# Welcome to BXA’s documentation!¶

## About Bayesian X-ray Analysis (BXA)¶

BXA connects the nested sampling algorithm MultiNest to the
X-ray spectral analysis environments Xspec/Sherpa
for **Bayesian Parameter Estimation** and **Model comparison**.

BXA provides the following features:

- parameter estimation in arbitrary dimensions, which involves:

- finding the best fit
- computing error bars
- computing marginal probability distributions

- plotting of spectral model vs. the data:

- for the best fit
- for each of the solutions (posterior samples)
- for each component

- model selection:

- computing the evidence for the considered model, ready for use in computing Bayes factors
- unlike likelihood-ratios, not limited to nested models

- model discovery:

- visualize deviations between model and data with Quantile-Quantile (QQ) plots. QQ-plots do not require binning and are more comprehensive than residuals. This will give you ideas on when to introduce more complex models, which may again be tested with model selection

## Usage¶

- We start with some notes on best practice in currently common Maximum Likelihood analysis (fitting) and Bayesian analysis.

The usage is similar in Sherpa and Xspec conceptionally:

## Get BXA¶

See the code repository page

## Citing BXA correctly¶

Refer to the accompaning paper Buchner et al. (2014) which gives introduction and detailed discussion on the methodology and its statistical footing.

We suggest giving credit to the developers of Sherpa/Xspec, MultiNest and of this software. As an example:

```
For analysing X-ray spectra, we use the analysis software BXA (\ref{Buchner2014}),
which connects the nested sampling algorithm MultiNest (\ref{FerozHobson2010})
with the fitting environment CIAO/Sherpa (\ref{Fruscione2006}).
```

Where the BibTex entries are:

for BXA, PyMultiNest software, and the contributions to X-ray spectral analysis methodology (model comparison, model discovery, Experiment design, Model discovery through QQ-plots):

- Buchner et al. (2014) A&A
- The paper is available at arXiv:1402.0004

for MultiNest: see MultiNest

for Sherpa: see Sherpa

for Xspec: see Xspec

## Installation¶

However, you need to have pymultinest and MultiNest installed and working.

- Installation for those two packages only
- Extensive PyMultiNest, PyAPEMoST, PyCuba installation instructions

You need to have Sherpa or Xspec installed and its environment loaded.

The following commands should not yield any error message:

```
$ python -c 'import pymultinest'
$ python -c 'import xspec'
$ sherpa
```

Install the required python packages, through your package manager, through pip or easy_install. For example:

```
$ yum install ipython python-matplotlib scipy numpy matplotlib
$ apt-get install python-numpy python-scipy python-matplotlib ipython
$ pip install tqdm corner --user
```

BXA itself can installed directly from PyPI using pip or easy_install:

```
$ pip install bxa # --user if you want to install locally
```

The source code is available from https://github.com/JohannesBuchner/BXA, so alternatively you can download and install it:

```
$ python setup.py install
```

Or if you only want to install it for the current user:

```
$ python setup.py install --user
```

## Running¶

In *Sherpa*, load the package:

```
jbuchner@ds42 ~ $ sherpa
-----------------------------------------------------
Welcome to Sherpa: CXC's Modeling and Fitting Package
-----------------------------------------------------
CIAO 4.4 Sherpa version 2 Tuesday, June 5, 2012
sherpa-1> import bxa.sherpa as bxa
sherpa-2> bxa.run_model?
```

For *Xspec*, start python or ipython:

```
jbuchner@ds42 ~ $ ipython
In [1]: import xspec
In [2]: import bxa.xspec as bxa
In [3]: bxa.standard_analysis?
```

Now you can use bxa.

## Documentation:¶

## Who is using BXA?¶

- Dr. Antonis Georgakakis (MPE, Munich)
- Dr. Mike Anderson (MPA, Munich)
- Dr. Franz Bauer (PUC, Santiago)
- Dr. Stéphane Paltani (ISDC, Geneva)
- Zhu Liu (NAO, Beijing)