R Interface to Stan

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Documentation for package ‘rstan’ version 2.32.6

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A C D E G I L M N O P Q R S T U V misc

rstan-package RStan - the R interface to Stan

-- A --

as.array.stanfit Create array, matrix, or data.frame objects from samples in a 'stanfit' object
as.data.frame.stanfit Create array, matrix, or data.frame objects from samples in a 'stanfit' object
as.matrix.stanfit Create array, matrix, or data.frame objects from samples in a 'stanfit' object
As.mcmc.list Create an mcmc.list from a stanfit object

-- C --

check_divergences Check HMC diagnostics after sampling
check_energy Check HMC diagnostics after sampling
check_hmc_diagnostics Check HMC diagnostics after sampling
check_treedepth Check HMC diagnostics after sampling
constrain_pars 'log_prob' and 'grad_log_prob' functions
constrain_pars-method 'log_prob' and 'grad_log_prob' functions

-- D --

dim.stanfit Create array, matrix, or data.frame objects from samples in a 'stanfit' object
dimnames.stanfit Create array, matrix, or data.frame objects from samples in a 'stanfit' object

-- E --

ess_bulk Convergence and efficiency diagnostics for Markov Chains
ess_tail Convergence and efficiency diagnostics for Markov Chains
expose_stan_functions Expose user-defined Stan functions to R for testing and simulation
extract Extract samples from a fitted Stan model
extract-method Extract samples from a fitted Stan model
extract_sparse_parts Extract the compressed representation of a sparse matrix

-- G --

get_adaptation_info Class 'stanfit': fitted Stan model
get_adaptation_info-method Class 'stanfit': fitted Stan model
get_bfmi Check HMC diagnostics after sampling
get_cppcode Class representing model compiled from C++
get_cppcode-method Class representing model compiled from C++
get_cppo_mode Class 'stanfit': fitted Stan model
get_cppo_mode-method Class 'stanfit': fitted Stan model
get_cxxflags Class representing model compiled from C++
get_cxxflags-method Class representing model compiled from C++
get_divergent_iterations Check HMC diagnostics after sampling
get_elapsed_time Class 'stanfit': fitted Stan model
get_elapsed_time-method Class 'stanfit': fitted Stan model
get_inits Class 'stanfit': fitted Stan model
get_inits-method Class 'stanfit': fitted Stan model
get_logposterior Class 'stanfit': fitted Stan model
get_logposterior-method Class 'stanfit': fitted Stan model
get_low_bfmi_chains Check HMC diagnostics after sampling
get_max_treedepth_iterations Check HMC diagnostics after sampling
get_num_divergent Check HMC diagnostics after sampling
get_num_leapfrog_per_iteration Check HMC diagnostics after sampling
get_num_max_treedepth Check HMC diagnostics after sampling
get_num_upars 'log_prob' and 'grad_log_prob' functions
get_num_upars-method 'log_prob' and 'grad_log_prob' functions
get_posterior_mean Class 'stanfit': fitted Stan model
get_posterior_mean-method Class 'stanfit': fitted Stan model
get_rng Expose user-defined Stan functions to R for testing and simulation
get_sampler_params Class 'stanfit': fitted Stan model
get_sampler_params-method Class 'stanfit': fitted Stan model
get_seed Class 'stanfit': fitted Stan model
get_seed-method Class 'stanfit': fitted Stan model
get_seeds Class 'stanfit': fitted Stan model
get_seeds-method Class 'stanfit': fitted Stan model
get_stancode Class 'stanfit': fitted Stan model
get_stancode-method Class 'stanfit': fitted Stan model
get_stancode-method Class representing model compiled from C++
get_stanmodel Class 'stanfit': fitted Stan model
get_stanmodel-method Class 'stanfit': fitted Stan model
get_stream Expose user-defined Stan functions to R for testing and simulation
gqs Draw samples of generated quantities from a Stan model
gqs-method Draw samples of generated quantities from a Stan model
grad_log_prob 'log_prob' and 'grad_log_prob' functions
grad_log_prob-method 'log_prob' and 'grad_log_prob' functions

