Gephi sees multiple edges between nodes as parallel, even though they have different time intervals

Question

I am using Gephi version 0.82, R version 3.1.2 and rgexf version 0.13.8

I have created a dynamic gexf file using R-package rgexf. Gephi identifies the time format used in the gexf file. However, when I try to open it, I get the warning "Parallel edges are not supported yet..." (even when I make sure the start and end dates of edges do not coincide) and all the edge weights for different time periods are combined into the first period's edge. How can I ensure that Gephi recognizes the output from R? Here's the code I use in R

'library(igraph)    
library(XML)
library(Rook)
library(rgexf)

year=2013

nodes_ini <- read.csv("network labels.csv")  
edges_ini <- read.csv("network edges dynamic3.csv")

nodes_ini <- as.matrix(nodes_ini[])
edges_ini <- as.matrix(edges_ini[])

edges <- edges_ini[,1:2]
nodes <- nodes_ini[,1:2]
edges <- data.frame(edges)
nodes <- data.frame(nodes)

edgeweight <- edges_ini[,3]
edgeweight <- as.matrix(edgeweight)
nodesatt <-nodes_ini[,3:9]
nodesatt <- as.matrix(nodesatt)
nodesize <- nodesatt[,(2014-year)]
nodesize <- as.matrix(as.numeric(nodesize))

edgetimes <- as.matrix(edges_ini[,4:5])
edgetimesdate1 <- as.Date(edgetimes[,1], "%Y-%m-%d")
edgetimesdate2 <- as.Date(edgetimes[,2], "%Y-%m-%d")
edgetimesdate11 <- data.frame(edgetimesdate1)
edgetimesdate22 <- data.frame(edgetimesdate2)
edgetimesdate <- cbind(edgetimesdate11, edgetimesdate22)



write.gexf(nodes,edges,edgesWeight = edgeweight,tFormat = "date",edgeDynamic = edgetimesdate,nodesVizAtt = list(size=nodesize),defaultedgetype="directed",output="C:/Users/gorkem/Desktop/exercise/gephi/rgexf/first3.gexf")`

Answer 1

The thing is that you are using a version with a bug (http://cran.r-project.org/web/packages/rgexf/news.html). Starting version 0.14.3 the option keepFactors handles factor data types. Previous versions didn't saw this, hence the edges/nodes labels (and ids) were got directly from the numeric part of the factor. Now, if the problem persists, report the bug https://bitbucket.org/gvegayon/rgexf/issues and I'll try to fix it.

Best regards,

George

Answer 2

However, when I try to open it, I get the warning "Parallel edges are not supported yet..." (even when I make sure the start and end dates of edges do not coincide) and all the edge weights for different time periods are combined into the first period's edge. How can I ensure that Gephi recognizes the output from R?

It's impossible using Gephi v0.8.2 (parallel edges will be merged unconditionally).