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
how to create initial configuraton for isoMDS
2 messages · LiLi (Z), Sarah Goslee
2 days later
Hi, Your matrix needs to either be symmetric or an object of class dist. Here's one way to reformat it: Note that calling it dist is a poor idea, since dist() is a base function. Also note that if the distance from 1-2 is 1 while distance from 2-1 is Inf, as in your original matrix, then you probably need to reconsider what you're doing. dconfig <- as.dist(t(dist)) loc <- isoMDS(dconfig) Sarah
LiLi (Z) wrote:
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