pystan

PyStan, a Python interface to Stan, a platform for statistical modeling. Documentation: https://pystan.readthedocs.io

https://github.com/stan-dev/pystan

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
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Academic publication links
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Committers with academic emails
6 of 16 committers (37.5%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.7%) to scientific vocabulary

Keywords from Contributors

closember bayes posterior

Last synced: 10 months ago · JSON representation

Repository

PyStan, a Python interface to Stan, a platform for statistical modeling. Documentation: https://pystan.readthedocs.io

Basic Info

Host: GitHub
Owner: stan-dev
License: isc
Language: Python
Default Branch: main
Homepage:
Size: 219 KB

Statistics

Stars: 354
Watchers: 14
Forks: 60
Open Issues: 13
Releases: 0

Created almost 9 years ago · Last pushed about 2 years ago

Metadata Files

Readme Funding License

README.rst

******
PyStan
******

**PyStan** is a Python interface to Stan, a package for Bayesian inference.

Stan® is a state-of-the-art platform for statistical modeling and
high-performance statistical computation. Thousands of users rely on Stan for
statistical modeling, data analysis, and prediction in the social, biological,
and physical sciences, engineering, and business.

Notable features of PyStan include:

* Automatic caching of compiled Stan models
* Automatic caching of samples from Stan models
* An interface similar to that of RStan
* Open source software: ISC License

Getting started
===============

Install PyStan with ``pip install pystan``. PyStan runs on Linux and macOS. You will also need a C++ compiler such as gcc ≥9.0 or clang ≥10.0.

The following block of code shows how to use PyStan with a model which studied coaching effects across eight schools (see Section 5.5 of Gelman et al (2003)). This hierarchical model is often called the "eight schools" model.

.. code-block:: python

    import stan

    schools_code = """
    data {
      int J;         // number of schools
      array[J] real y;              // estimated treatment effects
      array[J] real sigma; // standard error of effect estimates
    }
    parameters {
      real mu;                // population treatment effect
      real tau;      // standard deviation in treatment effects
      vector[J] eta;          // unscaled deviation from mu by school
    }
    transformed parameters {
      vector[J] theta = mu + tau * eta;        // school treatment effects
    }
    model {
      target += normal_lpdf(eta | 0, 1);       // prior log-density
      target += normal_lpdf(y | theta, sigma); // log-likelihood
    }
    """

    schools_data = {"J": 8,
                    "y": [28,  8, -3,  7, -1,  1, 18, 12],
                    "sigma": [15, 10, 16, 11,  9, 11, 10, 18]}

    posterior = stan.build(schools_code, data=schools_data)
    fit = posterior.sample(num_chains=4, num_samples=1000)
    eta = fit["eta"]  # array with shape (8, 4000)
    df = fit.to_frame()  # pandas `DataFrame`


Citation
========

We appreciate citations as they let us discover what people have been doing
with the software. Citations also provide evidence of use which can help in
obtaining grant funding.

To cite PyStan in publications use:

Riddell, A., Hartikainen, A., & Carter, M. (2021). PyStan (3.0.0). https://pypi.org/project/pystan

Or use the following BibTeX entry::

    @misc{pystan,
      title = {pystan (3.0.0)},
      author = {Riddell, Allen and Hartikainen, Ari and Carter, Matthew},
      year = {2021},
      month = mar,
      howpublished = {PyPI}
    }

Please also cite Stan.

Owner

Name: Stan
Login: stan-dev
Kind: organization
Email: mc.stanislaw@gmail.com

Website: https://mc-stan.org
Repositories: 50
Profile: https://github.com/stan-dev

GitHub Events

Total

Issues event: 1
Watch event: 19
Issue comment event: 2
Fork event: 4

Last Year

Issues event: 1
Watch event: 19
Issue comment event: 2
Fork event: 4

Committers

Last synced: about 1 year ago

All Time

Total Commits: 237
Total Committers: 16
Avg Commits per committer: 14.813
Development Distribution Score (DDS): 0.114

Past Year

Commits: 20
Committers: 3
Avg Commits per committer: 6.667
Development Distribution Score (DDS): 0.15

