Create a new
CmdStanModel
object from a file containing a Stan program
or from an existing Stan executable. The CmdStanModel
object stores the
path to a Stan program and compiled executable (once created), and provides
methods for fitting the model using Stan's algorithms.
See the compile
and ...
arguments for control over whether and how
compilation happens.
cmdstan_model(stan_file = NULL, exe_file = NULL, compile = TRUE, ...)
stan_file | (string) The path to a |
---|---|
exe_file | (string) The path to an existing Stan model executable. Can
be provided instead of or in addition to |
compile | (logical) Do compilation? The default is |
... | Optionally, additional arguments to pass to the
|
A CmdStanModel
object.
install_cmdstan()
, $compile()
,
$check_syntax()
The CmdStanR website (mc-stan.org/cmdstanr) for online documentation and tutorials.
The Stan and CmdStan documentation:
Stan documentation: mc-stan.org/users/documentation
CmdStan User’s Guide: mc-stan.org/docs/cmdstan-guide
# \dontrun{ library(cmdstanr) library(posterior) library(bayesplot) color_scheme_set("brightblue") # Set path to CmdStan # (Note: if you installed CmdStan via install_cmdstan() with default settings # then setting the path is unnecessary but the default below should still work. # Otherwise use the `path` argument to specify the location of your # CmdStan installation.) set_cmdstan_path(path = NULL)#># Create a CmdStanModel object from a Stan program, # here using the example model that comes with CmdStan file <- file.path(cmdstan_path(), "examples/bernoulli/bernoulli.stan") mod <- cmdstan_model(file) mod$print()#> data { #> int<lower=0> N; #> array[N] int<lower=0,upper=1> y; // or int<lower=0,upper=1> y[N]; #> } #> parameters { #> real<lower=0,upper=1> theta; #> } #> model { #> theta ~ beta(1,1); // uniform prior on interval 0,1 #> y ~ bernoulli(theta); #> }# Data as a named list (like RStan) stan_data <- list(N = 10, y = c(0,1,0,0,0,0,0,0,0,1)) # Run MCMC using the 'sample' method fit_mcmc <- mod$sample( data = stan_data, seed = 123, chains = 2, parallel_chains = 2 )#> Running MCMC with 2 parallel chains... #> #> Chain 1 Iteration: 1 / 2000 [ 0%] (Warmup) #> Chain 1 Iteration: 100 / 2000 [ 5%] (Warmup) #> Chain 1 Iteration: 200 / 2000 [ 10%] (Warmup) #> Chain 1 Iteration: 300 / 2000 [ 15%] (Warmup) #> Chain 1 Iteration: 400 / 2000 [ 20%] (Warmup) #> Chain 1 Iteration: 500 / 2000 [ 25%] (Warmup) #> Chain 1 Iteration: 600 / 2000 [ 30%] (Warmup) #> Chain 1 Iteration: 700 / 2000 [ 35%] (Warmup) #> Chain 1 Iteration: 800 / 2000 [ 40%] (Warmup) #> Chain 1 Iteration: 900 / 2000 [ 45%] (Warmup) #> Chain 1 Iteration: 1000 / 2000 [ 50%] (Warmup) #> Chain 1 Iteration: 1001 / 2000 [ 50%] (Sampling) #> Chain 1 Iteration: 1100 / 2000 [ 55%] (Sampling) #> Chain 1 Iteration: 1200 / 2000 [ 60%] (Sampling) #> Chain 1 Iteration: 1300 / 2000 [ 65%] (Sampling) #> Chain 1 Iteration: 1400 / 2000 [ 70%] (Sampling) #> Chain 1 Iteration: 1500 / 2000 [ 75%] (Sampling) #> Chain 1 Iteration: 1600 / 2000 [ 80%] (Sampling) #> Chain 1 Iteration: 1700 / 2000 [ 85%] (Sampling) #> Chain 1 Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 1 Iteration: 1900 / 2000 [ 95%] (Sampling) #> Chain 1 Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 2 Iteration: 1 / 2000 [ 0%] (Warmup) #> Chain 2 Iteration: 100 / 2000 [ 5%] (Warmup) #> Chain 2 Iteration: 200 / 2000 [ 10%] (Warmup) #> Chain 2 Iteration: 300 / 2000 [ 15%] (Warmup) #> Chain 2 Iteration: 400 / 2000 [ 20%] (Warmup) #> Chain 2 Iteration: 500 / 2000 [ 25%] (Warmup) #> Chain 2 Iteration: 600 / 2000 [ 30%] (Warmup) #> Chain 2 Iteration: 700 / 2000 [ 35%] (Warmup) #> Chain 2 Iteration: 800 / 2000 [ 40%] (Warmup) #> Chain 2 Iteration: 900 / 2000 [ 45%] (Warmup) #> Chain 2 Iteration: 1000 / 2000 [ 50%] (Warmup) #> Chain 2 Iteration: 1001 / 2000 [ 50%] (Sampling) #> Chain 2 Iteration: 1100 / 