[R] how to create initial configuraton for isoMDS

[LiLi (Z)]

Hi,

I'm trying to use isoMDS to project a directed graph to 2-dim vectors, but I got an error.

#here is the code to create the graph using igraph package and run isoMDS on it.
library(igraph)
library(MASS)
g<-make_graph(c(1,2, 2,3, 2,4, 3,4, 4,5, 5,6, 3,6, 1,6, 2,5),directed=TRUE)
dist<-distances(g, mode="out")
loc<-isoMDS(dist)

# below is content of the dist matrix
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    1    2    2    2    1
[2,]  Inf    0    1    1    1    2
[3,]  Inf  Inf    0    1    2    1
[4,]  Inf  Inf  Inf    0    1    2
[5,]  Inf  Inf  Inf  Inf    0    1
[6,]  Inf  Inf  Inf  Inf  Inf    0

# and here is the error message:
Error in isoMDS(dist) :
  an initial configuration must be supplied with NA/Infs in 'd'

It appears that isoMDS doesn't like the "Inf" values in the dist matrix, although help(isoMDS) suggests it accepts them if proper initial configuration is provided:
Arguments
d

distance structure of the form returned by dist, or a full, symmetric matrix. Data are assumed to be dissimilarities or relative distances, but must be positive except for self-distance. Both missing and infinite values are allowed.

y

An initial configuration. If none is supplied, cmdscale is used to provide the classical solution, unless there are missing or infinite dissimilarities.

k

The desired dimension for the solution, passed to cmdscale.


My questions is: how do I provide the y argument for this example to work?
Any help and suggestion is appreciated.
Li


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