Phylogenetically structured environmental responses | Species ordering | Fit the model | Phylogenetic fourth corner model | References

Hurdle beta GLLVM | Example | Ordered beta GLLVM | Adjusting ordered beta to data without ones | Setting shape parameter to common across species | Model fit | References

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

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

Structured and correlated community level random row effects | Structured and correlated latent variables | Structured latent variables | Correlated latent variables | References

References

Constrained ordination | Random slopes | Group-level unconstrained ordination | Fixed effects unconstrained ordination | Concurrent ordination | Partial constrained or concurrent ordination | References

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

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

References