Create¶
As we saw in Getting started, to create a MultiNorm object, you
pass a mean
vector, a covariance
matrix (both as Numpy arrays)
and optionally a list of parameter names
:
from multinorm import MultiNorm
mean = [10, 20, 30]
covariance = [[1, 0, 0], [0, 4, 0], [0, 0, 9]]
names = ["a", "b", "c"]
mn = MultiNorm(mean, covariance, names)
But where do these things come from?
On this page, we look at the most common scenarios.
From fit¶
TODO: show example using scipy.optimise.curve_fit`
To use multinorm
, we first need to fit some parameterised model
to obtain a best-fit parameter vector and covariance matrix.
Let’s use scipy.optimize_curve_fit to fit some data.
TODO: show example using iminuit
http://www.statsmodels.org/devel/examples/notebooks/generated/chi2_fitting.html https://github.com/cdeil/pyfit/blob/master/fitting_tutorial/src/tests/chi2_example.py https://lmfit.github.io https://iminuit.readthedocs.io https://sherpa.readthedocs.io
From points¶
A common way to analyse likelihood or in Bayesian analyses the posterior probability distributions is to use MCMC methods that sample the distribution. E.g. emcee or pymc are Python packages that generate this kind of output.
Estimating the multivariate normal distribution from samples well can be difficult, there are many methods with different trade-offs. We recommend using a different package for this task, e.g. sklearn.covariance.
That said, there is a method MultiNorm.from_points()
that calls numpy.std()
to compute the mean vector, and numpy.cov()
to compute what’s sometimes called
the “empirical” multivariate normal estimate.
Points should always be given as 2-dimensional arrays with shape (n_dim, n_points)
.
>>> points = mn.sample(size=100, random_state=0)
>>> MultiNorm.from_points(points)
MultiNorm(n=3)
names: ['par_0', 'par_1', 'par_2']
mean: [ 9.87581591 20.21250462 30.30156153]
err: [0.98090098 1.97394775 3.09360932]
cov:
[[ 0.96216674 -0.04439635 0.33802118]
[-0.04439635 3.89646972 -0.45369176]
[ 0.33802118 -0.45369176 9.57041861]]
From publication¶
TODO: show example how to take covar (or par errors) from a publication or blog post, i.e. as inputs.
From product¶
TODO: document MultiNorm.from_product()
Make example¶
TODO: document MultiNorm.make_example()