R Interface to 'CmdStan'
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Documentation for package ‘cmdstanr’ version 0.6.0.9000
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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_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.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.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 |
| CmdStanMCMC | CmdStanMCMC objects |
| CmdStanMLE | CmdStanMLE objects |
| CmdStanModel | CmdStanModel objects |
| CmdStanR | CmdStanR: the R interface to CmdStan |
| cmdstanr | CmdStanR: the R interface to CmdStan |
| cmdstanr_example | Fit models for use in examples |
| CmdStanVB | CmdStanVB 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 |
| 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_data_file | Save output and data files |
| fit-method-save_latent_dynamics_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 --
| 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 |
| 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-optimize | Run Stan's optimization algorithms |
| 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 --
| 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_data_file | Save output and data files |
| save_latent_dynamics_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 |