ChainConsumer¶
ChainConsumer is a python package designed to do one thing - consume the chains output from Monte Carlo processes like MCMC. ChainConsumer can utilise these chains to produce plots of the posterior surface inferred from the chain distributions, to plot the chains as walks (to check for mixing and convergence), and to output parameter summaries in the form of LaTeX tables. On top of all of this, if you have multiple models (chains), you can load them all in and perform some model comparison using AIC, BIC or DIC metrics.
To get things started, here is a basic example:
import numpy as np
from chainconsumer import ChainConsumer
mean = [0.0, 4.0]
data = np.random.multivariate_normal(mean, [[1.0, 0.7], [0.7, 1.5]], size=100000)
c = ChainConsumer()
c.add_chain(data, parameters=["$x_1$", "$x_2$"])
c.plotter.plot(filename="example.png", figsize="column", truth=mean)
The output figure is displayed below.
Or you can add more models and look at the summaries between them. Or a ton more, check the examples!
Check out the API and far more Examples below:
Contents¶
Installation¶
ChainConsumer requires the following dependencies, along with a LaTeX installation and dvipng
(a maptlotlib dependency):
numpy
scipy
matplotlib
statsmodels
ChainConsumer can be installed as follows:
pip install chainconsumer
Common Issues¶
Users on some Linux platforms have reported issues rendering plots using ChainConsumer.
The common error states that dvipng: not found
, and as per StackOverflow
post, it can be solved by explicitly install the matplotlib
dependency dvipng
via sudo apt-get install dvipng
.
Citing¶
You can cite ChainConsumer using the following BibTeX:
@ARTICLE{Hinton2016,
author = {{Hinton}, S.~R.},
title = "{ChainConsumer}",
journal = {The Journal of Open Source Software},
year = 2016,
month = aug,
volume = 1,
eid = {00045},
pages = {00045},
doi = {10.21105/joss.00045},
adsurl = {http://adsabs.harvard.edu/abs/2016JOSS....1...45H},
}
Contributing¶
Users that wish to contribute to this project may do so in a number of ways. Firstly, for any feature requests, bugs or general ideas, please raise an issue via Github.
If you wish to contribute code to the project, please simple fork the project on Github and then raise a pull request. Pull requests will be reviewed to determine whether the changes are major or minor in nature, and to ensure all changes are tested.