Welcome to BayesNetty’s webpage!

Please use the menu to the left to navigate through the documentation for BayesNetty or use the PDF of these webpages, bayesnetty.pdf.

Citation

Please use the following papers [3] and [4] to reference the BayesNetty software as follows:

@article{howey:etal:21,
author={Howey, R AND Clark, A D AND Naamane, N AND Reynard, L N AND Pratt, A G AND Cordell, H J},
title={{A Bayesian network approach incorporating imputation of missing data enables exploratory analysis of complex causal biological relationships}},
journal={PLOS Genetics},
month = {September},
volume={17},
number={9},
doi = {10.1371/journal.pgen.1009811},
url = {https://doi.org/10.1371/journal.pgen.1009811},
pages={e1009811},
year={2021}}

@article{howey:etal:20,
author = {Howey, R AND Shin, S-Y AND Relton, C AND Davey Smith, G AND Cordell, H J},
journal = {PLOS Genetics},
title = {Bayesian network analysis incorporating genetic anchors complements conventional Mendelian randomization approaches for exploratory analysis of causal relationships in complex data},
year = {2020},
month = {March},
volume = {16},
url = {https://doi.org/10.1371/journal.pgen.1008198},
pages = {1-35},
number = {3},
doi = {10.1371/journal.pgen.1008198}}

BayesNetty is copyright, 2015-present Richard Howey, GNU General Public License, version 3.

Contents

• Introduction
• Installation
• Using BayesNetty
  • Basic Options
  • Parameter file
  • Simple Example
  • Command-line Options
• Parallel BayesNetty
  • Compilation Scripts
• Input data
  • Options
  • Discrete data
  • Continuous data
  • Factor data
  • SNP data
  • Missing data
  • Data IDs
  • Example
• Input network
  • Options
  • Black lists
  • White lists
  • Soft Constraints
  • Network formats
  • Example
• bnlearn network
  • Network score
• deal network
  • Imaginary sample size
• Calculate network score
  • Options
  • Example
• Calculate posterior
  • Options
  • Example
• Search models
  • Options
  • Greedy search
  • Number of random restarts for the greedy algorithm
  • Number of jitter restarts for the greedy algorithm
  • Example
• Average network
  • Options
  • Score Method
  • Example
  • Parallel Example
• Impute Data
  • Options
  • Example
  • Parallel Example
• Estimate Imputation Benefit
  • Options
  • Example
• Calculate Recall and Precision
  • Options
  • Example
• Simulate network data
  • Options
  • Example 1: no data
  • Example 2: data and fitted network
  • Example 3: data and unknown network
• Markov blanket
  • Options
  • Example
• Output network
  • Options
  • Example
• Output priors (deal only)
  • Options
  • Example
• Output posteriors
  • Options
  • Example
• Network plotting
  • igraph
  • Example
• References

Contact

Please contact Richard Howey with any queries about the BayesNetty software.