RUNNING EXAMPLES IN cmdstan
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Unpacking Directories
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* $cmdstan is the directory in which cmdstan was unpacked

* $replication is the directory in which the replication examples were unpacked


Running Bernoulli MCMC example
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> cd $cmdstan
> make $replication/bernoulli
> cd $replication
> ./bernoulli sample data file=bernoulli.data.R random seed=2261934443 id=1 output file=output1.csv
> ./bernoulli sample data file=bernoulli.data.R random seed=2261934443 id=2 output file=output2.csv
> ./bernoulli sample data file=bernoulli.data.R random seed=2261934443 id=3 output file=output3.csv
> ./bernoulli sample data file=bernoulli.data.R random seed=2261934443 id=4 output file=output4.csv
> $cmdstan/bin/stansummary output*.csv


Running Bernoulli optimization example
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> cd $cmdstan
> make $replication/bernoulli
> cd $replication
> ./bernoulli optimize data file=bernoulli.data.R random seed=2261934443 id=1 output file=opt-fit.csv


Running Hierarchical binomial MCMC example
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> cd $cmdstan
> make $replication/hierarchical-binomial
> cd $replication
> ./hierarchical-binomial sample data file=hierarchical-binomial.data.R random seed=2261934443 id=1 output file=hier-output1.csv
> ./hierarchical-binomial sample data file=hierarchical-binomial.data.R random seed=2261934443 id=2 output file=hier-output2.csv
> ./hierarchical-binomial sample data file=hierarchical-binomial.data.R random seed=2261934443 id=3 output file=hier-output3.csv
> ./hierarchical-binomial sample data file=hierarchical-binomial.data.R random seed=2261934443 id=4 output file=hier-output4.csv
> $cmdstan/bin/stansummary hier-output*.csv



RUNNING EXAMPLES IN R
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First, you will need to install rstan from source or from CRAN.  Then

Running Bernoulli MCMC example
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> library("rstan")
> setwd("$replication")
> source("bernoulli.data.R")
> fit <- stan("bernoulli.stan", data = list(N = N, y = y))
> print(fit)


Running Bernoulli optimization example
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> bern_model <- stan_model("bernoulli.stan")
> opt_fit <- optimizing(bern_model, data = list(N = N, y = y))
> print(opt_fit)
