loop (version 1.1)

nmds.ordination: perform non-dimensional scaling of the nodes by employing the function 'isoMDS' from package 'MASS'

Description

this is to get the coordinates of each node/vertex in the two-diemsional spaces, which are used in plotting functions, including "fplot" and "groupplot".

Usage

nmds.ordination(gemat, type = "both", metric = "jaccard")

Arguments

gemat

standard square graph matrix

type

if type="both", the node similarity is calculated based on the the vertex similarity from the inward/outward links for each pair of nodes. if type="in", the node similarity is calculated based on the the vertex similarity from the inward links for each pair of nodes. if type="out", the node similarity is calculated based on the the vertex similarity from the outward links for each pair of nodes.

metric

node similarity methods, currently supporting two basic similarity indices: "jaccard" and "sorensen".

Value

coord

coordinates of each node in the space

names

names for the nodes

References

Chen Y (2012) loop: an R package for performing decomposition of weighted directed graphs, food web analysis and flexible network plotting. Submitted.

See Also

fplot, groupplot, node.similarity

Examples

mat=matrix(c(0,5,3,7,0,5,0,8,0,4,3,8,0,1,6,7,0,1,0,2,0,4,6,2,0),5,5)
nmds.ordination(gemat=mat)