pymc-labs · drbenvincent · May 1, 2023 · May 1, 2023
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -176,10 +176,10 @@ pyreverse -o png causalpy --output-directory img
 ```
 
 Classes
-![](img/classes.png)
+![](docs/source/_static/classes.png)
 
 Packages
-![](img/packages.png)
+![](docs/source/_static/packages.png)
 
 ---
 

diff --git a/README.md b/README.md
@@ -1,14 +1,20 @@
-# CausalPy
+<div align="center">
+  <a href="https://github.com/pymc-labs/CausalPy"><img width="60%" src="docs/source/_static/logo.png"></a>
+</div>
+
+----
 
 ![Build](https://github.com/pymc-labs/CausalPy/workflows/ci/badge.svg)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![PyPI version](https://badge.fury.io/py/CausalPy.svg)](https://badge.fury.io/py/CausalPy)
 ![GitHub Repo stars](https://img.shields.io/github/stars/pymc-labs/causalpy?style=social)
 ![Read the Docs](https://img.shields.io/readthedocs/causalpy)
 ![PyPI - Downloads](https://img.shields.io/pypi/dm/causalpy)
-![Interrogate](img/interrogate_badge.svg)
+![Interrogate](docs/source/_static/interrogate_badge.svg)
 [![codecov](https://codecov.io/gh/pymc-labs/CausalPy/branch/main/graph/badge.svg?token=FDKNAY5CZ9)](https://codecov.io/gh/pymc-labs/CausalPy)
 
+# CausalPy
+
 A Python package focussing on causal inference in quasi-experimental settings. The package allows for sophisticated Bayesian model fitting methods to be used in addition to traditional OLS.
 
 _**STATUS:** Feel free to explore and experiment with the repository, and we very much welcome feedback (via [Issues](https://github.com/pymc-labs/CausalPy/issues)). But be aware that this code is very alpha! Expect the codebase and API to change for a while, so it is not appropriate to rely on this package for in-production or research pipelines._
@@ -92,7 +98,7 @@ This is appropriate when you have multiple units, one of which is treated. You b
 
 | Frequentist | Bayesian |
 |--|--|
-| ![](img/synthetic_control_skl.svg) | ![](img/synthetic_control_pymc.svg) |
+| ![](docs/source/_static/synthetic_control_skl.svg) | ![](docs/source/_static/synthetic_control_pymc.svg) |
 
 > The data (treated and untreated units), pre-treatment model fit, and counterfactual (i.e. the synthetic control) are plotted (top). The causal impact is shown as a blue shaded region. The Bayesian analysis shows shaded Bayesian credible regions of the model fit and counterfactual. Also shown is the causal impact (middle) and cumulative causal impact (bottom).
 
@@ -112,7 +118,7 @@ This is appropriate for non-equivalent group designs when you have a single pre
 
 | Frequentist | Bayesian |
 |--|--|
-| coming soon | ![](img/anova_pymc.svg) |
+| coming soon | ![](docs/source/_static/anova_pymc.svg) |
 
 > The data from the control and treatment group are plotted, along with posterior predictive 94% credible intervals. The lower panel shows the estimated treatment effect.
 
@@ -131,7 +137,7 @@ Data is expected to be in the following form. Shown are just two units - one in
 
 | Frequentist | Bayesian |
 |--|--|
-| ![](img/difference_in_differences_skl.svg) | ![](img/difference_in_differences_pymc.svg) |
+| ![](docs/source/_static/difference_in_differences_skl.svg) | ![](docs/source/_static/difference_in_differences_pymc.svg) |
 
 >The data, model fit, and counterfactual are plotted. Frequentist model fits result in points estimates, but the Bayesian analysis results in posterior distributions, represented by the violin plots. The causal impact is the difference between the counterfactual prediction (treated group, post treatment) and the observed values for the treated group, post treatment.
 
@@ -150,7 +156,7 @@ Regression discontinuity designs are used when treatment is applied to units acc
 
 | Frequentist | Bayesian |
 |--|--|
-| ![](img/regression_discontinuity_skl.svg) | ![](img/regression_discontinuity_pymc.svg) |
+| ![](docs/source/_static/regression_discontinuity_skl.svg) | ![](docs/source/_static/regression_discontinuity_pymc.svg) |
 
 > The data, model fit, and counterfactual are plotted (top). Frequentist analysis shows the causal impact with the blue shaded region, but this is not shown in the Bayesian analysis to avoid a cluttered chart. Instead, the Bayesian analysis shows shaded Bayesian credible regions of the model fits. The Frequentist analysis visualises the point estimate of the causal impact, but the Bayesian analysis also plots the posterior distribution of the regression discontinuity effect (bottom).
 
@@ -173,7 +179,7 @@ Here are some general resources about causal inference:
 
 ## Support
 
-<img src="img/pymc-labs-log.png" align="right" width="50%" />
+<img src="docs/source/_static/pymc-labs-log.png" align="right" width="50%" />
 
 This repository is supported by [PyMC Labs](https://www.pymc-labs.io).
