Inferring, comparing and exploring ecological networks from time-series data through R packages constructnet, disgraph and dynet

TL;DR

This paper introduces three R packages—constructnet, disgraph, and dynet—that provide standardized tools for inferring, comparing, and simulating ecological networks from time-series data, facilitating accessible analysis for ecologists.

Contribution

The paper presents a coherent suite of R packages that implement various network inference, comparison, and simulation methods tailored for ecological data analysis.

Findings

Provides accessible R tools for ecological network inference

Enables comparison of network structures across datasets

Supports simulation of network processes for hypothesis testing

Abstract

Network inference is a major field of interest for the ecological community, especially in light of the high cost and difficulty of manual observation, and easy availability of remote, long term monitoring data. In addition, comparing across similar network structures, especially with spatial, environmental, or temporal variability and, simulating processes on networks to create toy models and hypotheses - are topics of considerable interest to the researchers. A large number of methods are being developed in the network science community to achieve these objectives but either don't have their code available or an implementation in R, the language preferred by ecologists and other biologists. We provide a suite of three packages which will provide a central suite of standardized network inference methods from time-series data (constructnet), distance metrics (disgraph) and (process) simulation models (dynet) to the growing R network analysis environment and would help ecologists and biologists to perform and compare methods under one roof. These packages are implemented in a coherent, consistent framework - making comparisons across methods and metrics easier. We hope that these tools in R will help increase the accessibility of network tools to ecologists and other biologists, who the language for most of their analysis.