Introduction | LM: A macro for complete linear models | Example logistic regression with mtcars | Example linear mixed model using ChickWeights | LINPRED | Generate a linear predictor from a formula | Factor/categorical covariates | Add a link function | Functions in formulas | Get default priors | Suppress the macro comments | Random effects | Include LINPRED in a complete model | LINPRED_PRIORS | FORLOOP | Writing Your Own Macros | Manually creating the macro | Using buildMacro to create the macro

Introduction | Working directory for running code | An example using nimble, jags, and stan. | Data vs. constants in nimble vs. JAGS and WinBUGS/OpenBUGS | MCMC efficiency and pace | What is timed | New MCMC configurations in nimble | Pre-defined configurations | Combining results from different calls to compareMCMCs. | Writing new comparison metrics. | Converting parameters to match each other across different MCMCs | Example | Converting parameters outside of compareMCMCs | How to specify conversions | Writing new page component plugins. | More about the make function. | Format of combined metrics provided to the make function. | Using a new page component | Pre-defined page components and defaults | Writing new MCMC package plugins.

What is nimble? | Getting help | The concept of using new distributions for ecological model components. | Illustration: A simple occupancy model | MCMC with both versions of the example occupancy model. | Build the model | Simulate data | Configure and build the MCMC | Compile the model and MCMC | Run the MCMC and extract the samples | Do it all for the new version of the model | Use the new version for something different: maximum likelihood or maximum a posteriori estimation. | Support for automatic differentiation with nimbleEcology. | Distributions provided in nimbleEcology | A note on static typing | Capture-recapture (dCJS) | CJS distributions in nimbleEcology | Hidden Markov models (HMMs) and Dynamic hidden Markov models (DHMMs) | HMM and DHMM distributions in nimbleEcology | Occupancy | Occupancy models in nimbleEcology | Dynamic occupancy | Dynamic occupancy models in nimbleEcology | N-mixture | N-mixture models in nimbleEcology