All functions

AICc(<gllvm>) nobs(<gllvm>)

Corrected Akaike information criterion and number of observations

anova(<gllvm>)

Analysis Of Deviance for gllvm

coefplot(<gllvm>)

Plot covariate coefficients and confidence intervals

confint(<gllvm>)

Confidence intervals for model parameters

optima(<gllvm>) tolerances(<gllvm>)

Functions to extract ecological quantities of the latent variables from a GLLVM, if species are a quadratic function of the latent variables.

getLV(<gllvm>)

Extract latent variables

getPredictErr(<gllvm>)

Extract prediction errors for latent variables from gllvm object

getResidualCor(<gllvm>)

Extract residual correlations from gllvm object

getResidualCov(<gllvm>)

Extract residual covariance matrix from gllvm object

gllvm()

Generalized Linear Latent Variable Models

logLik(<gllvm>)

Log-likelihood of gllvm

microbialdata

Microbial community data

ordiplot(<gllvm>)

Plot latent variables from gllvm model

plot(<gllvm>)

Plot Diagnostics for an gllvm Object

predict(<gllvm>)

Predict Method for gllvm Fits

predictLVs(<gllvm>)

Predict latent variables for gllvm Fits

randomCoefplot(<gllvm>)

Plot random slope coefficients

residuals(<gllvm>)

Dunn-Smyth residuals for gllvm model

se(<gllvm>)

Standard errors for gllvm model

simulate(<gllvm>)

Simulate data from gllvm fit

sim_bacteria

Simulated bacteria data

summary(<gllvm>) print(<summary.gllvm>)

Summarizing gllvm model fits

vcov(<gllvm>)

Returns variance-covariance matrix of coefficients in a GLLVM.