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# Based on https://github.com/actions/starter-workflows/blob/main/pages/static.yml | ||
name: documentation | ||
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on: | ||
push: | ||
branches: [$default-branch] | ||
workflow_dispatch: | ||
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permissions: | ||
contents: write | ||
pages: write | ||
id-token: write | ||
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jobs: | ||
docs: | ||
environment: | ||
name: github-pages | ||
url: ${{ steps.deployment.outputs.page_url }} | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v4 | ||
- name: Set up Python for Docs | ||
uses: actions/setup-python@v5 | ||
with: | ||
python-version: '3.x' | ||
- name: Install sphinx | ||
run: | | ||
python -m pip install --upgrade pip | ||
pip install sphinx sphinx-rtd-theme | ||
- name: Build Docs | ||
run: | | ||
sphinx-build docs docs/_build | ||
- name: Upload artifact | ||
uses: actions/upload-pages-artifact@v3 | ||
with: | ||
path: './docs/_build' | ||
- name: Deploy to GitHub Pages | ||
id: deployment | ||
uses: actions/deploy-pages@v4 |
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# Minimal makefile for Sphinx documentation | ||
# | ||
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# You can set these variables from the command line, and also | ||
# from the environment for the first two. | ||
SPHINXOPTS ?= | ||
SPHINXBUILD ?= sphinx-build | ||
SOURCEDIR = . | ||
BUILDDIR = _build | ||
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# Put it first so that "make" without argument is like "make help". | ||
help: | ||
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) | ||
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.PHONY: help Makefile | ||
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# Catch-all target: route all unknown targets to Sphinx using the new | ||
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). | ||
%: Makefile | ||
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) |
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# Configuration file for the Sphinx documentation builder. | ||
# | ||
# For the full list of built-in configuration values, see the documentation: | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html | ||
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# path | ||
import os | ||
import sys | ||
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sys.path.insert(0, os.path.abspath('..')) | ||
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# -- Project information ----------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information | ||
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project = 'mssm' | ||
copyright = '2024, Joshua Krause' | ||
author = 'Joshua Krause' | ||
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# -- General configuration --------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration | ||
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extensions = ['sphinx.ext.autodoc'] | ||
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templates_path = ['_templates'] | ||
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] | ||
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# -- Options for HTML output ------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output | ||
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html_theme = 'sphinx_rtd_theme' | ||
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html_theme_options = { | ||
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# Toc options | ||
'collapse_navigation': True, | ||
'sticky_navigation': True, | ||
'navigation_depth': 8 | ||
} | ||
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html_static_path = ['_static'] |
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.. mssm documentation master file, created by | ||
sphinx-quickstart on Fri Sep 27 15:37:49 2024. | ||
You can adapt this file completely to your liking, but it should at least | ||
contain the root `toctree` directive. | ||
mssm documentation | ||
================== | ||
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This is the documentation for the **exposed** API of ``mssm``. The source code for internal functions is available on `GitHub <https://github.com/JoKra1/mssm>`_ and can be | ||
consulted to understand their implementation. ``mssm`` is a toolbox to estimate Generalized Additive Mixed Models (GAMMs), Generalized Additive Mixed Models of Location Scale | ||
and Shape (GAMMLSS), and more general (mixed) smooth models in the sense defined by `Wood, Pya, & Säfken (2016) <https://doi.org/10.1080/01621459.2016.1180986>`_. | ||
mssm is an excellent choice for the modeling of multi-level time-series data, often estimating additive models with separate smooths for thousands of levels in a couple of minutes. | ||
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Currently, ``mssm`` supports Gaussian (G)AMMs (:func:`mssm.src.python.exp_fam.Gaussian`), Gamma GAMMs (:func:`mssm.src.python.exp_fam.Gamma`), and Binomial GAMMs (:func:`mssm.src.python.exp_fam.Binomial`). | ||
For GAMMLSS models, Gaussian models (:func:`mssm.src.python.exp_fam.GAUMLSS`), Gamma models (:func:`mssm.src.python.exp_fam.GAMMALS`), and Multionimal models (:func:`mssm.src.python.exp_fam.MULNOMLSS`) are supported. | ||
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If you are missing a family, don't worry - all you need to do is to implement the :func:`mssm.src.python.exp_fam.Family` template class for GAMM models and the :func:`mssm.src.python.exp_fam.GAMLSSFamily` template class for GAMMLSS models. | ||
To estimate the most general kind of smooth model, you only have to implement the :func:`mssm.src.python.exp_fam.GENSMOOTHFamily` template class. | ||
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To get started with ``mssm`` the tutorial and visualization code available `here <https://github.com/JoKra1/mssm_tutorials>`_ might also be helpful. | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
:caption: Contents: | ||
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modules |
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@ECHO OFF | ||
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pushd %~dp0 | ||
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REM Command file for Sphinx documentation | ||
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if "%SPHINXBUILD%" == "" ( | ||
set SPHINXBUILD=sphinx-build | ||
) | ||
set SOURCEDIR=. | ||
set BUILDDIR=_build | ||
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%SPHINXBUILD% >NUL 2>NUL | ||
if errorlevel 9009 ( | ||
echo. | ||
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx | ||
echo.installed, then set the SPHINXBUILD environment variable to point | ||
echo.to the full path of the 'sphinx-build' executable. Alternatively you | ||
echo.may add the Sphinx directory to PATH. | ||
echo. | ||
echo.If you don't have Sphinx installed, grab it from | ||
echo.https://www.sphinx-doc.org/ | ||
exit /b 1 | ||
) | ||
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if "%1" == "" goto help | ||
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% | ||
goto end | ||
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:help | ||
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% | ||
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:end | ||
popd |
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src | ||
=== | ||
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.. toctree:: | ||
:maxdepth: 4 | ||
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mssm |
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mssm package | ||
============ | ||
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Subpackages | ||
----------- | ||
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.. toctree:: | ||
:maxdepth: 4 | ||
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mssm.src | ||
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Submodules | ||
---------- | ||
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mssm.models module | ||
------------------ | ||
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.. automodule:: mssm.models | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: | ||
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mssm.src.python package | ||
======================= | ||
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Submodules | ||
---------- | ||
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mssm.src.python.compare module | ||
------------------------------ | ||
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.. automodule:: mssm.src.python.compare | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: | ||
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mssm.src.python.constraints module | ||
---------------------------------- | ||
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.. automodule:: mssm.src.python.constraints | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: | ||
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mssm.src.python.exp\_fam module | ||
------------------------------- | ||
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.. automodule:: mssm.src.python.exp_fam | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: | ||
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mssm.src.python.formula module | ||
------------------------------ | ||
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.. automodule:: mssm.src.python.formula | ||
:members: Formula, VarType,lhs,reparam | ||
:undoc-members: | ||
:show-inheritance: | ||
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mssm.src.python.terms module | ||
---------------------------- | ||
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.. automodule:: mssm.src.python.terms | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: | ||
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mssm.src.python.utils module | ||
---------------------------- | ||
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.. automodule:: mssm.src.python.utils | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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mssm.src package | ||
================ | ||
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Subpackages | ||
----------- | ||
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.. toctree:: | ||
:maxdepth: 4 | ||
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mssm.src.python |
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