# R Interface to 'CmdStan'

## Documentation for package ‘cmdstanr’ version 0.8.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A C D E F G H I L M N O P R S T U V W

cmdstanr-package | CmdStanR: the R interface to CmdStan

## -- A --

as.CmdStanDiagnose | Coercion methods for CmdStan objects
as.CmdStanGQ | Coercion methods for CmdStan objects
as.CmdStanLaplace | Coercion methods for CmdStan objects
as.CmdStanMCMC | Coercion methods for CmdStan objects
as.CmdStanMLE | Coercion methods for CmdStan objects
as.CmdStanPathfinder | Coercion methods for CmdStan objects
as.CmdStanVB | Coercion methods for CmdStan objects
as_cmdstan_fit | Read CmdStan CSV files into R
as_draws | Create a 'draws' object from a CmdStanR fitted model object
as_draws.CmdStanGQ | Create a 'draws' object from a CmdStanR fitted model object
as_draws.CmdStanLaplace | Create a 'draws' object from a CmdStanR fitted model object
as_draws.CmdStanMCMC | Create a 'draws' object from a CmdStanR fitted model object
as_draws.CmdStanMLE | Create a 'draws' object from a CmdStanR fitted model object
as_draws.CmdStanPathfinder | Create a 'draws' object from a CmdStanR fitted model object
as_draws.CmdStanVB | Create a 'draws' object from a CmdStanR fitted model object
as_mcmc.list | Convert 'CmdStanMCMC' to 'mcmc.list'

## -- C --

check_cmdstan_toolchain | Install CmdStan or clean and rebuild an existing installation
check_syntax | Check syntax of a Stan program
CmdStanDiagnose | CmdStanDiagnose objects
CmdStanGQ | CmdStanGQ objects
CmdStanLaplace | CmdStanLaplace objects
CmdStanMCMC | CmdStanMCMC objects
CmdStanMLE | CmdStanMLE objects
CmdStanModel | CmdStanModel objects
CmdStanPathfinder | CmdStanPathfinder objects
CmdStanR | CmdStanR: the R interface to CmdStan
cmdstanr | CmdStanR: the R interface to CmdStan
cmdstanr_example | Fit models for use in examples
cmdstanr_global_options | CmdStanR global options
CmdStanVB | CmdStanVB objects
cmdstan_coercion | Coercion methods for CmdStan objects
cmdstan_diagnose | Run CmdStan's 'stansummary' and 'diagnose' utilities
cmdstan_make_local | Install CmdStan or clean and rebuild an existing installation
cmdstan_model | Create a new CmdStanModel object
cmdstan_path | Get or set the file path to the CmdStan installation
cmdstan_summary | Run CmdStan's 'stansummary' and 'diagnose' utilities
cmdstan_version | Get or set the file path to the CmdStan installation
code | Return Stan code
compile | Compile a Stan program
config_files | Save output and data files
constrain_variables | Transform a set of unconstrained parameter values to the constrained scale

## -- D --

data_file | Save output and data files
diagnose | Run Stan's diagnose method
diagnostic_summary | Sampler diagnostic summaries and warnings
draws | Extract posterior draws
draws_to_csv | Write posterior draws objects to CSV files suitable for running standalone generated quantities with CmdStan.

## -- E --

eng_cmdstan | CmdStan knitr engine for Stan
expose_functions | Expose Stan functions to R

## -- F --

fit-method-cmdstan_diagnose | Run CmdStan's 'stansummary' and 'diagnose' utilities
fit-method-cmdstan_summary | Run CmdStan's 'stansummary' and 'diagnose' utilities
fit-method-code | Return Stan code
fit-method-constrain_variables | Transform a set of unconstrained parameter values to the constrained scale
fit-method-data_file | Save output and data files
fit-method-diagnostic_summary | Sampler diagnostic summaries and warnings
fit-method-draws | Extract posterior draws
fit-method-expose_functions | Expose Stan functions to R
fit-method-gradients | Extract gradients after diagnostic mode
fit-method-grad_log_prob | Calculate the log-probability and the gradient w.r.t. each input for a given vector of unconstrained parameters
fit-method-hessian | Calculate the log-probability , the gradient w.r.t. each input, and the hessian for a given vector of unconstrained parameters
fit-method-init | Extract user-specified initial values
fit-method-init_model_methods | Compile additional methods for accessing the model log-probability function and parameter constraining and unconstraining.
fit-method-inv_metric | Extract inverse metric (mass matrix) after MCMC
fit-method-latent_dynamics_files | Save output and data files
fit-method-log_prob | Calculate the log-probability given a provided vector of unconstrained parameters.
fit-method-loo | Leave-one-out cross-validation (LOO-CV)
fit-method-lp | Extract log probability (target)
fit-method-metadata | Extract metadata from CmdStan CSV files
fit-method-mle | Extract (penalized) maximum likelihood estimate after optimization
fit-method-num_chains | Extract number of chains after MCMC
fit-method-output | Access console output
fit-method-output_files | Save output and data files
fit-method-print | Compute a summary table of estimates and diagnostics
fit-method-profiles | Return profiling data
fit-method-profile_files | Save output and data files
fit-method-return_codes | Extract return codes from CmdStan
fit-method-sampler_diagnostics | Extract sampler diagnostics after MCMC
fit-method-save_config_files | Save output and data files
fit-method-save_data_file | Save output and data files
fit-method-save_latent_dynamics_files | Save output and data files
fit-method-save_metric_files | Save output and data files
fit-method-save_object | Save fitted model object to a file
fit-method-save_output_files | Save output and data files
fit-method-save_profile_files | Save output and data files
fit-method-summary | Compute a summary table of estimates and diagnostics
fit-method-time | Report timing of CmdStan runs
fit-method-unconstrain_draws | Transform all parameter draws to the unconstrained scale
fit-method-unconstrain_variables | Transform a set of parameter values to the unconstrained scale
fit-method-variable_skeleton | Return the variable skeleton for 'relist'
format | Run stanc's auto-formatter on the model code.

## -- G --

generate_quantities | Run Stan's standalone generated quantities method
gradients | Extract gradients after diagnostic mode
grad_log_prob | Calculate the log-probability and the gradient w.r.t. each input for a given vector of unconstrained parameters

## -- H --

hessian | Calculate the log-probability , the gradient w.r.t. each input, and the hessian for a given vector of unconstrained parameters

## -- I --

init | Extract user-specified initial values
init_model_methods | Compile additional methods for accessing the model log-probability function and parameter constraining and unconstraining.
install_cmdstan | Install CmdStan or clean and rebuild an existing installation
inv_metric | Extract inverse metric (mass matrix) after MCMC

## -- L --

laplace | Run Stan's Laplace algorithm
latent_dynamics_files | Save output and data files
log_prob | Calculate the log-probability given a provided vector of unconstrained parameters.
loo | Leave-one-out cross-validation (LOO-CV)
lp | Extract log probability (target)
lp_approx | Extract log probability (target)

## -- M --

metadata | Extract metadata from CmdStan CSV files
metric_files | Save output and data files
mle | Extract (penalized) maximum likelihood estimate after optimization
model-method-check_syntax | Check syntax of a Stan program
model-method-compile | Compile a Stan program
model-method-diagnose | Run Stan's diagnose method
model-method-expose_functions | Expose Stan functions to R
model-method-format | Run stanc's auto-formatter on the model code.
model-method-generate-quantities | Run Stan's standalone generated quantities method
model-method-laplace | Run Stan's Laplace algorithm
model-method-optimize | Run Stan's optimization algorithms
model-method-pathfinder | Run Stan's Pathfinder Variational Inference Algorithm
model-method-sample | Run Stan's MCMC algorithms
model-method-sample_mpi | Run Stan's MCMC algorithms with MPI
model-method-variables | Input and output variables of a Stan program
model-method-variational | Run Stan's variational approximation algorithms

## -- N --

num_chains | Extract number of chains after MCMC

## -- O --

optimize | Run Stan's optimization algorithms
output | Access console output
output_files | Save output and data files

## -- P --

pathfinder | Run Stan's Pathfinder Variational Inference Algorithm
print.CmdStanMCMC | Compute a summary table of estimates and diagnostics
print.CmdStanMLE | Compute a summary table of estimates and diagnostics
print.CmdStanVB | Compute a summary table of estimates and diagnostics
print_example_program | Fit models for use in examples
profiles | Return profiling data
profile_files | Save output and data files

## -- R --

read_cmdstan_csv | Read CmdStan CSV files into R
rebuild_cmdstan | Install CmdStan or clean and rebuild an existing installation
register_knitr_engine | Register CmdStanR's knitr engine for Stan
return_codes | Extract return codes from CmdStan

## -- S --

sample | Run Stan's MCMC algorithms
sampler_diagnostics | Extract sampler diagnostics after MCMC
sample_mpi | Run Stan's MCMC algorithms with MPI
save_config_files | Save output and data files
save_data_file | Save output and data files
save_latent_dynamics_files | Save output and data files
save_metric_files | Save output and data files
save_object | Save fitted model object to a file
save_output_files | Save output and data files
save_profile_files | Save output and data files
set_cmdstan_path | Get or set the file path to the CmdStan installation
summary | Compute a summary table of estimates and diagnostics

## -- T --

time | Report timing of CmdStan runs

## -- U --

unconstrain_draws | Transform all parameter draws to the unconstrained scale
unconstrain_variables | Transform a set of parameter values to the unconstrained scale

## -- V --

variables | Input and output variables of a Stan program
variable_skeleton | Return the variable skeleton for 'relist'
variational | Run Stan's variational approximation algorithms

## -- W --

write_stan_file | Write Stan code to a file
write_stan_json | Write data to a JSON file readable by CmdStan