-- I --

is.array.stanfit Create array, matrix, or data.frame objects from samples in a 'stanfit' object

-- L --

log_prob 'log_prob' and 'grad_log_prob' functions
log_prob-method 'log_prob' and 'grad_log_prob' functions
loo Approximate leave-one-out cross-validation
loo-method Approximate leave-one-out cross-validation
loo.stanfit Approximate leave-one-out cross-validation
lookup Look up the Stan function that corresponds to a R function or name.
loo_moment_match Moment matching for efficient approximate leave-one-out cross-validation (LOO)
loo_moment_match-method Moment matching for efficient approximate leave-one-out cross-validation (LOO)
loo_moment_match.stanfit Moment matching for efficient approximate leave-one-out cross-validation (LOO)

-- M --

makeconf_path Obtain the full path of file 'Makeconf'
monitor Compute summaries of MCMC draws and monitor convergence

-- N --

names.stanfit Create array, matrix, or data.frame objects from samples in a 'stanfit' object
names<-.stanfit Create array, matrix, or data.frame objects from samples in a 'stanfit' object
nlist Created named lists

-- O --

optimizing Obtain a point estimate by maximizing the joint posterior
optimizing-method Obtain a point estimate by maximizing the joint posterior

-- P --

pairs.stanfit Create a matrix of output plots from a 'stanfit' object
plot-method Plots for stanfit objects
plot.sbc Simulation Based Calibration (sbc)
print.sbc Simulation Based Calibration (sbc)
print.simsummary Compute summaries of MCMC draws and monitor convergence
print.stanfit Print a summary for a fitted model represented by a 'stanfit' object

-- Q --

quietgg ggplot2 for RStan

-- R --

read_rdump Read data in an R dump file to a list
read_stan_csv Read CSV files of samples generated by (R)Stan into a 'stanfit' object
Rhat Convergence and efficiency diagnostics for Markov Chains
rstan RStan - the R interface to Stan
rstan-plotting-functions RStan Plotting Functions
rstan.package.skeleton Create a Skeleton for a New Source Package with Stan Programs
rstan_ggtheme_options Set default appearance options
rstan_gg_options Set default appearance options
rstan_options Set and read options used in RStan

-- S --

sampling Draw samples from a Stan model
sampling-method Draw samples from a Stan model
sbc Simulation Based Calibration (sbc)
set_cppo Defunct function to set the compiler optimization level
sflist2stanfit Merge a list of stanfit objects into one
show-method Class 'stanfit': fitted Stan model
show-method Class representing model compiled from C++
stan Fit a model with Stan
stanc Translate Stan model specification to C++ code
stanc_builder Translate Stan model specification to C++ code
stanfit Class 'stanfit': fitted Stan model
stanfit-class Class 'stanfit': fitted Stan model
stanmodel-class Class representing model compiled from C++
stan_ac ggplot2 for RStan
stan_demo Demonstrate examples included in Stan
stan_dens ggplot2 for RStan
stan_diag RStan Diagnostic plots
stan_ess RStan Diagnostic plots
stan_hist ggplot2 for RStan
stan_mcse RStan Diagnostic plots
stan_model Construct a Stan model
stan_par RStan Diagnostic plots
stan_plot ggplot2 for RStan
stan_rdump Dump the data for a Stan model to R dump file in the limited format that Stan can read.
stan_rhat RStan Diagnostic plots
stan_scat ggplot2 for RStan
stan_trace ggplot2 for RStan
stan_version Obtain the version of Stan
summary-method Summary method for stanfit objects

-- T --

traceplot Markov chain traceplots
traceplot-method Markov chain traceplots

-- U --

unconstrain_pars 'log_prob' and 'grad_log_prob' functions
unconstrain_pars-method 'log_prob' and 'grad_log_prob' functions

-- V --

vb Run Stan's variational algorithm for approximate posterior sampling
vb-method Run Stan's variational algorithm for approximate posterior sampling

-- misc --

[.simsummary Compute summaries of MCMC draws and monitor convergence