2000 [ 55%] (Sampling) #> Chain 2 Iteration: 1200 / 2000 [ 60%] (Sampling) #> Chain 2 Iteration: 1300 / 2000 [ 65%] (Sampling) #> Chain 2 Iteration: 1400 / 2000 [ 70%] (Sampling) #> Chain 2 Iteration: 1500 / 2000 [ 75%] (Sampling) #> Chain 2 Iteration: 1600 / 2000 [ 80%] (Sampling) #> Chain 2 Iteration: 1700 / 2000 [ 85%] (Sampling) #> Chain 2 Iteration: 1800 / 2000 [ 90%] (Sampling) #> Chain 2 Iteration: 1900 / 2000 [ 95%] (Sampling) #> Chain 2 Iteration: 2000 / 2000 [100%] (Sampling) #> Chain 1 finished in 0.0 seconds. #> Chain 2 finished in 0.0 seconds. #> #> Both chains finished successfully. #> Mean chain execution time: 0.0 seconds. #> Total execution time: 0.2 seconds. #># Use 'posterior' package for summaries fit_mcmc$summary()#> # A tibble: 2 × 10 #> variable mean median sd mad q5 q95 rhat ess_bulk ess_tail #> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 lp__ -7.30 -7.03 0.721 0.380 -8.82 -6.75 1.00 902. 1006. #> 2 theta 0.247 0.233 0.122 0.129 0.0786 0.470 1.00 762. 712.#> # A draws_array: 1000 iterations, 2 chains, and 2 variables #> , , variable = lp__ #> #> chain #> iteration 1 2 #> 1 -6.8 -6.8 #> 2 -6.9 -6.8 #> 3 -7.0 -7.0 #> 4 -6.9 -7.1 #> 5 -6.7 -7.0 #> #> , , variable = theta #> #> chain #> iteration 1 2 #> 1 0.28 0.21 #> 2 0.19 0.20 #> 3 0.16 0.17 #> 4 0.20 0.36 #> 5 0.25 0.34 #> #> # ... with 995 more iterations#> # A draws_df: 1000 iterations, 2 chains, and 2 variables #> lp__ theta #> 1 -6.8 0.28 #> 2 -6.9 0.19 #> 3 -7.0 0.16 #> 4 -6.9 0.20 #> 5 -6.7 0.25 #> 6 -7.1 0.36 #> 7 -9.0 0.55 #> 8 -7.2 0.15 #> 9 -6.8 0.23 #> 10 -7.5 0.42 #> # ... with 1990 more draws #> # ... hidden reserved variables {'.chain', '.iteration', '.draw'}#># Call CmdStan's diagnose and stansummary utilities fit_mcmc$cmdstan_diagnose()#> Processing csv files: /var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpmzUYEz/bernoulli-202203181224-1-1bc5e7.csv, /var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpmzUYEz/bernoulli-202203181224-2-1bc5e7.csv #> #> Checking sampler transitions treedepth. #> Treedepth satisfactory for all transitions. #> #> Checking sampler transitions for divergences. #> No divergent transitions found. #> #> Checking E-BFMI - sampler transitions HMC potential energy. #> E-BFMI satisfactory. #> #> Effective sample size satisfactory. #> #> Split R-hat values satisfactory all parameters. #> #> Processing complete, no problems detected.fit_mcmc$cmdstan_summary()#> Inference for Stan model: bernoulli_model #> 2 chains: each with iter=(1000,1000); warmup=(0,0); thin=(1,1); 2000 iterations saved. #> #> Warmup took (0.0050, 0.0050) seconds, 0.010 seconds total #> Sampling took (0.018, 0.016) seconds, 0.034 seconds total #> #> Mean MCSE StdDev 5% 50% 95% N_Eff N_Eff/s R_hat #> #> lp__ -7.3 2.6e-02 0.72 -8.8 -7.0 -6.8 781 22972 1.0 #> accept_stat__ 0.92 8.3e-03 0.13 0.64 0.97 1.0 2.3e+02 6.9e+03 1.0e+00 #> stepsize__ 0.95 7.9e-02 0.079 0.87 1.0 1.0 1.0e+00 3.0e+01 2.0e+13 #> treedepth__ 1.4 1.1e-02 0.48 1.0 1.0 2.0 1.9e+03 5.5e+04 1.0e+00 #> n_leapfrog__ 2.5 1.4e-01 1.3 1.0 3.0 3.0 8.9e+01 2.6e+03 1.0e+00 #> divergent__ 0.00 nan 0.00 0.00 0.00 0.00 nan nan nan #> energy__ 7.8 3.6e-02 1.00 6.8 7.5 9.6 7.7e+02 2.3e+04 1.0e+00 #> #> theta 0.25 4.3e-03 0.12 0.079 0.23 0.47 796 23422 1.0 #> #> Samples were drawn using hmc with nuts. #> For each parameter, N_Eff is a crude measure of effective sample size, #> and R_hat is the potential scale reduction factor on split chains (at #> convergence, R_hat=1).