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Network Comparison

An R package implementing the Netdis and NetEMD alignment-free network comparison measures.

⚠️ BETA: Package under construction (pre-release) ⚠️

Until this package hits release 1.0 anything can change with no notice.

Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. GitHub release Build

Codecov license Github All Releases

Usage

See "Quick start" vignettes in documentation for example usage.

Parallel processing support

The gdd_for_all_graphs method will make use of multiple threads to calculate graphlet-based degree distributions for multiple graphs in parallel. However, this is only supported on unix-like systems (e.g. Linux and Mac OSX), as the underlying mcapply method requires system support for forks. The gdd_for_all_graphs method will run on Windows, but the number of cores will be restricted to 1, regardless of the value of mc.cores provided to gdd_for_all_graphs or set in the R environment.

Installing package from source

When published to the CRAN package repository, the library and all documentation will be installed in the standard manner using install.packages("netdist"), which will also install all dependencies from CRAN. However, prior to publication on CRAN, the package can be installed from Github using the devtools package.

Prerequisites

  • Install the devtools package using install.packages("devtools")

Installing package and core dependencies needed to use it

Core dependencies are listed in the Imports section of the package DEPENDENCIES file and will be automatically installed when installing / updating the package using devtools as described below.

Install the latest package from GitHub using:

  • devtools::install_github("alan-turing-institute/network-comparison")

Installing additional optional dependencies

Additional optional packages required to generate documentation, run tests or develop the package are listed in the Suggests section of the package DEPENDENCIES file. These will not be automatically installed by devtools::install() and, if required, each optional package will need to be separately installed using devtools::install("<package_name>").

Example optional libraries are:

  • testthat for running tests via devtools::test() or generating package documentation using devtools::document()
  • knitr for building the package long-form documentation vignettes using devtools::build_vignettes()

Documentation

You can browse a list of long form examples illustrating how to use the package using browseVignettes(package = "netdist").

You can list the functions available in the package with library(help = "netdist") and get more detailed help on individual functions using ?function_name (e.g. ?net_emd). In RStudio, typing ?netdist:: should also provide a drop down list of functions you can select to load the more detailed help.

References

NetEMD

Anatol E. Wegner, Luis Ospina-Forero, Robert E. Gaunt, Charlotte M. Deane, Gesine Reinert; Identifying networks with common organizational principles. arXiv:1704.00387 [stat.ML] (Open Access pre-print)

NetDis

Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun, Charlotte M. Deane; Alignment-free protein interaction network comparison. Bioinformatics 2014; 30 (17): i430-i437. https://doi.org/10.1093/bioinformatics/btu447 (Open Access)