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Posteriors Sampling Diagnostic

Source: R/diagnostic_posterior.R
diagnostic_posterior.Rd

Extract diagnostic metrics (Effective Sample Size (ESS), Rhat and Monte Carlo Standard Error MCSE).

Usage

diagnostic_posterior(posterior, ...)

# Default S3 method
diagnostic_posterior(posterior, diagnostic = c("ESS", "Rhat"), ...)

# S3 method for class 'stanreg'
diagnostic_posterior(
  posterior,
  diagnostic = "all",
  effects = c("fixed", "random", "all"),
  component = c("location", "all", "conditional", "smooth_terms", "sigma",
    "distributional", "auxiliary"),
  parameters = NULL,
  ...
)

# S3 method for class 'brmsfit'
diagnostic_posterior(
  posterior,
  diagnostic = "all",
  effects = c("fixed", "random", "all"),
  component = c("conditional", "zi", "zero_inflated", "all"),
  parameters = NULL,
  ...
)

Arguments

posterior

A stanreg, stanfit, brmsfit, or blavaan object.

...

Currently not used.

diagnostic

Diagnostic metrics to compute. Character (vector) or list with one or more of these options: "ESS", "Rhat", "MCSE" or "all".

effects

Should parameters for fixed effects, random effects or both be returned? Only applies to mixed models. May be abbreviated.

component

Should all predictor variables, predictor variables for the conditional model, the zero-inflated part of the model, the dispersion term or the instrumental variables be returned? Applies to models with zero-inflated and/or dispersion formula, or to models with instrumental variable (so called fixed-effects regressions). May be abbreviated. Note that the conditional component is also called count or mean component, depending on the model.

parameters

Regular expression pattern that describes the parameters that should be returned.

Details

Effective Sample (ESS) should be as large as possible, although for most applications, an effective sample size greater than 1000 is sufficient for stable estimates (Bürkner, 2017). The ESS corresponds to the number of independent samples with the same estimation power as the N autocorrelated samples. It is is a measure of "how much independent information there is in autocorrelated chains" (Kruschke 2015, p182-3).

Rhat should be the closest to 1. It should not be larger than 1.1 (Gelman and Rubin, 1992) or 1.01 (Vehtari et al., 2019). The split Rhat statistic quantifies the consistency of an ensemble of Markov chains.

Monte Carlo Standard Error (MCSE) is another measure of accuracy of the chains. It is defined as standard deviation of the chains divided by their effective sample size (the formula for mcse() is from Kruschke 2015, p. 187). The MCSE "provides a quantitative suggestion of how big the estimation noise is".

References

  • Gelman, A., & Rubin, D. B. (1992). Inference from iterative simulation using multiple sequences. Statistical science, 7(4), 457-472.

  • Vehtari, A., Gelman, A., Simpson, D., Carpenter, B., and Bürkner, P. C. (2019). Rank-normalization, folding, and localization: An improved Rhat for assessing convergence of MCMC. arXiv preprint arXiv:1903.08008.

  • Kruschke, J. (2014). Doing Bayesian data analysis: A tutorial with R, JAGS, and Stan. Academic Press.

Examples

# \donttest{
# rstanarm models
# -----------------------------------------------
model <- suppressWarnings(
  rstanarm::stan_glm(mpg ~ wt + gear, data = mtcars, chains = 2, iter = 200, refresh = 0)
)
diagnostic_posterior(model)
#>     Parameter      Rhat      ESS       MCSE
#> 1 (Intercept) 0.9980336 182.6025 0.36283152
#> 2        gear 0.9917174 206.3058 0.06519599
#> 3          wt 0.9978902 186.7773 0.04770867

# brms models
# -----------------------------------------------
model <- brms::brm(mpg ~ wt + cyl, data = mtcars)
#> Compiling Stan program...
#> Start sampling
#> 
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
#> Chain 1: 
#> Chain 1: Gradient evaluation took 7e-06 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1: 
#> Chain 1: 
#> Chain 1: Iteration:    1 / 2000 [  0%]  (Warmup)
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#> Chain 1: 
#> Chain 1:  Elapsed Time: 0.023 seconds (Warm-up)
#> Chain 1:                0.018 seconds (Sampling)
#> Chain 1:                0.041 seconds (Total)
#> Chain 1: 
#> 
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
#> Chain 2: 
#> Chain 2: Gradient evaluation took 3e-06 seconds
#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
#> Chain 2: Adjust your expectations accordingly!
#> Chain 2: 
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#> Chain 2: 
#> Chain 2:  Elapsed Time: 0.025 seconds (Warm-up)
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#> Chain 2:                0.05 seconds (Total)
#> Chain 2: 
#> 
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 3).
#> Chain 3: 
#> Chain 3: Gradient evaluation took 4e-06 seconds
#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
#> Chain 3: Adjust your expectations accordingly!
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#> Chain 3: 
#> Chain 3:  Elapsed Time: 0.024 seconds (Warm-up)
#> Chain 3:                0.021 seconds (Sampling)
#> Chain 3:                0.045 seconds (Total)
#> Chain 3: 
#> 
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 4).
#> Chain 4: 
#> Chain 4: Gradient evaluation took 3e-06 seconds
#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
#> Chain 4: Adjust your expectations accordingly!
#> Chain 4: 
#> Chain 4: 
#> Chain 4: Iteration:    1 / 2000 [  0%]  (Warmup)
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#> Chain 4: 
#> Chain 4:  Elapsed Time: 0.022 seconds (Warm-up)
#> Chain 4:                0.023 seconds (Sampling)
#> Chain 4:                0.045 seconds (Total)
#> Chain 4: 
diagnostic_posterior(model)
#>     Parameter     Rhat      ESS       MCSE
#> 1 b_Intercept 1.000297 4618.359 0.02593799
#> 2       b_cyl 1.003470 1868.916 0.01002953
#> 3        b_wt 1.003250 1697.213 0.01926801
# }