Introduction | Listing and loading models | Example data | Sampling settings | A test model | Zheng et al (2006) Barrier Effects Model | Count responses | Structure of the fitted object | Interpreting the fit | Count responses (alternative parametrization) | Dichotomous responses | Trichotomous responses | Zheng et al (2006) Group Prevalence Model | Maltiel et al (2015) Barrier Effects Model | Maltiel et al (2015) Random Degree Model | Maltiel et al (2015) Transmission Bias Model | Maltiel et al (2015) Combined Model | Where to go from here | References

Summary statistics | Extracting posterior draws/samples | Structured draws similar to rstan::extract() | Plotting the draws of a vector

Introduction | Installing CmdStan | Compiling a model | Running MCMC | Posterior summary statistics | Summaries from the posterior package | CmdStan's stansummary utility | Posterior draws | Extracting draws | Plotting draws | Sampler diagnostics | Extracting diagnostic values for each iteration and chain | Sampler diagnostic warnings and summaries | CmdStan's diagnose utility | Running optimization and variational inference | Optimization | Laplace Approximation | Variational (ADVI) | Variational (Pathfinder) | Running standalone generated quantities | Saving fitted model objects | Comparison with RStan | Additional resources

Introduction | Compilation | Immediate compilation | Delayed compilation | Pedantic check | Stan model variables | Executable location | Processing data | Named list of R objects | JSON file | R dump file | Writing CmdStan output to CSV | Default temporary files | Non-temporary files | Reading CmdStan output into R | Lazy CSV reading | read_cmdstan_csv() | as_cmdstan_fit() | Saving and accessing advanced algorithm info (latent dynamics) | Developing using CmdStanR | Compiling Stan models during package installation | Troubleshooting and debugging

Introduction | Adding profiling statements to a Stan program | Accessing the profiling information from R | Comparing to a faster version of the model | Per-gradient timings and autodiff variable counts | Accessing and saving the profile files | References

Option 1: Using RStan for all chunks | Option 2: Using CmdStanR for all chunks | Example | Option 3: Using both RStan and CmdStanR in the same R Markdown document | Caching chunks | Running interactively