nmds.ordination: perform non-dimensional scaling of the nodes by employing the...

In loop: loop decomposition of weighted directed graphs for life cycle analysis, providing flexbile network plotting methods, and analyzing food chain properties in ecology

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

Author(s)

Youhua Chen <[e-mail]>

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)

Example output

Loading required package: grid
Loading required package: MASS
initial  value 0.000000 
final  value 0.000000 
converged
$coord
              [,1]       [,2]
[1,]  4.138236e-01 -0.1274755
[2,] -4.138236e-01 -0.1274755
[3,] -3.185091e-16  0.5099020
[4,] -4.138236e-01 -0.1274755
[5,]  4.138236e-01 -0.1274755

$names
[1] 1 2 3 4 5

loop documentation built on May 2, 2019, 9:07 a.m.