CmdStanMCMC objects — CmdStanMCMC • cmdstanr
Description: A CmdStanMCMC object is the fitted model object returned by the $sample() method of a CmdStanModel object. Like CmdStanModel objects, CmdStanMCMC objects are R6 objects.

# CmdStanMCMC objects

Source: `R/fit.R`
`CmdStanMCMC.Rd`

A `CmdStanMCMC` object is the fitted model object returned by the `$sample()` method of a `CmdStanModel` object. Like `CmdStanModel` objects, `CmdStanMCMC` objects are R6 objects.

## Methods

`CmdStanMCMC` objects have the following associated methods, all of which have their own (linked) documentation pages.

### Extract contents of fitted model object

Method | Description
`$draws()` | Return posterior draws using formats from the posterior package.
`$sampler_diagnostics()` | Return sampler diagnostics as a `draws_array`.
`$lp()` | Return the total log probability density (`target`).
`$inv_metric()` | Return the inverse metric for each chain.
`$init()` | Return user-specified initial values.
`$metadata()` | Return a list of metadata gathered from the CmdStan CSV files.
`$num_chains()` | Return the number of MCMC chains.
`$code()` | Return Stan code as a character vector.

### Summarize inferences and diagnostics

Method | Description
`$print()` | Run `posterior::summarise_draws()`.
`$summary()` | Run `posterior::summarise_draws()`.
`$diagnostic_summary()` | Get summaries of sampler diagnostics and warning messages.
`$cmdstan_summary()` | Run and print CmdStan's `bin/stansummary`.
`$cmdstan_diagnose()` | Run and print CmdStan's `bin/diagnose`.
`$loo()` | Run `loo::loo.array()` for approximate LOO-CV

### Save fitted model object and temporary files

Method | Description
`$save_object()` | Save fitted model object to a file.
`$save_output_files()` | Save output CSV files to a specified location.
`$save_data_file()` | Save JSON data file to a specified location.
`$save_latent_dynamics_files()` | Save diagnostic CSV files to a specified location.

### Report run times, console output, return codes

Method | Description
`$output()` | Return the stdout and stderr of all chains or pretty print the output for a single chain.
`$time()` | Report total and chain-specific run times.
`$return_codes()` | Return the return codes from the CmdStan runs.

### Expose Stan functions and additional methods to R

Method | Description
`$expose_functions()` | Expose Stan functions for use in R.
`$init_model_methods()` | Expose methods for log-probability, gradients, parameter constraining and unconstraining.
`$log_prob()` | Calculate log-prob.
`$grad_log_prob()` | Calculate log-prob and gradient.
`$hessian()` | Calculate log-prob, gradient, and hessian.
`$constrain_variables()` | Transform a set of unconstrained parameter values to the constrained scale.
`$unconstrain_variables()` | Transform a set of parameter values to the unconstrained scale.
`$unconstrain_draws()` | Transform all parameter draws to the unconstrained scale.
`$variable_skeleton()` | Helper function to re-structure a vector of constrained parameter values.

## See also

The CmdStanR website (mc-stan.org/cmdstanr) for online documentation and tutorials.

The Stan and CmdStan documentation:

- Stan documentation: mc-stan.org/users/documentation

- CmdStan User’s Guide: mc-stan.org/docs/cmdstan-guide

Other fitted model objects: `CmdStanDiagnose`, `CmdStanGQ`, `CmdStanMLE`, `CmdStanVB`