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Magics for defining stan code in notebooks.

Project description

jupyterstan

jupyterstan is a package to help development of Stan models (using pystan) in jupyter notebooks.

The package is heavily based on Arvinds-ds stanmagic package, but provides an interface that simply returns a pystan.Model object.

In addition, it bundles Arvinds-ds stan_code_helper package to improve syntax highlighting for stan cells.

## Installation

To install the library:

pip install git+https://github.com/janfreyberg/jupyterstan.git

To enable the syntax highlighting:

jupyter nbextension install --py stan_syntax --sys-prefix
jupyter nbextension enable stan_syntax --py --sys-prefix

Usage

To use the magic in your notebook, you need to lead the extension:

%load_ext jupyterstan

To define a stan model inside a jupyter notebook, start a cell with the %%stan magic. You can also provide a variable name, which is the variable name that the pystan.Model object will be assigned to. For example:

%%stan paris_female_births
data {
    int male;
    int female;
}

parameters {
    real<lower=0, upper=1> p;
}

model {
    female ~ binomial(male + female, p);
}

Then, to use your defined model:

fit = paris_female_births.sampling(
    data={'male': 251527, 'female': 241945},
    iter=1000,
    chains=4
)

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