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=TRUE, verbose=FALSE)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.
A matrix with lower trophic level species as rows, higher trophic level species as columns and number of interactions as entries.
An optional name for the data file generated by the function.
Logical; is the web quantitative and should hence a weighted edge list be produced? Defaults to TRUE.
Logical; shall each link be represented twice, i.e. once from A to B and also from B to A? Defaults to FALSE.
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.
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.
Logical; shall the edge list be returned by this function (for future use in R)? Defaults to TRUE. Setting return to FALSE will cause writing of files to the hard drive!
Logical; shall some feedback tell you that the files have been generated? Defaults to FALSE.
Carsten F. Dormann carsten.dormann@biom.uni-freiburg.de
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.
data(Safariland)
web2edges(Safariland)
web2edges(as.one.mode(Safariland, project="lower"), is.one.mode=TRUE)
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