Statistical methods for the analysis of populations of directed graphs

This contains the source code of the beta version of StatGraph, including all of the methods that were implemented for the directed code, which were used for the development of the simulations and plots in the paper 'Statistical methods for the analysis of populations of directed graphs'. This is a beta version. Please see the official StatGraph website in RCran for updated versions.

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StatGraph

Contains statistical methods to analyze graphs, such as graph parameter estimation, model selection based on the GIC (Graph Information Criterion), statistical tests to discriminate two or more populations of graphs (ANOGVA - Analysis of Graph Variability), correlation between graphs, and clustering of graphs.

References:

• Takahashi et al. (2012) doi:10.1371/journal.pone.0049949,
• Futija et al. (2017) doi:10.3389/fnins.2017.00066,
• Fujita et al. (2017) doi:10.1016/j.csda.2016.11.016,
• Tang et al. (2017) doi:10.3150/15-BEJ789,
• Tang et al. (2017) doi:10.1080/10618600.2016.1193505,
• Ghoshdastidar et al. (2017) arXiv:1705.06168,
• Ghoshdastidar et al. (2017) arXiv:1707.00833,
• Cerqueira et al. (2017) doi:10.1109/TNSE.2017.2674026,
• Fraiman and Fraiman (2018) doi:10.1038/s41598-018-23152-5,
• Fujita et al. (2019) doi:10.1093/comnet/cnz028.

For Developers:

Building:

Before attempting to build this project, make sure that you have all of the requirements needed by running:

apt install -y r-base libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev r-cran-tinytex texlive texinfo texlive-fonts-extra curl libcurl4 libharfbuzz-dev libfribidi-dev libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev

Once the requirements are installed, you can build the project by running:

./build.r`

or

Rscript build.r

This will generate a statGraph_{version}.pdf file containing the documentation and a statGraph_{version}.tar.gz file containing the finished library.

Testing

Test files are located in directory statGraph/tests/testthat/. It is not advisable to attempt to run the test script files directly.

In order to perform tests, run the following:

./test.r [Arguments]

The test.r script file has three modes of operation, which can be selected using by passing the appropriate argument.

The arguments that can be passed to test.r consist of the following:

-a [or no argument passed] - Runs all tests
-i TEST1,TEST2,TEST3...    - Runs only the tests described in the argument following -i. This has to be a comma separated list of test names.
-e TEST1,TEST2,TEST3...    - Runs all but the tests described in the argument following -e. This has to be a comma separated list of test names.

For example, the following command only runs the tests graph.param.estimator and graph.model.selection

./test.r -i graph.param.estimator,graph.model.selection

Structure of this project

This project uses the structured of a standard R project. To find out more: https://r-pkgs.org/whole-game.html

In short: Methods should be added to .R files located in statGraph/R/. To make them public, they have to be exported by adding the corresponding @export tag before their constructors.

More specific guidelines for the structure of this codebase can be found on statGraph/R/README.md and statGraph/tests/testthat/README.md