Getting the data into R

Every network can be read straight into R with read.csv(); no package is needed. The files are plain CSV in UTF-8, with species names exactly as in the downloads. The examples use network M_PL_006; replace it with any network ID.

One network

# Interaction matrix, species names as row and column names
m <- as.matrix(read.csv("https://www.web-of-life.es/api/v1/networks/M_PL_006/matrix.csv",
                        row.names = 1, check.names = FALSE))

# One row per interaction: network, row_species, column_species, row_role, column_role, strength
edges <- read.csv("https://www.web-of-life.es/api/v1/networks/M_PL_006/edges.csv")

# The species: side of the matrix, role, kingdom, order, family, number of interactions, abundance
species <- read.csv("https://www.web-of-life.es/api/v1/networks/M_PL_006/species.csv")

All networks

# One row per network: type, size, connectance, nestedness, modularity, location, reference
networks <- read.csv("https://www.web-of-life.es/api/v1/networks.csv")

# Several networks at once, e.g. all weighted pollination networks
ids <- networks$network[networks$interaction_type == "Pollination" & networks$weighted == 1]
matrices <- lapply(ids, function(id) as.matrix(read.csv(
  paste0("https://www.web-of-life.es/api/v1/networks/", id, "/matrix.csv"), row.names = 1, check.names = FALSE)))
names(matrices) <- ids

Everything at once, with one table of all interactions of all networks: download the zip of all published networks.

Files

Address	Content
`/api/v1/networks.csv`	All networks with their metadata and structure.
`/api/v1/networks/<ID>/matrix.csv`	The matrix of one network, without abundances.
`/api/v1/networks/<ID>/edges.csv`	Its interactions, one per row.
`/api/v1/networks/<ID>/species.csv`	Its species with their role and taxonomy.
`/download/everything/`	A zip with all of the above for every published network.

Earlier addresses

The addresses of the previous site keep working with the same output, for the rweboflife package and existing scripts: get_networks.php, get_network_info.php, get_species_info.php, get_networks_by_species.php, get_taxize_info.php and networkjson.php. For example: https://www.web-of-life.es/get_networks.php?network_name=M_PL_006.

Nestedness and modularity

Nestedness is computed as in rweboflife::nestedness (Fortuna et al. 2019, Evolution 73: 1001–1011), from 0 to 1. Modularity is Barber's bipartite modularity (Physical Review E 76: 066102, 2007) of the binary matrix, maximised by repeated searches; the number of modules is that of the best partition found.

How to cite

Please cite the original study of each network and mention the database: "This work has used the Web of Life database (www.web-of-life.es)". Each network's sheet has a How to cite button with BibTeX and RIS files.