Skip to content

Commit

Permalink
docs styling
Browse files Browse the repository at this point in the history
  • Loading branch information
Andrew McCluskey committed Apr 23, 2020
1 parent ce39da4 commit 56485dd
Show file tree
Hide file tree
Showing 2 changed files with 9 additions and 12 deletions.
19 changes: 8 additions & 11 deletions docs/source/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -6,31 +6,31 @@
making Bayesian modelling easy(er)
==================================

``uravu`` is about the relationship between some data and a function that may be used to describe the data.
:py:mod:`uravu` is about the relationship between some data and a function that may be used to describe the data.

The aim of ``uravu`` is to make using the **amazing** Bayesian inference libraries that are available in Python as easy as `scipy.optimize.curve_fit`_.
The aim of :py:mod:`uravu` is to make using the **amazing** Bayesian inference libraries that are available in Python as easy as :py:function:`scipy.optimize.curve_fit`.
Therefore enabling many more to make use of these exciting tools and powerful libraries.
Plus, we have some nice plotting functionalities available in the :mod:`plotting` module, capable of generating publication quality figures.

.. image:: sample_fig.png
:alt: An example of the type of figures that uravu can produce. Showing straight line distribution with increasing uncertainty.

In an effort to make the ``uravu`` API friendly to those new to Bayesian inference, ``uravu`` is *opinionated*, making assumptions about priors amoung other things.
In an effort to make the :py:mod:`uravu` API friendly to those new to Bayesian inference, :py:mod:`uravu` is *opinionated*, making assumptions about priors amoung other things.
However, we have endevoured to make it straightforward to ignore these opinions.

In addition to the library and API, we also have some `basic tutorials`_ discussing how Bayesian inference methods can be used in the analysis of data.

``uravu`` is under active development, more details of which can be found on `Github`_.
:py:mod:`uravu` is under active development, more details of which can be found on `Github`_.

Bayesian inference in Python
----------------------------

There are a couple of fantastic Bayesian inference libraries available in Python that `uravu` makes use of:
There are a couple of fantastic Bayesian inference libraries available in Python that :py:mod:`uravu` makes use of:

- `emcee`_: enables the use of the `Goodman & Weare’s Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler`_ to evaluate the structure of the model parameter posterior distributions,
- `dynesty`_: implements the `nested sampling`_ algorithm for evidence estimation.
- :py:mod:`emcee`: enables the use of the `Goodman & Weare’s Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler`_ to evaluate the structure of the model parameter posterior distributions,
- :py:mod:`dynesty`: implements the `nested sampling`_ algorithm for evidence estimation.

To see which publications you should reference in your work, the :class:`Relationship` has a property that will return the relevant citations based on what analyses have been performed.
To see which publications you should reference in your work, the :py:class:`~uravu.relationship.Relationship` has a property that will return the relevant citations based on what analyses have been performed.

.. code-block:: python
Expand All @@ -43,11 +43,8 @@ To see which publications you should reference in your work, the :class:`Relatio
print(modeller.citations)
.. _scipy.optimize.curve_fit: https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.curve_fit.html
.. _basic tutorials: ./tutorials.html
.. _Github: https://github.com/arm61/uravu
.. _emcee: https://emcee.readthedocs.io/
.. _dynesty: https://dynesty.readthedocs.io/
.. _Goodman & Weare’s Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler: https://doi.org/10.2140/camcos.2010.5.65
.. _nested sampling: https://doi.org/10.1063/1.1835238

Expand Down
2 changes: 1 addition & 1 deletion docs/source/installation.rst
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Installation
============

``uravu`` can be installed from the PyPI package manager with ``pip``:
:py:mod:`uravu` can be installed from the PyPI package manager with py:mod:`pip`:

.. code-block:: bash
Expand Down

0 comments on commit 56485dd

Please sign in to comment.