.. _hyperparameters:

================
Hyper-parameters
================

This short guide will illustrate how to estimate hyper-parameters from
posterior samples using :code:`bilby` using a simplistic problem.

Setting up the problem
----------------------

We are given three data sets labelled by a, b, and c. Each data set consists of
:math:`N` observations of a variable :math:`y` taken at a dependent variable
:math:`x`. Notationally, we can write these three data sets as :math:`(y_i^a,
x_i^a),(y_i^b, x_i^b),(y_i^c, x_i^c)` where :math:`i \in [0, N]` labels the
indexes of each data set.

Plotting the data, we see that all three look like they could be modelled by
a linear function with some slope and some intercept:

.. image:: images/hyper_parameter_data.png

Given any individual data set, you could write down a linear model :math:`y(x)
= c_0 + c_1 x` and infer the intercept and gradient. For example, given the
a-data set, you could calculate :math:`P(c_0|y_i^a, x_i^a)` by fitting the
model to the data. Here is a figure demonstrating the posteriors on the
intercept, for the three data sets given above

.. image:: images/hyper_parameter_combined_posteriors.png

While the data looks noise, the overlap in the :math:`c_0` posteriors might
(especially given context about how the data was produced and the physical
setting) make you believe all data sets share a common intercept. How would
you go about estimating this? You could just take the mean of the means of the
posterior and that would give you a pretty good estimate. However, we'll now
discuss how to do this with hyper parameters.

Understanding the population using hyperparameters
--------------------------------------------------

We first need to define our hyperparameterized model. In this case, it is
as simple as

.. math::

   c_0 \sim \mathcal{N}(\mu_{c_0}, \sigma_{c_0})


That is, we model the population :math:`c_0` (from which each of the data sets
was drawn) as coming from a normal distribution with some mean and some
standard deviation.

To do - write in details of the likelihood and its derivation

For the samples in the figure above, the posterior on these hyperparamters
is given by

.. image:: images/hyper_parameter_corner.png
