Commit 8297a6e0 authored by Gregory Ashton's avatar Gregory Ashton

Add documentation for basic of PE

parent eaf8d4d7
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Basics of parameter estimation
==============================
In this example, we'll go into some of the basics of parameter estimation and
how they are implemented in `tupak`.
Firstly, consider a situation where you have discrete data :math:`\{y_0,
y_1,\ldots, y_n\}` taken at a set of times :math:`\{t_0, t_1, \ldots, y_n\}`.
Further, we know that this data is generated by a process which can be modelled
by a linear function of the form :math:`y(t) = m t + c`. We will refer to
this model as :math:`H`. Given a set of data,
how can we figure out the coefficients :math:`m` and :math:`c`?
This is a well studied problem known as `linear regression
<https://en.wikipedia.org/wiki/Linear_regression>`_ and there already exists
many ways to estimate the coefficients (you may already be familiar with a
least squares estimator for example).
Here, we will describe a Bayesian approach using `nested sampling
<https://en.wikipedia.org/wiki/Nested_sampling_algorithm>`_ which might feel
like overkill for this problem. However, it is a useful way to introduce some
of the basic features of `tupak` before seeing them in more complicated
settings.
The maths
---------
Given the data, the posterior distribution for the model parameters is given
by
.. math::
P(m, c| \{y_i, t_i\}, H) \propto P(\{y_i, t_i\}| m, c, H) \times P(m, c| H)
where the first term on the right-hand-side is the *likelihood* while the
second is the *prior*. In the model :math:`H`, the likelihood of the data point
:math:`y_i, t_i`, given a value for the coefficients we will define to be
Gaussian distributed as such:
.. math::
P(y_i, t_i| m, c, H) = \frac{1}{\sqrt{2\pi\sigma^2}}
\mathrm{exp}\left(\frac{-(y_i - (t_i x + c))^2}{2\sigma^2}\right)
Next, we assume that all data points are independent. As such,
.. math::
P(\{y_i, t_i\}| m, c, H) = \prod_{i=1}^n P(y_i, t_i| m, c, H)
When solving problems on a computer, it is often convienient to work with
the log-likelihood. Indeed, a `tupak` *likelihood* must have a `log_likelihood()`
method. For the normal distribution, the log-likelihood for *n* data points is
.. math::
\log(P(\{y_i, t_i\}| m, c, H)) = -\frac{1}{2}\left[
\sum_{i=1}^n \left(\frac{(y_i - (t_i x + c))}{\sigma}\right)^2
+ n\log\left(2\pi\sigma^2\right)\right]
Finally, we need to specify a *prior*. In this case we will use uncorrelated
uniform priors
.. math::
P(m, c| H) = P(m| H) \times P(c| H) = \textrm{Unif}(0, 5) \times \textrm{Unif}(-2, 2)
the choice of prior in general should be guided by physical knowledge about the
system and not the data in question.
The key point to take away here is that the **likelihood** and **prior** are
the inputs to figuring out the **posterior**. There are many ways to go about
this, we will now show how to do so in `tupak`. In this case, we explicitly
show how to write the `GaussianLikelihood` so that one can see how the
maths above gets implemented. For the prior, this is done implicitly by the
naming of the priors.
The code
--------
In the following example, also available under
`examples/other_examples/linear_regression.py
<https://git.ligo.org/Monash/tupak/tree/master/examples/other_examples/linear_regression.py>`_
we will step through the process of generating some simulated data, writing
a likelihood and prior, and running nested sampling using `tupak`.
.. literalinclude:: /../examples/other_examples/linear_regression.py
:language: python
:emphasize-lines: 12,15-18
:linenos:
Running the script above will make a few images. Firstly, the plot of the data:
.. image:: images/linear-regression_data.png
The dashed red line here shows the simulated signal.
Secondly, because we used the `plot=True` argument in `run_sampler` we generate
a corner plot
.. image:: images/linear-regression_corner.png
The solid lines indicate the simulated values which are recovered quite
easily. Note, you can also make a corner plot with `result.plot_corner()`.
Final thoughts
--------------
While this example is somewhat trivial, hopefully you can see how this script
can be easily modified to perform parameter estimation for almost any
time-domain data where you can model the background noise as Gaussian and write
the signal model as a python function (i.e., replacing `model`).
......@@ -8,6 +8,7 @@ Welcome to tupak's documentation!
:maxdepth: 3
:caption: Contents:
basics-of-parameter-estimation
likelihood
samplers
writing-documentation
......
......@@ -48,7 +48,7 @@ ax.plot(time, model(time, **injection_parameters), '--r', label='signal')
ax.set_xlabel('time')
ax.set_ylabel('y')
ax.legend()
fig.savefig('{}/data.png'.format(outdir))
fig.savefig('{}/{}_data.png'.format(outdir, label))
# Parameter estimation: we now define a Gaussian Likelihood class relevant for
......
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