Top Committers

Name	Email	Commits
Allen Riddell	r**n@i**u	210
Ari Hartikainen	h**i@g**m	5
Matthew Carter	m**2@l**k	5
Ari Hartikainen	a**n@r**i	4
Ari Hartikainen	a****n	2
A. Riddell	r**a@i**u	1
Anthony Sottile	a**e@u**u	1
Hartikainen Ari	a**n@a**i	1
Javier Burroni	j**i@g**m	1
Jonah Gabry	j**y@g**m	1
Michael Clerx	m**x@n**k	1
Semyeong Oh	s**h@g**m	1
ahartikainen	a**n@g**m	1
amas	a**1@g**m	1
er-eis	e**0@g**m	1
mikediessner	m**2@n**k	1

Committer Domains (Top 20 + Academic)

indiana.edu: 2 newcastle.ac.uk: 1 github.com: 1 nottingham.ac.uk: 1 aalto.fi: 1 umich.edu: 1 ramboll.fi: 1 liverpool.ac.uk: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time

Total issues: 77
Total pull requests: 48
Average time to close issues: 2 months
Average time to close pull requests: 16 days
Total issue authors: 48
Total pull request authors: 13
Average comments per issue: 3.21
Average comments per pull request: 1.17
Merged pull requests: 33
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 2.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

riddell-stan (15)
ahartikainen (11)
beew (2)
mrv-king (2)
ForceBru (2)
MichaelClerx (2)
ansarrice (2)
BrandonReeve (1)
coenvdm (1)
rrod515 (1)
W-L-W (1)
loulakiX (1)
8one6 (1)
ideasrule (1)
adaly (1)

Pull Request Authors

riddell-stan (34)
afuetterer (4)
ahartikainen (3)
abelowska (2)
monikavila (2)
cclauss (1)
thechopkins (1)
tillahoffmann (1)
MichaelClerx (1)
seeky-camelid (1)
er-eis (1)
asottile (1)

Top Labels

Issue Labels

bug (40) wontfix (24) help wanted (3) enhancement (3) question (1)

Pull Request Labels

Packages

Total packages: 3
Total downloads:
- pypi 595,958 last-month
Total docker downloads: 5,321,880

Total dependent packages: 42
(may contain duplicates)
Total dependent repositories: 1,424
(may contain duplicates)
Total versions: 83
Total maintainers: 2

pypi.org: pystan

Python interface to Stan, a package for Bayesian inference

Homepage: https://mc-stan.org
Documentation: https://pystan.readthedocs.io
License: ISC
Latest release: 3.10.0
published about 2 years ago

Versions: 67
Dependent Packages: 35
Dependent Repositories: 1,380
Downloads: 595,958 Last month
Docker Downloads: 5,321,880

Rankings

Downloads: 0.3%

Dependent repos count: 0.3%

Dependent packages count: 0.5%

Docker downloads count: 0.6%

Average: 1.8%

Stargazers count: 3.7%

Forks count: 5.7%

Maintainers (2)

ahartikainen ariddell

Last synced: 10 months ago

conda-forge.org: pystan

PyStan provides a Python interface to Stan, a package for Bayesian inference using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.

Homepage: http://mc-stan.org/interfaces/pystan.html
License: ISC
Latest release: 3.3.0
published almost 4 years ago

Versions: 10
Dependent Packages: 7
Dependent Repositories: 22

Rankings

Dependent repos count: 7.6%

Dependent packages count: 8.0%

Average: 16.5%

Stargazers count: 24.1%

Forks count: 26.1%

Last synced: 10 months ago

anaconda.org: pystan

PyStan provides a Python interface to Stan, a package for Bayesian inference using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.

Homepage: https://mc-stan.org/interfaces/pystan.html
License: ISC
Latest release: 3.10.0
published about 1 year ago

Versions: 6
Dependent Packages: 0
Dependent Repositories: 22

Rankings

Dependent repos count: 30.9%

Stargazers count: 36.7%

Forks count: 38.7%

Average: 39.3%

Dependent packages count: 51.0%

Last synced: 11 months ago

Dependencies

docs-requirements.txt pypi

sphinx *
sphinx-rtd-theme *

pyproject.toml pypi

autoflake ^1.4 develop
black 22.6.0 develop
flake8 ^4.0 develop
isort ^5.9 develop
mypy 0.961 develop
pandas ^1.0 develop
pytest ^6.2 develop
pytest-asyncio ^0.18.3 develop
sphinx ^4.2 develop
sphinx-rtd-theme ^1.0 develop
types-setuptools ^57.4 develop
aiohttp ^3.6
clikit ^0.6
httpstan ~4.8
numpy ^1.19
pysimdjson ^3.2
python ^3.8
setuptools *

.github/workflows/main.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

.github/workflows/publish.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite