ecological-complexity-lab / emln

An R package for handling and manipulating multilayer network data, mainly for ecological networks

👋 About

This repository contains the code for the R package EMLN. EMLN is an R package that standardizes workflows for creating, storing and converting mulilayer network data. It also contains data sets of ecological multilayer networks for analysis. Although designed with ecological dcata in mind, it is flexible and can handle data from other research domains.

📄 Paper and citing

Frydman N, Freilikhman S, Talpaz I, Pilosof S. Practical guidelines and the EMLN R package for handling ecological multilayer networks. Methods in Ecology and Evolution. 2023. DOI:10.1111/2041-210X.14225. Please cite the paper when implementing the guidelines we describe or when using the package, this helps us a lot!

📦 Installation

Current installation uses devtools. CRAN version will come next.

package.list=c("tidyverse", "magrittr","igraph","Matrix","DT","hablar","devtools")
loaded <-  package.list %in% .packages()
package.list <-  package.list[!loaded]
installed <-  package.list %in% .packages(TRUE)
if (!all(installed)) install.packages(package.list[!installed],repos="http://cran.rstudio.com/")

devtools::install_github('Ecological-Complexity-Lab/emln', force=T)
library(emln)

🌐 Website

Detailed explanations on workflows accomanied by examples for handling monolayer and multilayer data using emln are in: https://ecological-complexity-lab.github.io/emln_package/.

emln's Issues

Problem when creating a network with interlayer links

I am having a problem to create a network with interlayer links. First of all, I have two layers loaded ("asia" and "neot"). Then, I specified the layer attributes.

# Specify the layers
layer_attributes = tibble(layer_id=1:2, layer_name=c('Indo-Malayan-Australasian',
                                                     'Neotropics'))

Then I created my interlayer links object:

> interlayer <- tibble(layer_from=c('Neotropics','Neotropics','Neotropics','Neotropics','Neotropics','Neotropics','Neotropics','Neotropics'),
                     node_from=c('Anacardiaceae', 'Araucariaceae','Clusiaceae','Euphorbiaceae','Fabaceae','Moraceae','Myrtaceae','Pinaceae'),
                     layer_to=c('Indo-Malayan-Australasia','Indo-Malayan-Australasia','Indo-Malayan-Australasia','Indo-Malayan-Australasia','Indo-Malayan-Australasia','Indo-Malayan-Australasia','Indo-Malayan-Australasia','Indo-Malayan-Australasia'), 
                     node_to=c('Anacardiaceae', 'Araucariaceae','Clusiaceae','Euphorbiaceae','Fabaceae','Moraceae','Myrtaceae','Pinaceae'),
                     weight=1)

Finally, I created the multilayer network object:

mult_resin = create_multilayer_network(list_of_layers = list(asia,neot),
                                             interlayer_links = interlayer,
                                             layer_attributes = layer_attributes,
                                             bipartite = T,
                                             directed = F)

But I obtained the following error:

Error in x[[jj]][iseq] <- vjj : replacement has length zero

How can I fix it?