.. _output-network:

Output network
==============

A network may be output using the `-output-network` task. The network may be output in one of three different formats.
The `-output-network-igraph-file-prefix` option can also be used to output igraph files, see :ref:`plot-network` for more details.


The output network task can also be used to output node data using the `-output-network-node-data-file-prefix` option and optionally the `-output-network-node-data-bed-file` option. 

.. _output-network-options:

Options
-------

The options are as follows:

.. list-table:: 
    :header-rows: 1

    * - Option
      - Description
      - Default

    * - -output-network
      - do a task to output a network or network data to file
      -   

    * - -output-network-name name
      - label the task with a name
      - Task-n

    * - -output-network-network-name network
      - output this network
      - previous network (or the default model given by a node for each data variable and no edges if there is no previous network)

    * - -output-network-file network.dat
      - output the network in a format where the nodes and then the edges are listed
      -

    * - -output-network-file2 network2.dat
      - output the network in this style of format: [a][b|a][c|a:b]
      -

    * - -output-network-equivalent-networks-file equiv-networks.dat
      - output a list of equivalent networks to file equiv-networks.dat
      -

    * - -output-network-igraph-file-prefix mygraph
      - output igraph format files consisting of mygraph-nodes.dat, mygraph-edges.dat and R code mygraph-plot.R
      -

    * - -output-network-node-data-file-prefix mydata
      - output network discrete data to mydata-discrete.dat and continuous data to mydata-cts.dat
      -

    * - -output-network-node-data-bed-file
      - output SNP data to files mydata.bed, mydata.bim and mydata.fam and not to files mydata-discrete.dat and mydata-cts.dat
      -

    * - -output-network-node-data-start-indiv a
      - start output of data from individual a
      - 1

    * - -output-network-node-data-end-indiv b
      - stop output of data at individual b
      - last individual

    * - -output-network-node-data-job i t
      - only output individuals for subset i from a total of t subsets
      -


.. _output-network-example:


Example
-------

The following is an example parameter file to output a network.

.. code-block:: none

    #input continuous data
    -input-data
    -input-data-file example-cts.dat
    -input-data-cts

    #input discrete data
    -input-data
    -input-data-file example-discrete.dat
    -input-data-discrete

    #input SNP data as discrete data
    -input-data
    -input-data-file example.bed
    -input-data-discrete-snp

    #search network models
    -search-models

    #output the fitted network
    -output-network
    -output-network-file fittedNetwork.dat


This parameter file, `paras-output-network.txt`, can be found in `example.zip <https://github.com/NewcastleRSE/BayesNetty/raw/refs/heads/main/docs/resources/example.zip>`_ and can be used as follows:


.. code-block:: none

    ./bayesnetty paras-output-network.txt

Which should produce output that looks like something as follows:

.. code-block:: none

    BayesNetty: Bayesian Network software, v1.00
    --------------------------------------------------
    Copyright 2015-present Richard Howey, GNU General Public License, v3
    Institute of Genetic Medicine, Newcastle University

    Random seed: 1551716789
    --------------------------------------------------
    Task name: Task-1
    Loading data
    Continuous data file: example-cts.dat
    Number of ID columns: 2
    Including (all) 2 variables in analysis
    Each variable has 1500 data entries
    Missing value: not set
    --------------------------------------------------
    --------------------------------------------------
    Task name: Task-2
    Loading data
    Discrete data file: example-discrete.dat
    Number of ID columns: 2
    Including the 1 and only variable in analysis
    Each variable has 1500 data entries
    Missing value: NA
    --------------------------------------------------
    --------------------------------------------------
    Task name: Task-3
    Loading data
    SNP binary data file: example.bed
    SNP data treated as discrete data
    Total number of SNPs: 2
    Total number of subjects: 1500
    Number of ID columns: 2
    Including (all) 2 variables in analysis
    Each variable has 1500 data entries
    --------------------------------------------------
    --------------------------------------------------
    Task name: Task-4
    Searching network models
    --------------------------------------------------
    Loading defaultNetwork network
    Network type: bnlearn
    Network score type: BIC
    Total number of nodes: 5 (Discrete: 3 | Factor: 0 | Continuous: 2)
    Total number of edges: 0
    Network Structure: [express][pheno][mood][rs1][rs2]
    Total data at each node: 1495
    Missing data at each node: 5
    --------------------------------------------------
    Network: defaultNetwork
    Search: Greedy
    Random restarts: 0
    Random jitter restarts: 0
    Network Structure: [mood][rs1][rs2][express|rs1:rs2][pheno|express:mood]
    Network score type: BIC
    Network score = -8213.45
    --------------------------------------------------
    --------------------------------------------------
    Task name: Task-5
    Outputting network
    Network: defaultNetwork
    Network Structure: [mood][rs1][rs2][express|rs1:rs2][pheno|express:mood]
    Network output to file: fittedNetwork.dat
    --------------------------------------------------

    Run time: less than one second

The data is loaded, a search is performed and then the network is output to a file.