 

diff --git a/docs/Makefile b/docs/Makefile
@@ -5,7 +5,7 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
+SOURCEDIR     = source
 BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".

diff --git a/img/anova_pymc.svg → docs/source/_static/anova_pymc.svg b/img/anova_pymc.svg → docs/source/_static/anova_pymc.svg
diff --git a/img/classes.png → docs/source/_static/classes.png b/img/classes.png → docs/source/_static/classes.png
diff --git a/img/difference_in_differences_pymc.svg → ...static/difference_in_differences_pymc.svg b/img/difference_in_differences_pymc.svg → ...static/difference_in_differences_pymc.svg
diff --git a/img/difference_in_differences_skl.svg → ..._static/difference_in_differences_skl.svg b/img/difference_in_differences_skl.svg → ..._static/difference_in_differences_skl.svg
diff --git a/img/interrogate_badge.svg → docs/source/_static/interrogate_badge.svg b/img/interrogate_badge.svg → docs/source/_static/interrogate_badge.svg
diff --git a/docs/source/_static/logo.png b/docs/source/_static/logo.png
diff --git a/img/packages.png → docs/source/_static/packages.png b/img/packages.png → docs/source/_static/packages.png
diff --git a/img/pymc-labs-log.png → docs/source/_static/pymc-labs-log.png b/img/pymc-labs-log.png → docs/source/_static/pymc-labs-log.png
diff --git a/img/regression_discontinuity_pymc.svg → ..._static/regression_discontinuity_pymc.svg b/img/regression_discontinuity_pymc.svg → ..._static/regression_discontinuity_pymc.svg
diff --git a/img/regression_discontinuity_skl.svg → .../_static/regression_discontinuity_skl.svg b/img/regression_discontinuity_skl.svg → .../_static/regression_discontinuity_skl.svg
diff --git a/img/synthetic_control_pymc.svg → ...source/_static/synthetic_control_pymc.svg b/img/synthetic_control_pymc.svg → ...source/_static/synthetic_control_pymc.svg
diff --git a/img/synthetic_control_skl.svg → .../source/_static/synthetic_control_skl.svg b/img/synthetic_control_skl.svg → .../source/_static/synthetic_control_skl.svg
diff --git a/docs/api_datasets.rst → docs/source/api_datasets.rst b/docs/api_datasets.rst → docs/source/api_datasets.rst
diff --git a/docs/api_plot_utils.rst → docs/source/api_plot_utils.rst b/docs/api_plot_utils.rst → docs/source/api_plot_utils.rst
diff --git a/docs/api_pymc_experiments.rst → docs/source/api_pymc_experiments.rst b/docs/api_pymc_experiments.rst → docs/source/api_pymc_experiments.rst
diff --git a/docs/api_pymc_models.rst → docs/source/api_pymc_models.rst b/docs/api_pymc_models.rst → docs/source/api_pymc_models.rst
diff --git a/docs/api_skl_experiments.rst → docs/source/api_skl_experiments.rst b/docs/api_skl_experiments.rst → docs/source/api_skl_experiments.rst
diff --git a/docs/api_skl_models.rst → docs/source/api_skl_models.rst b/docs/api_skl_models.rst → docs/source/api_skl_models.rst
diff --git a/docs/conf.py → docs/source/conf.py b/docs/conf.py → docs/source/conf.py
@@ -78,9 +78,10 @@
 
 html_theme = "sphinx_rtd_theme"
 html_static_path = ["_static"]
-# TODO: version seems not to be displayed despite setting this to True
+html_logo = "logo.png"
 html_theme_options = {
-    "display_version": True,
+    "logo_only": True,
+    "display_version": False,
 }
 
 # -- Options for autodoc ----------------------------------------------------

diff --git a/docs/examples.rst → docs/source/examples.rst b/docs/examples.rst → docs/source/examples.rst
diff --git a/docs/glossary.md → docs/source/glossary.md b/docs/glossary.md → docs/source/glossary.md
diff --git a/docs/index.rst → docs/source/index.rst b/docs/index.rst → docs/source/index.rst
@@ -1,7 +1,8 @@
-.. CausalPy documentation master file, created by
-   sphinx-quickstart on Mon Nov 14 18:28:13 2022.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+.. image:: _static/logo.png
+   :width: 80 %
+   :align: center
+   :alt: CausalPy logo
+
 
 CausalPy - causal inference for quasi-experiments
 =================================================
@@ -75,7 +76,7 @@ Synthetic control
 
 This is appropriate when you have multiple units, one of which is treated. You build a synthetic control as a weighted combination of the untreated units.
 
-.. image:: ../img/synthetic_control_pymc.svg
+.. image:: _static/synthetic_control_pymc.svg
 
 Geographical Lift / Geolift
 """"""""""""""""""""""""""""
@@ -86,28 +87,28 @@ ANCOVA
 
 This is appropriate when you have a single pre and post intervention measurement and have a treament and a control group.
 
-.. image:: ../img/anova_pymc.svg
+.. image:: _static/anova_pymc.svg
 
 Difference in differences
 """""""""""""""""""""""""
 
 This is appropriate when you have pre and post intervention measurement(s) and have a treament and a control group.
 
-.. image:: ../img/difference_in_differences_pymc.svg
+.. image:: _static/difference_in_differences_pymc.svg
 
 Regression discontinuity
 """"""""""""""""""""""""
 
 Regression discontinuity designs are used when treatment is applied to units according to a cutoff on a running variable, which is typically not time. By looking for the presence of a discontinuity at the precise point of the treatment cutoff then we can make causal claims about the potential impact of the treatment.
 
-.. image:: ../img/regression_discontinuity_pymc.svg
+.. image:: _static/regression_discontinuity_pymc.svg
 
 Support
 -------
 
 This repository is supported by `PyMC Labs <https://www.pymc-labs.io>`_.
 
-.. image:: ../img/pymc-labs-log.png
+.. image:: _static/pymc-labs-log.png
    :align: center
    :target: https://www.pymc-labs.io
    :scale: 50 %

diff --git a/docs/notebooks/ancova_pymc.ipynb → docs/source/notebooks/ancova_pymc.ipynb b/docs/notebooks/ancova_pymc.ipynb → docs/source/notebooks/ancova_pymc.ipynb
diff --git a/docs/notebooks/did_pymc.ipynb → docs/source/notebooks/did_pymc.ipynb b/docs/notebooks/did_pymc.ipynb → docs/source/notebooks/did_pymc.ipynb
diff --git a/docs/notebooks/did_pymc_banks.ipynb → docs/source/notebooks/did_pymc_banks.ipynb b/docs/notebooks/did_pymc_banks.ipynb → docs/source/notebooks/did_pymc_banks.ipynb
diff --git a/docs/notebooks/did_skl.ipynb → docs/source/notebooks/did_skl.ipynb b/docs/notebooks/did_skl.ipynb → docs/source/notebooks/did_skl.ipynb
diff --git a/docs/notebooks/generate_plots.ipynb → docs/source/notebooks/generate_plots.ipynb b/docs/notebooks/generate_plots.ipynb → docs/source/notebooks/generate_plots.ipynb
diff --git a/docs/notebooks/geolift.csv → docs/source/notebooks/geolift.csv b/docs/notebooks/geolift.csv → docs/source/notebooks/geolift.csv
diff --git a/docs/notebooks/geolift1.ipynb → docs/source/notebooks/geolift1.ipynb b/docs/notebooks/geolift1.ipynb → docs/source/notebooks/geolift1.ipynb
diff --git a/docs/notebooks/its_covid.ipynb → docs/source/notebooks/its_covid.ipynb b/docs/notebooks/its_covid.ipynb → docs/source/notebooks/its_covid.ipynb
diff --git a/docs/notebooks/rd_pymc.ipynb → docs/source/notebooks/rd_pymc.ipynb b/docs/notebooks/rd_pymc.ipynb → docs/source/notebooks/rd_pymc.ipynb
diff --git a/docs/notebooks/rd_pymc_drinking.ipynb → docs/source/notebooks/rd_pymc_drinking.ipynb b/docs/notebooks/rd_pymc_drinking.ipynb → docs/source/notebooks/rd_pymc_drinking.ipynb
diff --git a/docs/notebooks/rd_skl.ipynb → docs/source/notebooks/rd_skl.ipynb b/docs/notebooks/rd_skl.ipynb → docs/source/notebooks/rd_skl.ipynb
diff --git a/docs/notebooks/rd_skl_drinking.ipynb → docs/source/notebooks/rd_skl_drinking.ipynb b/docs/notebooks/rd_skl_drinking.ipynb → docs/source/notebooks/rd_skl_drinking.ipynb
diff --git a/docs/notebooks/sc2_pymc.ipynb → docs/source/notebooks/sc2_pymc.ipynb b/docs/notebooks/sc2_pymc.ipynb → docs/source/notebooks/sc2_pymc.ipynb
diff --git a/docs/notebooks/sc2_skl.ipynb → docs/source/notebooks/sc2_skl.ipynb b/docs/notebooks/sc2_skl.ipynb → docs/source/notebooks/sc2_skl.ipynb
diff --git a/docs/notebooks/sc_pymc.ipynb → docs/source/notebooks/sc_pymc.ipynb b/docs/notebooks/sc_pymc.ipynb → docs/source/notebooks/sc_pymc.ipynb
diff --git a/docs/notebooks/sc_pymc_brexit.ipynb → docs/source/notebooks/sc_pymc_brexit.ipynb b/docs/notebooks/sc_pymc_brexit.ipynb → docs/source/notebooks/sc_pymc_brexit.ipynb
diff --git a/docs/notebooks/sc_skl.ipynb → docs/source/notebooks/sc_skl.ipynb b/docs/notebooks/sc_skl.ipynb → docs/source/notebooks/sc_skl.ipynb