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Demonstrate examples included in Stan

stan_demo.Rd

Stan includes a variety of examples and most of the BUGS example models that are translated into Stan modeling language. One example is chosen from a list created from matching user input and gets fitted in the demonstration.

Usage

stan_demo(model = character(0), 
            method = c("sampling", "optimizing", "meanfield", "fullrank"), ...)

Arguments

model

A character string for model name to specify which model will be used for demonstration. The default is an empty string, which prompts the user to select one the available models. If model = 0, a character vector of all models is returned without any user intervention. If model = i where i > 0, then the ith available model is chosen without user intervention, which is useful for testing.

method

Whether to call sampling (the default), optimizing, or one of the variants of vb for the demonstration

...

Further arguments passed to method.

Value

An S4 object of stanfit, unless model = 0, in which case a character vector of paths to available models is returned.

References

The Stan Development Team Stan Modeling Language User's Guide and Reference Manual. https://mc-stan.org/.

See also

sampling, optimizing

Examples

  # \dontrun{
     dogsfit <- stan_demo("dogs") # run the dogs model
#> 
#> > n_dogs <- 31
#> 
#> > n_trials <- 25
#> 
#> > y <- structure(c(0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
#> +     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
#> +     1, 0, 1, 1, 1, 0, 1, 1, 1,  .... [TRUNCATED] 
#> 
#> SAMPLING FOR MODEL 'dogs' NOW (CHAIN 1).
#> Chain 1: 
#> Chain 1: Gradient evaluation took 0.0002 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1: 
#> Chain 1: 
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#> Chain 1: 
#> Chain 1:  Elapsed Time: 2.053 seconds (Warm-up)
#> Chain 1:                2.064 seconds (Sampling)
#> Chain 1:                4.117 seconds (Total)
#> Chain 1: 
#> 
#> SAMPLING FOR MODEL 'dogs' NOW (CHAIN 2).
#> Chain 2: 
#> Chain 2: Gradient evaluation took 0.00019 seconds
#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.9 seconds.
#> Chain 2: Adjust your expectations accordingly!
#> Chain 2: 
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#> Chain 2: 
#> Chain 2:  Elapsed Time: 2.225 seconds (Warm-up)
#> Chain 2:                2.061 seconds (Sampling)
#> Chain 2:                4.286 seconds (Total)
#> Chain 2: 
#> 
#> SAMPLING FOR MODEL 'dogs' NOW (CHAIN 3).
#> Chain 3: 
#> Chain 3: Gradient evaluation took 0.000194 seconds
#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.94 seconds.
#> Chain 3: Adjust your expectations accordingly!
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#> Chain 3: 
#> Chain 3:  Elapsed Time: 2.174 seconds (Warm-up)
#> Chain 3:                1.965 seconds (Sampling)
#> Chain 3:                4.139 seconds (Total)
#> Chain 3: 
#> 
#> SAMPLING FOR MODEL 'dogs' NOW (CHAIN 4).
#> Chain 4: 
#> Chain 4: Gradient evaluation took 0.000194 seconds
#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.94 seconds.
#> Chain 4: Adjust your expectations accordingly!
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#> Chain 4: 
#> Chain 4:  Elapsed Time: 2.125 seconds (Warm-up)
#> Chain 4:                2.019 seconds (Sampling)
#> Chain 4:                4.144 seconds (Total)
#> Chain 4: 
     fit1 <- stan_demo(1) # run model_names[1]
#> 
#> > "score1" <- c(0.446, 0.334, -0.233, -0.304, -0.256, 
#> +     0.515, -0.652, 0.271, -0.556, 0.955, 0.307, -0.434, -0.272, 
#> +     -0.404, 0.415, 0.39, - .... [TRUNCATED] 
#> 
#> > "party" <- c(1, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 0, 
#> +     0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 
#> +     0, 0, 0, 1, 1, 0, 1, 0, 1 .... [TRUNCATED] 
#> 
#> > "x" <- c(0.62073, 0.50803, 0.38243, 0.29769, 0.32751, 
#> +     0.53766, 0.20003, 0.52211, 0.31267, 0.64143, 0.69113, 0.4386, 
#> +     0.30166, 0.25836,  .... [TRUNCATED] 
#> 
#> > "N" <- 357
#> 
#> SAMPLING FOR MODEL 'ideo_interactions' NOW (CHAIN 1).
#> Chain 1: 
#> Chain 1: Gradient evaluation took 9e-06 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds.
#> Chain 1: Adjust your expectations accordingly!
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#> Chain 1: 
#> Chain 1:  Elapsed Time: 0.11 seconds (Warm-up)
#> Chain 1:                0.127 seconds (Sampling)
#> Chain 1:                0.237 seconds (Total)
#> Chain 1: 
#> 
#> SAMPLING FOR MODEL 'ideo_interactions' NOW (CHAIN 2).
#> Chain 2: 
#> Chain 2: Gradient evaluation took 4e-06 seconds
#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
#> Chain 2: Adjust your expectations accordingly!
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#> Chain 2: 
#> Chain 2:  Elapsed Time: 0.11 seconds (Warm-up)
#> Chain 2:                0.127 seconds (Sampling)
#> Chain 2:                0.237 seconds (Total)
#> Chain 2: 
#> 
#> SAMPLING FOR MODEL 'ideo_interactions' NOW (CHAIN 3).
#> Chain 3: 
#> Chain 3: Gradient evaluation took 3e-06 seconds
#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
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#> Chain 3:  Elapsed Time: 0.111 seconds (Warm-up)
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#> Chain 3:                0.222 seconds (Total)
#> Chain 3: 
#> 
#> SAMPLING FOR MODEL 'ideo_interactions' NOW (CHAIN 4).
#> Chain 4: 
#> Chain 4: Gradient evaluation took 4e-06 seconds
#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
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#> Chain 4: 
  # }