Motivation | Load packages | Culcita example: near-complete separation | Gopher tortoise example: mitigate singular fit | Zero-inflation | TO DO/FIX ME | Development issues | References

Introduction/quick start | Preliminaries: packages and data | Sample timings

Overview | The AR(1) covariance structure | Demonstration on simulated data | Increasing the sample size | The unstructured covariance | The Toeplitz structure | Compound symmetry | Anova tables | Adding coordinate information | Ornstein–Uhlenbeck | Spatial correlations | Matérn | Gaussian | Exponential | A spatial covariance example | Mappings | Unstructured | Generalized latent variable model | Reduced-rank | Proportional | Equal | Construction of structured covariance matrices | References

model checking and diagnostics | Inference | Extracting coefficients, coefficient plots and tables | influence measures | Robust sandwich standard errors | to do

Warnings | Model convergence problem; non-positive-definite Hessian matrix; NA values for likelihood/AIC/etc. | Example 1. | Example 2. | Example 3. | Model convergence problem: eigenvalue problems | NA/NaN function evaluation | false convergence | Errors | NA/NaN gradient evaluation | gradient length

Overview | Setup | Salamander example | Metropolis-Hastings (DIY) | tmbstan | Sleep study example

Simulating from a fitted model | Simulating from scratch (de novo) | example 1: linear regression | example 2: random effects (including correlations) | example 3: AR1 model | FIXME/TO DO

Adding a family | C++ | modify glmmTMB.cpp | R code | modifying family.R | modifying glmmTMB.R | updating NAMESPACE | updating enum.R | Finishing up | Reinstall | Test | Additional distributional parameters | Adding a covariance structure | C++ code | Structure of a glmmTMB object

Notes on OpenMP support | System information

Beta dispersion model