# For models fit using MCMC, if you like working with RStan's stanfit objects # then you can create one with rstan::read_stan_csv() # stanfit <- rstan::read_stan_csv(fit_mcmc$output_files()) # Run 'optimize' method to get a point estimate (default is Stan's LBFGS algorithm) # and also demonstrate specifying data as a path to a file instead of a list my_data_file <- file.path(cmdstan_path(), "examples/bernoulli/bernoulli.data.json") fit_optim <- mod$optimize(data = my_data_file, seed = 123)#> Initial log joint probability = -9.51104 #> Iter log prob ||dx|| ||grad|| alpha alpha0 # evals Notes #> 6 -5.00402 0.000103557 2.55661e-07 1 1 9 #> Optimization terminated normally: #> Convergence detected: relative gradient magnitude is below tolerance #> Finished in 0.1 seconds.fit_optim$summary()#> # A tibble: 2 × 2 #> variable estimate #> <chr> <dbl> #> 1 lp__ -5.00 #> 2 theta 0.2# Run 'variational' method to approximate the posterior (default is meanfield ADVI) fit_vb <- mod$variational(data = stan_data, seed = 123)#> ------------------------------------------------------------ #> EXPERIMENTAL ALGORITHM: #> This procedure has not been thoroughly tested and may be unstable #> or buggy. The interface is subject to change. #> ------------------------------------------------------------ #> Gradient evaluation took 6e-06 seconds #> 1000 transitions using 10 leapfrog steps per transition would take 0.06 seconds. #> Adjust your expectations accordingly! #> Begin eta adaptation. #> Iteration: 1 / 250 [ 0%] (Adaptation) #> Iteration: 50 / 250 [ 20%] (Adaptation) #> Iteration: 100 / 250 [ 40%] (Adaptation) #> Iteration: 150 / 250 [ 60%] (Adaptation) #> Iteration: 200 / 250 [ 80%] (Adaptation) #> Success! Found best value [eta = 1] earlier than expected. #> Begin stochastic gradient ascent. #> iter ELBO delta_ELBO_mean delta_ELBO_med notes #> 100 -6.262 1.000 1.000 #> 200 -6.263 0.500 1.000 #> 300 -6.307 0.336 0.007 MEDIAN ELBO CONVERGED #> Drawing a sample of size 1000 from the approximate posterior... #> COMPLETED. #> Finished in 0.1 seconds.fit_vb$summary()#> # A tibble: 3 × 7 #> variable mean median sd mad q5 q95 #> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 lp__ -7.18 -6.94 0.588 0.259 -8.36 -6.75 #> 2 lp_approx__ -0.515 -0.221 0.692 0.303 -2.06 -0.00257 #> 3 theta 0.263 0.246 0.115 0.113 0.106 0.481#># Specifying initial values as a function fit_mcmc_w_init_fun <- mod$sample( data = stan_data, seed = 123, chains = 2, refresh = 0, init = function() list(theta = runif(1)) )#> Running MCMC with 2 sequential chains... #> #> Chain 1 finished in 0.0 seconds. #> Chain 2 finished in 0.0 seconds. #> #> Both chains finished successfully. #> Mean chain execution time: 0.0 seconds. #> Total execution time: 0.3 seconds. #>fit_mcmc_w_init_fun_2 <- mod$sample( data = stan_data, seed = 123, chains = 2, refresh = 0, init = function(chain_id) { # silly but demonstrates optional use of chain_id list(theta = 1 / (chain_id + 1)) } )#> Running MCMC with 2 sequential chains... #> #> Chain 1 finished in 0.0 seconds. #> Chain 2 finished in 0.0 seconds. #> #> Both chains finished successfully. #> Mean chain execution time: 0.0 seconds. #> Total execution time: 0.3 seconds. #>fit_mcmc_w_init_fun_2$init()#> [[1]] #> [[1]]$theta #> [1] 0.5 #> #> #> [[2]] #> [[2]]$theta #> [1] 0.3333333 #> #># Specifying initial values as a list of lists fit_mcmc_w_init_list <- mod$sample( data = stan_data, seed = 123, chains = 2, refresh = 0, init = list( list(theta = 0.75), # chain 1 list(theta = 0.25) # chain 2 ) )#> Running MCMC with 2 sequential chains... #> #> Chain 1 finished in 0.0 seconds. #> Chain 2 finished in 0.0 seconds. #> #> Both chains finished successfully. #> Mean chain execution time: 0.0 seconds. #> Total execution time: 0.3 seconds. #>fit_optim_w_init_list <- mod$optimize( data = stan_data, seed = 123, init = list( list(theta = 0.75) ) )#> Initial log joint probability = -11.6657 #> Iter log prob ||dx|| ||grad|| alpha alpha0 # evals Notes #> 6 -5.00402 0.000237915 9.55309e-07 1 1 9 #> Optimization terminated normally: #> Convergence detected: relative gradient magnitude is below tolerance #> Finished in 0.1 seconds.fit_optim_w_init_list$init()#> [[1]] #> [[1]]$theta #> [1] 0.75 #> #># }