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Problem with shortestPath in igraph and qgraph

3 messages · Zahra Tofighi, Jeff Newmiller

Zahra Tofighi
# 
hello,

I have a graph and i use qgraph package to calculate centrality parameters.
Now I want to know the maximum value of shortest path for each vertex with
discarding the Inf value in short pathes. For this I use the
ShortestPathLengths of centrality function in qgraph. but when I want to
get the maximum the result is wrong. here is my code:

cen<-centrality(Q)

tmp3<-cen$ShortestPathLengths
shp<-matrix(1:ncol(tmp3),ncol(tmp3),1)for(i in ncol(tmp3)){
shp[i,]=max(tmp3[i,][tmp3[i,]!=Inf)}

when I display the valu of shp the result is same as initial value (form
one to ncol). I also test with shortest.paths function. the result was
same. what is my wrong?
Jeff Newmiller
# 
Hard to follow data analysis without data. Try making your example reproducible [1][2][3] and post in plain text (a setting in your emailer). Read the Posting Guide mentioned in the footer to avoid other posting pitfalls. 

[1] http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

[2] http://adv-r.had.co.nz/Reproducibility.html

[3] https://cran.r-project.org/web/packages/reprex/index.html
Zahra Tofighi
# 
I hope this new post be according to  your tips.
My database is big so i upload it in Dropbox and here is the link to
download it:
https://www.dropbox.com/pri/get/cognitiveEdges.csv?_subject_uid=680429290&w=AADQFwqcK-l66BiR4hcJayEc8dFbn0YNHdzeJ7ErqiKr1g

and here is code to run in R studio (3.4.0) :
 rm(list = ls())
library("igraph")
library("qgraph")
library("data.table")
links <- read.csv("C:/result21/CognitiveEdges.csv", header=T, as.is=T) #
Address of file
nrow(links); nrow(unique(links[,c("From", "To")]))
nrow(unique(links[,c("From", "To")]))
net <- graph_from_data_frame(d=links, directed=T)
Q<-qgraph(as_adjacency_matrix(net))
cen<-centrality(Q)
 tmp3 <- shortest.paths(net,V(net),V(net))
cen<-centrality(Q)
tmp3<-cen$ShortestPathLengths
re<-function(tmp3){
shp<-matrix(1:ncol(tmp3),ncol(tmp3),1)
for(i in ncol(tmp3))
{
shp[i,]<-max(tmp3[i,][tmp3[i,]!=Inf])}
return(shp)
}
mm<-re(tmp3)### my problem is here Line 21
max(tmp3[1,][tmp3[1,]!=Inf]) # line 22

my problem is at line 21. Why the result of mm[1,] is not same as line 22??
for other elements of mm also i didn't get the true result.
With Regards,

On Wed, Jun 21, 2017 at 9:35 AM, Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
wrote: