diff --git a/docs/source/index.rst b/docs/source/index.rst index 6247534..3367291 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -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 @@ -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 diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 2c0cec2..00d4646 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -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