README.md

In lsaravia/EcoNetwork: Ecological network analyses including multiplex networks

multiweb

This is an R package to analize ecological networks, including multilayer networks, recently developed network metrics and also some old ones conveniently in the same place. Functions to read, plot and a big set of networks are also included in the package.

Instalation

require(devtools)
install_github("lsaravia/multiweb")

Examples

Read the example data included in the package

require(multiweb)

fileName <- c(system.file("extdata",  package = "multiweb"))
fileName <- system.file("extdata", "BarentsBoreal_FW.csv", package = "multiweb")
g <- readNetwork(fileName)

Read multiple interaction network in different layers as a list

fileName <- c(system.file("extdata",  package = "multiweb"))
dn <- list.files(fileName,pattern = "^Kefi2015.*\\.txt$")
g <- readNetwork(dn,fileName, skipColumn = 2)

Convert to mgraph type

gt <- fromIgraphToMgraph(g,c("Negative","Positive","Antagonistic"))

Read multiple interaction network with a function

types <- c("Negative","Positive","Antagonistic")
gt <- readMultiplex(dn,types,fileName, skipColumn = 2)

Calculate QSS (quasi-sign-stability) for multiple interactions networks (mgraph)

calc_QSS(gt)

References

1. Marina, T. I., Saravia, L. A., Cordone, G., Salinas, V., Doyle, S. R., & Momo, F. R. (2018). Architecture of marine food webs: To be or not be a ‘small-world.’ PLoS ONE, 13(5), 1–13. https://doi.org/10.1371/journal.pone.0198217

2. Saravia, L. A., Marina, T. I., Kristensen, N. P., De Troch, M., & Momo, F. R. (2022). Ecological network assembly: How the regional metaweb influences local food webs. Journal of Animal Ecology, 91(3), 630–642. https://doi.org/10.1111/1365-2656.13652

lsaravia/EcoNetwork documentation built on March 20, 2024, 3:27 p.m.