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Introduction

Energy landscape analysis (ELA) is a systematic method for analyzing an energy landscape represented as a weighted network (Fig. 1).

Figure 1: A schematic　of ELA

Figure 1. A schematic illustration of ELA.


  • In the energy landscape, the nodes of the network represent unique community compositions, and the links represent the transition paths between them.
  • The community composition is described as a binary vector that represents the presence (1) and absence (0) of a species, and the links connect all nodes that differ only in the presence or absence of one species (Fig. 1B).
  • The nodes are weighted by their energies, and the difference in energy level drives the direction of transitions in community composition (Fig.1D).
  • The energy is assigned by a pairwise maximum entropy model or its extension with an external force (environmental effect) term (Fig.1C).

Platforms

We currently provided several software platforms for running ELA.

R package

R package of ELA is currently available on Windows, Mac(including arm64), and Linux.

The package is not currently distributed via repositories and can be only installed from a local file after the download.

For details see: https://github.com/kecosz/rELA

Python package

Python package of ELA is currently available only on Mac(including arm64) or Linux.

The installation of python package is also not yet supported via online repositories, pip or conda.
The user need to download all the modules from the git repository and need the manual instllation.

For details see: https://github.com/sotarotakano/ELApy

Mathematica

Download the package from the github page and run in the Mathematica environment.
For details see: https://github.com/kecosz/ela

References and Citations

Main publication

Suzuki, K., Nakaoka, S., Fukuda, S., & Masuya, H. (2021). "Energy landscape analysis elucidates the multistability of ecological communities across environmental gradients." Ecological Monographs.
https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecm.1469

ELA in journal articles

Representative articles using ELA packages.


Citations

total citations

The full article list citing ELA or the related papers.


Data collection is conducted using the OpenCitations platform.