README.md

In MarcOhlmann/metanetwork: Handling and Representing Trophic Networks in Space and Time

R package ‘metanetwork’

Marc Ohlmann 15/03/22

Description

A collection of tools in R to represent and analyse trophic networks in space across aggregation levels. The package contains a layout algorithm specifically designed for trophic networks, using trophic levels and dimension reduction on a diffusion kernel.

Package installation

For the last stable version, use the CRAN version

install.packages("metanetwork")

For the development version, use the github install

install_github("MarcOhlmann/metanetwork")

Loading the package

library(metanetwork)

Loading ‘igraph’ is also strongly recommended since ‘metanetwork’ objects are built from ‘igraph’ objects

library(igraph)

Introduction and basics

What is a metanetwork ?

In ecological networks literature, metanetwork refers to a set of networks in space. In R package ‘metanetwork’, we stick to a widespread (however restrictive) case:

• a potential interaction network (the metaweb, can be built using expert knowledge)
• local abundance tables, local networks are then induced subgraph of the metaweb by local abundances

Additional information might be considered (and used in ‘metanetwork’) as:

• a trophic table indicating a hierarchy of nodes of the metaweb, in order to study the metanetwork at different aggregation levels

See vignettes for application of ‘metanetwork’ on several datasets.

What ‘metanetwork’ package provides ?

data("meta_angola")
#Angola dataset
ggmetanet(meta_angola,beta = 0.05,legend = "Phylum")

‘metanetwork’ map

Authors

This package is currently developed by Marc Ohlmann from Laboratoire d’Ecologie Alpine, Grenoble and Jimmy Garnier and Laurent Vuillon from Laboratoire de Mathématiques, Chambéry. It is supported by the ANR Globnets and ANR Econet.

About

https://marcohlmann.github.io/metanetwork/ https://cran.r-project.org/web/packages/metanetwork/index.html

MarcOhlmann/metanetwork documentation built on July 1, 2023, 6:27 a.m.