library(stanflow)
stan_logo()
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#> G08GLG80Gstanflow is a lightweight metapackage that sets up a Stan-based Bayesian workflow. It attaches a core toolkit for model analysis (posterior, loo, projpred, bayesplot, shinystan) and helps you install/configure Stan interfaces (cmdstanr, rstan, brms, rstanarm).
Attach stanflow
Startup messages list attached packages and any namespace clashes. You can re-print that status later with flow_check(), or just the namespace conflicts with stanflow_conflicts().
flow_check()
#> ── Attaching Stan processing packages ─────────────────── stanflow 0.0.0.9000 ──
#> ✔ bayesplot 1.15.0 ✔ projpred 2.10.0
#> ✔ loo 2.9.0 ✔ shinystan 2.7.0
#> ✔ posterior 1.6.1
#> ── Available Stan interfaces ────────────────────────────── setup_interface() ──
#> ✔ brms 2.23.0 • rstan 2.32.7
#> ✔ cmdstanr 0.9.0 • rstanarm 2.32.2
#> ── Conflicts ─────────────────────────────────────────── stanflow_conflicts() ──
#> ✖ brms::ar() masks stats::ar()
#> ✖ brms::do_call() masks projpred::do_call()
#> ✖ brms::rhat() masks posterior::rhat(), bayesplot::rhat()
#> ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
stanflow_conflicts()
#> ── Conflicts ─────────────────────────────────────────── stanflow_conflicts() ──
#> ✖ brms::ar() masks stats::ar()
#> ✖ brms::do_call() masks projpred::do_call()
#> ✖ brms::rhat() masks posterior::rhat(), bayesplot::rhat()
#> ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorsChoose interface backends
Use setup_interface() to install (if needed), attach, and configure interfaces. This example prefers the cmdstanr backend for brms. Running this command will attach both packages and ensure that brms calls rely on cmdstanr by default.
setup_interface(
interface = "brms",
brms_backend = "cmdstanr",
cores = 2,
quiet = TRUE,
force = TRUE # only required for non-interactive usage
)
#> ℹ Adding cmdstanr to setup because `brms_backend = 'cmdstanr'`
#> ℹ Attaching brms...
#> ℹ Configured brms: set `options(mc.cores = 2)` and `options(brms.backend = 'cmdstanr')`
#> ℹ Attaching cmdstanr...
#> ! CmdStan binaries are missing or force-reinstall requested.
#> ℹ Installing CmdStan (this can take some time)...
#> * Latest CmdStan release is v2.38.0
#> * Installing CmdStan v2.38.0 in /home/runner/.cmdstan/cmdstan-2.38.0
#> * Downloading cmdstan-2.38.0.tar.gz from GitHub...
#> * Download complete
#> * Unpacking archive...
#> * Building CmdStan binaries...
