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In Ecological-Complexity-Lab/infomap_ecology_package: Community Detection using Infomap, Inspired by Ecological Networks

Updated: 2021-09-26

This site is an extension of the paper Identifying flow modules in ecological networks using Infomap It contains installation instructions and very detailed Infomap commands and R code that we use in the examples that are presented in the paper. Infomap is a very rich implementation of the map equation, fully covered in https://www.mapequation.org/. In this knowledge base we present what is most relevant for ecological network analysis and the R package infomapecology. The package is a convenient interface to use Infomap within R and to santdardize network data structures for a better workflow with other package such as igraph and bipartite. We will be updating this knowledge base with every improvement of infomapecology.

Installation of Infomap and infomapecology

Currently, infomapecology uses a standalone version of Infomap. We are working hard to integrate Infomap directly into R. Until that happens, install Infomap and infomapecology as specified here.

Infomap's basics

The basics of Infomap's input and output are here.

Examples from the paper

• Bipartite monolayer network example
• Monolayer directed network with hierarchical structure
• Monolayer directed network with node attributes
• Flow models
• Hypothesis testing
• Temporal multilayer network with global relax rates
• Temporal multilayer network with interlayer edges

Acknowledgements

This work was supported by research grant ISF (Israel Science Foundation) 1281/20 to Shai Pilosof.

Ecological-Complexity-Lab/infomap_ecology_package documentation built on June 6, 2024, 5:28 a.m.