point Contact
logLik | Log-likelihood of gllvm
logLik.gllvm | Log-likelihood of gllvm
microbialdata | Microbial community data
nobs | Corrected Akaike information criterion and number of observations
nobs.gllvm | Corrected Akaike information criterion and number of observations
optima | Functions to extract ecological quantities of the latent variables from a GLLVM, if species are a quadratic function of the latent variables.
optima.gllvm | Functions to extract ecological quantities of the latent variables from a GLLVM, if species are a quadratic function of the latent variables.
ordiplot | Plot latent variables from gllvm model
ordiplot.gllvm | Plot latent variables from gllvm model
phyloplot | Plot phylogenetic random effects from gllvm
phyloplot.gllvm | Plot phylogenetic random effects from gllvm
plot.gllvm | Plot Diagnostics for an gllvm Object
plot.predictSR.gllvm | Predict species richness from a gllvm object
plot.summary.gllvm | Summarizing gllvm model fits
plot.VP.gllvm | Calculate variance partitioning
plotVarPartitioning | Calculate variance partitioning
plotVP | Calculate variance partitioning
predict | Predict Method for gllvm Fits
predict.gllvm | Predict Method for gllvm Fits
predict.glmmVA | Predict method for glmmVA objects
predictLVs | Predict latent variables for gllvm Fits
predictLVs.gllvm | Predict latent variables for gllvm Fits
predictPairwise | Predict co-occurrence from a gllvm object
predictPairwise.gllvm | Predict co-occurrence from a gllvm object
predictSR | Predict species richness from a gllvm object
predictSR.gllvm | Predict species richness from a gllvm object
print.summary.gllvm | Summarizing gllvm model fits
print.VP.gllvm | Calculate variance partitioning
randomCoefplot | Plot random slope coefficients
randomCoefplot.gllvm | Plot random slope coefficients
ranef | Generic function for extracting random effects
ranef.glmmVA | Extract random effects from a glmmVA object
residuals.gllvm | Dunn-Smyth residuals for gllvm model
residuals.predictSR.gllvm | Dunn-Smyth residuals for species richness from a gllvm object
se | Standard errors for gllvm model
se.gllvm | Standard errors for gllvm model
simulate | Simulate data from gllvm fit
simulate.gllvm | Simulate data from gllvm fit
Skabbholmen | Skabbholmen island data
summary.gllvm | Summarizing gllvm model fits
tolerances | Functions to extract ecological quantities of the latent variables from a GLLVM, if species are a quadratic function of the latent variables.
tolerances.gllvm | Functions to extract ecological quantities of the latent variables from a GLLVM, if species are a quadratic function of the latent variables.
update | Update and Re-fit a gllvm Model Call
update.gllvm | Update and Re-fit a gllvm Model Call
varPartitioning | Calculate variance partitioning
varPartitioning.gllvm | Calculate variance partitioning
vcov | Returns variance-covariance matrix of coefficients in a GLLVM.
vcov.gllvm | Returns variance-covariance matrix of coefficients in a GLLVM.
VP | Calculate variance partitioning
VP.gllvm | Calculate variance partitioning