| Title: | Facilitates Bayesian Analysis using STAN with CmdStanR |
|---|---|
| Description: | Facilitates Bayesian Analysis using STAN with CmdStanR. This builds on smbr, which uses rstan. |
| Authors: | Seb Dalgarno [aut, cre] (ORCID: <https://orcid.org/0000-0002-3658-4517>) |
| Maintainer: | Seb Dalgarno <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.0.0.9000 |
| Built: | 2026-06-03 22:04:10 UTC |
| Source: | https://github.com/poissonconsulting/smbr2 |
Generic function for diagnosing analysis objects.
See documentation for specific methods:
diagnose(x, ...)diagnose(x, ...)
x |
An analysis object. |
... |
Additional arguments passed to methods. |
Diagnostic output (format depends on the analysis type).
Provides diagnostic information for CmdStan MCMC analysis objects.
For more details on diagnostics and how to address issues see:
https://mc-stan.org/docs/cmdstan-guide/diagnose.html
## S3 method for class 'cmdstan_mcmc_analysis' diagnose(x, ...)## S3 method for class 'cmdstan_mcmc_analysis' diagnose(x, ...)
x |
A cmdstan_mcmc_analysis object. |
... |
Additional arguments (unused). |
Output from CmdStan's diagnostic function.
Provides diagnostic information for CmdStan Pathfinder analysis objects.
For more details on diagnostics and how to address issues see:
https://mc-stan.org/docs/cmdstan-guide/diagnose.html
## S3 method for class 'cmdstan_pathfinder_analysis' diagnose(x, ...)## S3 method for class 'cmdstan_pathfinder_analysis' diagnose(x, ...)
x |
A cmdstan_pathfinder_analysis object. |
... |
Additional arguments (unused). |
Output from CmdStan's diagnostic function.
Provides diagnostic information for CmdStan Variational analysis objects.
For more details on diagnostics and how to address issues see:
https://mc-stan.org/docs/cmdstan-guide/diagnose.html
## S3 method for class 'cmdstan_variational_analysis' diagnose(x, ...)## S3 method for class 'cmdstan_variational_analysis' diagnose(x, ...)
x |
A cmdstan_variational_analysis object. |
... |
Additional arguments (unused). |
Output from CmdStan's diagnostic function.
Provides a one-row summary of Laplace approximation analysis results.
## S3 method for class 'cmdstan_laplace_analysis' glance(x, ...)## S3 method for class 'cmdstan_laplace_analysis' glance(x, ...)
x |
A |
... |
Additional arguments (unused). |
Diagnostic interpretation:
return_code: Should be 0. Non-zero values indicate the optimizer failed to find the posterior mode, invalidating the Laplace approximation.
A tibble with one row containing:
Number of observations in the dataset
Number of parameters
Logical indicating optimization convergence
Optimization return code for mode finding. Problem indicators: Non-zero values indicate mode-finding issues
Provides a one-row summary of key diagnostics for MCMC analysis results.
## S3 method for class 'cmdstan_mcmc_analysis' glance(x, ...)## S3 method for class 'cmdstan_mcmc_analysis' glance(x, ...)
x |
A |
... |
Additional arguments (unused). |
Diagnostic interpretation:
Divergent transitions: Should be 0. Any divergent transitions indicate the sampler had numerical issues and results may be unreliable.
Max treedepth: Should be 0 or very low. High values suggest the sampler
is working hard and may benefit from increased adapt_delta.
E-BFMI: Should be > 0.2. Values < 0.2 suggest poor adaptation, often requiring longer warmup or model reparameterization.
A tibble with one row containing:
Number of observations in the dataset
Number of parameters
Number of MCMC chains
Number of iterations per chain (post-warmup)
Thinning interval
Logical indicating convergence (TRUE if max R-hat < rhat threshold)
Number of divergent transitions across all chains. Problem indicators: Any value > 0 indicates sampling issues
Number of transitions that hit maximum tree depth. Problem indicators: Values > 0 may indicate inefficient sampling
Minimum Energy Bayesian Fraction of Missing Information across chains. Problem indicators: Values < 0.2 indicate poor adaptation/warmup
Provides a one-row summary of optimization analysis results.
## S3 method for class 'cmdstan_optimize_analysis' glance(x, ...)## S3 method for class 'cmdstan_optimize_analysis' glance(x, ...)
x |
A |
... |
Additional arguments (unused). |
Diagnostic interpretation:
return_code: Should be 0. Non-zero values indicate the optimizer encountered issues (e.g., 1 = max iterations reached, 2 = convergence issues).
A tibble with one row containing:
Number of observations in the dataset
Number of parameters
Logical indicating optimization convergence
Optimization return code. Problem indicators: Non-zero values indicate optimization issues
Provides a one-row summary of key diagnostics for Pathfinder analysis results.
## S3 method for class 'cmdstan_pathfinder_analysis' glance(x, ...)## S3 method for class 'cmdstan_pathfinder_analysis' glance(x, ...)
x |
A |
... |
Additional arguments (unused). |
Diagnostic interpretation:
return_code: Should be 0. Non-zero values indicate pathfinder failed to find a good approximation.
A tibble with one row containing:
Number of observations in the dataset
Number of parameters
Logical indicating pathfinder convergence
Pathfinder return code. Problem indicators: Non-zero values indicate pathfinder issues
Provides a one-row summary of variational inference analysis results.
## S3 method for class 'cmdstan_variational_analysis' glance(x, ...)## S3 method for class 'cmdstan_variational_analysis' glance(x, ...)
x |
A |
... |
Additional arguments (unused). |
Diagnostic interpretation:
return_code: Should be 0. Non-zero values indicate the variational algorithm failed to converge to a stable ELBO (Evidence Lower BOund).
A tibble with one row containing:
Number of observations in the dataset
Number of parameters
Logical indicating ELBO convergence
Optimization return code. Problem indicators: Non-zero values indicate convergence issues
Tests whether x is an object of class 'cmdstan_analysis'
is.cmdstan_analysis(x)is.cmdstan_analysis(x)
x |
The object to test. |
A flag indicating whether the test was positive.
Tests whether x is an object of class 'cmdstan_mcmc_analysis'
is.cmdstan_mcmc_analysis(x)is.cmdstan_mcmc_analysis(x)
x |
The object to test. |
A flag indicating whether the test was positive.
Print Method for CmdStan MCMC Diagnostics
## S3 method for class 'cmdstan_diagnostics' print(x, ...)## S3 method for class 'cmdstan_diagnostics' print(x, ...)
x |
A cmdstan_mcmc_diagnostics object. |
... |
Additional arguments (currently unused). |