#> ar: creating stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a
#> ar: creating stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a
#> ar: creating stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a
#> ar: creating stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a
#> /home/runner/.cmdstan/cmdstan-2.38.0/stan/lib/stan_math/lib/tbb_2020.3/build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=gcc target=linux runtime=cc13.3.0_libc2.39_kernel6.11.0
#> In file included from ../tbb_2020.3/src/tbb/concurrent_hash_map.cpp:17:
#> ../tbb_2020.3/include/tbb/concurrent_hash_map.h:347:23: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
#> 347 | : public std::iterator<std::forward_iterator_tag,Value>
#> | ^~~~~~~~
#> In file included from /usr/include/c++/13/bits/stl_construct.h:61,
#> from /usr/include/c++/13/bits/stl_tempbuf.h:61,
#> from /usr/include/c++/13/memory:66,
#> from ../tbb_2020.3/include/tbb/tbb_stddef.h:452,
#> from ../tbb_2020.3/include/tbb/concurrent_hash_map.h:23:
#> /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
#> 127 | struct _GLIBCXX17_DEPRECATED iterator
#> | ^~~~~~~~
#> cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics
#> In file included from ../tbb_2020.3/src/tbb/concurrent_queue.cpp:22:
#> ../tbb_2020.3/include/tbb/internal/_concurrent_queue_impl.h:749:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
#> 749 | public std::iterator<std::forward_iterator_tag,Value> {
#> | ^~~~~~~~
#> In file included from /usr/include/c++/13/bits/stl_construct.h:61,
#> from /usr/include/c++/13/bits/stl_tempbuf.h:61,
#> from /usr/include/c++/13/memory:66,
#> from ../tbb_2020.3/include/tbb/tbb_stddef.h:452,
#> from ../tbb_2020.3/src/tbb/concurrent_queue.cpp:17:
#> /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
#> 127 | struct _GLIBCXX17_DEPRECATED iterator
#> | ^~~~~~~~
#> ../tbb_2020.3/include/tbb/internal/_concurrent_queue_impl.h:1013:21: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
#> 1013 | public std::iterator<std::forward_iterator_tag,Value> {
#> | ^~~~~~~~
#> /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
#> 127 | struct _GLIBCXX17_DEPRECATED iterator
#> | ^~~~~~~~
#> cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics
#> * Finished installing CmdStan to /home/runner/.cmdstan/cmdstan-2.38.0
#> CmdStan path set to: /home/runner/.cmdstan/cmdstan-2.38.0
#> ✔ Installing CmdStan (this can take some time)... ... done
#>
#> ℹ Configured cmdstanr: set `options(mc.cores = 2)`
#> ✔ Setup complete. brms, cmdstanr packages are attached; you do not need to run `library()`.
flow_check()
#> ── Attaching Stan processing packages ─────────────────── stanflow 0.0.0.9000 ──
#> ✔ bayesplot 1.15.0 ✔ projpred 2.10.0
#> ✔ loo 2.9.0 ✔ shinystan 2.7.0
#> ✔ posterior 1.6.1
#> ── Available Stan interfaces ────────────────────────────── setup_interface() ──
#> ✔ brms 2.23.0 • rstan 2.32.7
#> ✔ cmdstanr 0.9.0 • rstanarm 2.32.2
#> ── Conflicts ─────────────────────────────────────────── stanflow_conflicts() ──
#> ✖ brms::ar() masks stats::ar()
#> ✖ brms::do_call() masks projpred::do_call()
#> ✖ brms::rhat() masks posterior::rhat(), bayesplot::rhat()
#> ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorsIf you prefer RStan, you could just load it alongside brms.
setup_interface(
interface = c("rstan", "brms"),
cores = 2,
quiet = TRUE
)A tiny workflow
With the core packages attached, you can generate, summarise, and visualise draws immediately. Here we create fake draws, compute a simple loo object, and plot a quick histogram with bayesplot.
set.seed(0)
draws <- as_draws_df(
matrix(rnorm(4000), ncol = 1, dimnames = list(NULL, "theta"))
)
summarise_draws(draws, mean, sd, rhat, ess_bulk)
#> # A tibble: 1 × 5
#> variable mean sd rhat ess_bulk
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 theta 0.00750 0.990 1.00 4038.
mcmc_hist(draws, pars = "theta")
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.
log_lik <- matrix(rnorm(4000 * 10, -1, 0.2), ncol = 10)
loo(log_lik)
#>
#> Computed from 4000 by 10 log-likelihood matrix.
#>
#> Estimate SE
#> elpd_loo -10.2 0.0
#> p_loo 0.4 0.0
#> looic 20.4 0.0
#> ------
#> MCSE of elpd_loo is 0.0.
#> MCSE and ESS estimates assume independent draws (r_eff=1).
#>
#> All Pareto k estimates are good (k < 0.7).
#> See help('pareto-k-diagnostic') for details.Keep the flow fresh
Check whether your Stan workflow packages are up to date (stable releases by default, or dev builds with dev = TRUE). Set recursive to check the full dependency closure.
stanflow_update(recursive = TRUE)