Conversion of a network matrix into a (weighted) edge list
This helper function converts a bipartite matrix into an edge list, optionally weighted, as used by other packages and software, and writes this to the hard drive (optionally)
web2edges(web, webName=NULL, weight.column=TRUE, both.directions=FALSE,
is.one.mode=FALSE, out.files=c("edges", "names", "groups")[1:2],
return=FALSE, verbose=FALSE)web |
A matrix with lower trophic level species as rows, higher trophic level species as columns and number of interactions as entries. |
webName |
An optional name for the data file generated by the function. |
weight.column |
Logical; is the web quantitative and should hence a weighted edge list be produced? Defaults to TRUE. |
both.directions |
Logical; shall each link be represented twice, i.e. once from A to B and also from B to A? Defaults to FALSE. |
is.one.mode |
Logical; if TRUE, labels for species will be used as they currently are in the web; otherwise, species will be re-labelled so that the first column will have number NROW(web) + 1. This is also the default. |
out.files |
String indicating which files to produce: "edges" writes an edge list, "names" writes a list with names belonging to the edges and "groups" writes a file assigning the species to higher and lower trophic levels. The default produces the edge list and the names file. |
return |
Logical; shall the edge list be returned by this function (for future use in R)? Defaults to FALSE. Setting return to TRUE will prevent writing of files to the hard drive! |
verbose |
Logical; shall some feedback tell you that the files have been generated? Defaults to FALSE. |
Many network programs (e.g. Pajek) require input in the form of an edge list. Here each species is a number. The edge list has two column, one with the target and one with the origin of the connection. That means an interaction between 1 and 6 would be written (in one line) as: 1 6. In a weighted edge list, a third column represents the strength of the interaction: 1 6 4.77.
All this function does is to transform the typical interaction matrix used in bipartite into an edge list. Within R this could be used e.g. in the package tnet; outside R by Pajek or others.
Similar to as.one.mode this function is there to increase interchange between different coding standards and packages.
A matrix (“edge list”) with two (unweighted) or three (weighted) columns.
If return=FALSE, this matrix (and possibly names and groups) are written to a text-file in the working directory.
The function is used as export helper (default) or as link to tnet (with return=TRUE).
Carsten F. Dormann carsten.dormann@ufz.de
data(Safariland) web2edges(Safariland, return=TRUE)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.